cpgIslandExt CpG Islands CpG Islands (Islands < 300 Bases are Light Green) Expression and Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
cpgIslandSuper CpG Islands CpG Islands (Islands < 300 Bases are Light Green) Expression and Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
rmsk RepeatMasker Repeating Elements by RepeatMasker Variation and Repeats Description This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. Some newer assemblies have been made with Dfam, not Repbase. You can find the details for how we make our database data here in our &quot;makeDb/doc/&quot; directory. When analyzing the data tables of this track, keep in mind that Repbase is not the same as the Repeatmasker sequence database and that the repeat names in the Repeatmasker output are not the same as the sequence names in the Repeatmasker database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker output and this track, but there is not necessarily a single sequence "L1PA4" in the Repeatmasker database. This is because Repeatmasker creates annotations by joining matches to partial pieces of the database together so there is no 1:1 relationship between its sequence database and the annotations. To learn more, you can read the Repeatmasker paper, its source code or reach out to the Repeatmasker authors, your local expert on transposable elements or us. Display Conventions and Configuration In full display mode, this track displays up to ten different classes of repeats: Short interspersed nuclear elements (SINE), which include ALUs Long interspersed nuclear elements (LINE) Long terminal repeat elements (LTR), which include retroposons DNA repeat elements (DNA) Simple repeats (micro-satellites) Low complexity repeats Satellite repeats RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) Other repeats, which includes class RC (Rolling Circle) Unknown The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading. A &quot;?&quot; at the end of the &quot;Family&quot; or &quot;Class&quot; (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the &quot;?&quot; will be removed or the classification will be changed. Methods Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Repbase Update is described in: Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072 For a discussion of repeats in mammalian genomes, see: Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616 Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846 
robustPeaks TSS peaks FANTOM5 DPI peak, robust set Expression and Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as a robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to Shuhei Noguchi, the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M Hrydziuszko O, Vitezic M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556; PMC: PMC4681433 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
fantom5 FANTOM5 FANTOM5 Expression and Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as a robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to Shuhei Noguchi, the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M Hrydziuszko O, Vitezic M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556; PMC: PMC4681433 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
Total_counts_multiwig Total counts Total counts of CAGE reads Expression and Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as a robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to Shuhei Noguchi, the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M Hrydziuszko O, Vitezic M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556; PMC: PMC4681433 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
TotalCounts_Rev Total counts of CAGE reads (rev) Total counts of CAGE reads reverse Expression and Regulation 
TotalCounts_Fwd Total counts of CAGE reads (fwd) Total counts of CAGE reads forward Expression and Regulation 
Max_counts_multiwig Max counts Max counts of CAGE reads Expression and Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as a robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to Shuhei Noguchi, the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M Hrydziuszko O, Vitezic M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556; PMC: PMC4681433 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
MaxCounts_Rev Max counts of CAGE reads (rev) Max counts of CAGE reads reverse Expression and Regulation 
MaxCounts_Fwd Max counts of CAGE reads (fwd) Max counts of CAGE reads forward Expression and Regulation 
refSeqComposite NCBI RefSeq RefSeq genes from NCBI Genes and Gene Predictions Description The NCBI RefSeq Genes composite track shows dog protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences between the annotation coordinates provided by UCSC and NCBI. For RNA-seq analysis, we advise using NCBI aligned tables like RefSeq All or RefSeq Curated. See the Methods section for more details about how the different tracks were created. Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track is a composite track that contains differing data sets. To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide. Note: Not all subtracts are available on all assemblies. The possible subtracks include: RefSeq aligned annotations and UCSC alignment of RefSeq annotations RefSeq All &ndash; all curated and predicted annotations provided by RefSeq. RefSeq Curated &ndash; subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.) They were manually curated, based on publications describing transcripts and manual reviews of evidence which includes EST and full-length cDNA alignments, protein sequences, splice sites and any other evidence available in databases or the scientific literature. The resulting sequences can differ from the genome, they exist independently from a particular human genome build, and so must be aligned to the genome to create a track. The "RefSeq Curated" track is NCBI's mapping of these transcripts to the genome. Another alignment track exists for these, the "UCSC RefSeq" track (see beloow). RefSeq Predicted &ndash; subset of RefSeq All that includes those annotations whose accessions begin with XM or XR. They were predicted based on protein, cDNA, EST and RNA-seq alignments to the genome assembly by the NCBI Gnomon prediction software. RefSeq Other &ndash; all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks. Examples are untranscribed pseudogenes or gene clusters, such as HOX or protocadherin alpha. They were manually curated from publications or databases but are not typical transcribed genes. RefSeq Alignments &ndash; alignments of RefSeq RNAs to the dog genome provided by the RefSeq group, following the display conventions for PSL tracks. RefSeq Diffs &ndash; alignment differences between the dog reference genome(s) and RefSeq curated transcripts. (Track not currently available for every assembly.) UCSC RefSeq &ndash; annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the dog genome. This track was previously known as the &quot;RefSeq Genes&quot; track. RefSeq Select (subset, only on hg38) &ndash; Subset of RefSeq Curated, transcripts marked as part of the RefSeq Select dataset. A single Select transcript is chosen as representative for each protein-coding gene. See NCBI RefSeq Select. RefSeq HGMD (subset) &ndash; Subset of RefSeq Curated, transcripts annotated by the Human Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. It is the most restricted RefSeq subset, targeting clinical diagnostics. The RefSeq All, RefSeq Curated, RefSeq Predicted, and UCSC RefSeq tracks follow the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq. Color Level of review Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information. Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff. Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted. The item labels and codon display properties for features within this track can be configured through the check-box controls at the top of the track description page. To adjust the settings for an individual subtrack, click the wrench icon next to the track name in the subtrack list . Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name or OMIM identifier instead of the gene name, show all or a subset of these labels including the gene name, OMIM identifier and accession names, or turn off the label completely. Codon coloring: This track has an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. The RefSeq Diffs track contains five different types of inconsistency between the reference genome sequence and the RefSeq transcript sequences. The five types of differences are as follows: mismatch &ndash; aligned but mismatching bases, plus HGVS g. to show the genomic change required to match the transcript and HGVS c./n. to show the transcript change required to match the genome. short gap &ndash; genomic gaps that are too small to be introns (arbitrary cutoff of &lt; 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. showing differences. shift gap &ndash; shortGap items whose placement could be shifted left and/or right on the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region in transcript. Here, thin and thick lines are used -- the thin line shows the span of the repetitive sequence, and the thick line shows the rightmost shifted gap. double gap &ndash; genomic gaps that are long enough to be introns but that skip over transcript sequence (invisible in default setting), with HGVS c./n. deletion. skipped &ndash; sequence at the beginning or end of a transcript that is not aligned to the genome (invisible in default setting), with HGVS c./n. deletion HGVS Terminology (Human Genome Variation Society): g. = genomic sequence ; c. = coding DNA sequence ; n. = non-coding RNA reference sequence. When reporting HGVS with RefSeq sequences, to make sure that results from research articles can be mapped to the genome unambiguously, please specify the RefSeq annotation release displayed on the transcript's Genome Browser details page and also the RefSeq transcript ID with version (e.g. NM_012309.4 not NM_012309). Methods Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found here. The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments. The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks. RefSeq RNAs were aligned against the dog genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Data Access The raw data for these tracks can be accessed in multiple ways. It can be explored interactively using the REST API, Table Browser or Data Integrator. The tables can also be accessed programmatically through our public MySQL server or downloaded from our downloads server for local processing. The previous track versions are available in the archives of our downloads server. You can also access any RefSeq table entries in JSON format through our JSON API. The data in the RefSeq Other and RefSeq Diffs tracks are organized in bigBed file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows: genePred format: RefSeq All - ncbiRefSeq RefSeq Curated - ncbiRefSeqCurated RefSeq Predicted - ncbiRefSeqPredicted UCSC RefSeq - refGene PSL format: RefSeq Alignments - ncbiRefSeqPsl The first column of each of these tables is &quot;bin&quot;. This column is designed to speed up access for display in the Genome Browser, but can be safely ignored in downstream analysis. You can read more about the bin indexing system here. The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed files, which can be obtained from our downloads server here, ncbiRefSeqOther.bb and ncbiRefSeqDiffs.bb. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/canFam3/ncbiRefSeq/ncbiRefSeqOther.bb -chrom=chr16 -start=34990190 -end=36727467 stdout You can download a GTF format version of the RefSeq All table from the GTF downloads directory. The genePred format tracks can also be converted to GTF format using the genePredToGtf utility, available from the utilities directory on the UCSC downloads server. The utility can be run from the command line like so: genePredToGtf canFam3 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access section. A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, and RefSeq Predicted tracks can be found on our downloads server here. Please refer to our mailing list archives for questions. Previous versions of the ncbiRefSeq set of tracks can be found on our archive download server. Credits This track was produced at UCSC from data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
refGene UCSC RefSeq UCSC annotations of RefSeq RNAs (NM_* and NR_*) Genes and Gene Predictions Description The RefSeq Genes track shows known dog protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods RefSeq RNAs were aligned against the dog genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
ncbiRefSeqGenomicDiff RefSeq Diffs Differences between NCBI RefSeq Transcripts and the Reference Genome Genes and Gene Predictions 
ncbiRefSeqPsl RefSeq Alignments RefSeq Alignments of RNAs Genes and Gene Predictions 
ncbiRefSeqOther RefSeq Other NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) Genes and Gene Predictions 
ncbiRefSeqPredicted RefSeq Predicted NCBI RefSeq genes, predicted subset (XM_* or XR_*) Genes and Gene Predictions 
ncbiRefSeqCurated RefSeq Curated NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) Genes and Gene Predictions 
ncbiRefSeq RefSeq All NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) Genes and Gene Predictions 
TSS_activity_read_counts TSS activity(read counts) TSS activity per sample(read counts) Expression and Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as a robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to Shuhei Noguchi, the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M Hrydziuszko O, Vitezic M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556; PMC: PMC4681433 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
UniversalRNADogNormalTissuesBiochainPool1_CNhs10590_ctss_rev UniversalRna- Universal RNA - Dog Normal Tissues Biochain, pool1_CNhs10590_10006-101B2_reverse Expression and Regulation 
UniversalRNADogNormalTissuesBiochainPool1_CNhs10590_ctss_fwd UniversalRna+ Universal RNA - Dog Normal Tissues Biochain, pool1_CNhs10590_10006-101B2_forward Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor3_CNhs11310_ctss_rev MscBoneMarrowD3- Canine Mesenchymal stem cells - bone marrow derived, donor3_CNhs11310_11442-118I2_reverse Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor3_CNhs11310_ctss_fwd MscBoneMarrowD3+ Canine Mesenchymal stem cells - bone marrow derived, donor3_CNhs11310_11442-118I2_forward Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor2_CNhs11304_ctss_rev MscBoneMarrowD2- Canine Mesenchymal stem cells - bone marrow derived, donor2_CNhs11304_11370-118A2_reverse Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor2_CNhs11304_ctss_fwd MscBoneMarrowD2+ Canine Mesenchymal stem cells - bone marrow derived, donor2_CNhs11304_11370-118A2_forward Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor1_CNhs11291_ctss_rev MscBoneMarrowD1- Canine Mesenchymal stem cells - bone marrow derived, donor1_CNhs11291_11293-117A6_reverse Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor1_CNhs11291_ctss_fwd MscBoneMarrowD1+ Canine Mesenchymal stem cells - bone marrow derived, donor1_CNhs11291_11293-117A6_forward Expression and Regulation 
CanineHepatocytesDonor3_CNhs11308_ctss_rev HepatocyteD3- Canine hepatocytes, donor3_CNhs11308_11407-118E3_reverse Expression and Regulation 
CanineHepatocytesDonor3_CNhs11308_ctss_fwd HepatocyteD3+ Canine hepatocytes, donor3_CNhs11308_11407-118E3_forward Expression and Regulation 
CanineHepatocytesDonor2_CNhs11069_ctss_rev HepatocyteD2- Canine hepatocytes, donor2_CNhs11069_11325-117E2_reverse Expression and Regulation 
CanineHepatocytesDonor2_CNhs11069_ctss_fwd HepatocyteD2+ Canine hepatocytes, donor2_CNhs11069_11325-117E2_forward Expression and Regulation 
CanineHepatocytesDonor1_CNhs10873_ctss_rev HepatocyteD1- Canine hepatocytes, donor1_CNhs10873_11244-116E2_reverse Expression and Regulation 
CanineHepatocytesDonor1_CNhs10873_ctss_fwd HepatocyteD1+ Canine hepatocytes, donor1_CNhs10873_11244-116E2_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor3_CNhs11053_ctss_rev AorticSmcDiffD3- Canine Aortic Smooth Muscle cells - differentiated, donor3_CNhs11053_11472-119C5_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor3_CNhs11053_ctss_fwd AorticSmcDiffD3+ Canine Aortic Smooth Muscle cells - differentiated, donor3_CNhs11053_11472-119C5_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor2_CNhs11066_ctss_rev AorticSmcDiffD2- Canine Aortic Smooth Muscle cells - differentiated, donor2_CNhs11066_11471-119C4_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor2_CNhs11066_ctss_fwd AorticSmcDiffD2+ Canine Aortic Smooth Muscle cells - differentiated, donor2_CNhs11066_11471-119C4_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor3_CNhs11070_ctss_rev AorticSmcD3- Canine Aortic Smooth Muscle cells, donor3_CNhs11070_11446-118I6_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor3_CNhs11070_ctss_fwd AorticSmcD3+ Canine Aortic Smooth Muscle cells, donor3_CNhs11070_11446-118I6_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor2_CNhs11300_ctss_rev AorticSmcD2- Canine Aortic Smooth Muscle cells, donor2_CNhs11300_11374-118A6_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor2_CNhs11300_ctss_fwd AorticSmcD2+ Canine Aortic Smooth Muscle cells, donor2_CNhs11300_11374-118A6_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor1_CNhs11895_ctss_rev AorticSmcD1- Canine Aortic Smooth Muscle cells, donor1_CNhs11895_11297-117B1_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor1_CNhs11895_ctss_fwd AorticSmcD1+ Canine Aortic Smooth Muscle cells, donor1_CNhs11895_11297-117B1_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor1_CNhs12204_ctss_rev AorticSmcDiffD1- Canine Aortic Smooth Muscle cells - differentiated, donor1 _CNhs12204_11470-119C3_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor1_CNhs12204_ctss_fwd AorticSmcDiffD1+ Canine Aortic Smooth Muscle cells - differentiated, donor1 _CNhs12204_11470-119C3_forward Expression and Regulation 
cpgIslandExtUnmasked Unmasked CpG CpG Islands on All Sequence (Islands < 300 Bases are Light Green) Expression and Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
TSS_activity_TPM TSS activity(TPM) TSS activity per sample(TPM) Expression and Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as a robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to Shuhei Noguchi, the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M Hrydziuszko O, Vitezic M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556; PMC: PMC4681433 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
UniversalRNADogNormalTissuesBiochainPool1_CNhs10590_tpm_rev UniversalRna- Universal RNA - Dog Normal Tissues Biochain, pool1_CNhs10590_10006-101B2_reverse Expression and Regulation 
UniversalRNADogNormalTissuesBiochainPool1_CNhs10590_tpm_fwd UniversalRna+ Universal RNA - Dog Normal Tissues Biochain, pool1_CNhs10590_10006-101B2_forward Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor3_CNhs11310_tpm_rev MscBoneMarrowD3- Canine Mesenchymal stem cells - bone marrow derived, donor3_CNhs11310_11442-118I2_reverse Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor3_CNhs11310_tpm_fwd MscBoneMarrowD3+ Canine Mesenchymal stem cells - bone marrow derived, donor3_CNhs11310_11442-118I2_forward Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor2_CNhs11304_tpm_rev MscBoneMarrowD2- Canine Mesenchymal stem cells - bone marrow derived, donor2_CNhs11304_11370-118A2_reverse Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor2_CNhs11304_tpm_fwd MscBoneMarrowD2+ Canine Mesenchymal stem cells - bone marrow derived, donor2_CNhs11304_11370-118A2_forward Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor1_CNhs11291_tpm_rev MscBoneMarrowD1- Canine Mesenchymal stem cells - bone marrow derived, donor1_CNhs11291_11293-117A6_reverse Expression and Regulation 
CanineMesenchymalStemCellsBoneMarrowDerivedDonor1_CNhs11291_tpm_fwd MscBoneMarrowD1+ Canine Mesenchymal stem cells - bone marrow derived, donor1_CNhs11291_11293-117A6_forward Expression and Regulation 
CanineHepatocytesDonor3_CNhs11308_tpm_rev HepatocyteD3- Canine hepatocytes, donor3_CNhs11308_11407-118E3_reverse Expression and Regulation 
CanineHepatocytesDonor3_CNhs11308_tpm_fwd HepatocyteD3+ Canine hepatocytes, donor3_CNhs11308_11407-118E3_forward Expression and Regulation 
CanineHepatocytesDonor2_CNhs11069_tpm_rev HepatocyteD2- Canine hepatocytes, donor2_CNhs11069_11325-117E2_reverse Expression and Regulation 
CanineHepatocytesDonor2_CNhs11069_tpm_fwd HepatocyteD2+ Canine hepatocytes, donor2_CNhs11069_11325-117E2_forward Expression and Regulation 
CanineHepatocytesDonor1_CNhs10873_tpm_rev HepatocyteD1- Canine hepatocytes, donor1_CNhs10873_11244-116E2_reverse Expression and Regulation 
CanineHepatocytesDonor1_CNhs10873_tpm_fwd HepatocyteD1+ Canine hepatocytes, donor1_CNhs10873_11244-116E2_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor3_CNhs11053_tpm_rev AorticSmcDiffD3- Canine Aortic Smooth Muscle cells - differentiated, donor3_CNhs11053_11472-119C5_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor3_CNhs11053_tpm_fwd AorticSmcDiffD3+ Canine Aortic Smooth Muscle cells - differentiated, donor3_CNhs11053_11472-119C5_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor2_CNhs11066_tpm_rev AorticSmcDiffD2- Canine Aortic Smooth Muscle cells - differentiated, donor2_CNhs11066_11471-119C4_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor2_CNhs11066_tpm_fwd AorticSmcDiffD2+ Canine Aortic Smooth Muscle cells - differentiated, donor2_CNhs11066_11471-119C4_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor3_CNhs11070_tpm_rev AorticSmcD3- Canine Aortic Smooth Muscle cells, donor3_CNhs11070_11446-118I6_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor3_CNhs11070_tpm_fwd AorticSmcD3+ Canine Aortic Smooth Muscle cells, donor3_CNhs11070_11446-118I6_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor2_CNhs11300_tpm_rev AorticSmcD2- Canine Aortic Smooth Muscle cells, donor2_CNhs11300_11374-118A6_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor2_CNhs11300_tpm_fwd AorticSmcD2+ Canine Aortic Smooth Muscle cells, donor2_CNhs11300_11374-118A6_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor1_CNhs11895_tpm_rev AorticSmcD1- Canine Aortic Smooth Muscle cells, donor1_CNhs11895_11297-117B1_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDonor1_CNhs11895_tpm_fwd AorticSmcD1+ Canine Aortic Smooth Muscle cells, donor1_CNhs11895_11297-117B1_forward Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor1_CNhs12204_tpm_rev AorticSmcDiffD1- Canine Aortic Smooth Muscle cells - differentiated, donor1 _CNhs12204_11470-119C3_reverse Expression and Regulation 
CanineAorticSmoothMuscleCellsDifferentiatedDonor1_CNhs12204_tpm_fwd AorticSmcDiffD1+ Canine Aortic Smooth Muscle cells - differentiated, donor1 _CNhs12204_11470-119C3_forward Expression and Regulation 
transMapEnsemblV5 TransMap Ensembl TransMap Ensembl and GENCODE Mappings Version 5 Genes and Gene Predictions Description This track contains GENCODE or Ensembl alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. GENCODE is Ensembl for human and mouse, for other Ensembl sources, only ones with full gene builds are used. Projection Ensembl gene annotations will not be used as sources. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in dog. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the dog (canFam3) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the dog genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - canFam3.ensembl.transMapV4.bigPsl TransMap RefGene - canFam3.refseq.transMapV4.bigPsl TransMap RNA - canFam3.rna.transMapV4.bigPsl TransMap ESTs - canFam3.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/canFam3/transMap/V4/canFam3.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapV5 TransMap V5 TransMap Alignments Version 5 Genes and Gene Predictions Description These tracks contain cDNA and gene alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered LASTZ or BLASTZ alignment chains, resulting in a prediction of the orthologous genes in dog. For more distant organisms, reciprocal best alignments are used. TransMap maps genes and related annotations in one species to another using synteny-filtered pairwise genome alignments (chains and nets) to determine the most likely orthologs. For example, for the mRNA TransMap track on the human assembly, more than 400,000 mRNAs from 25 vertebrate species were aligned at high stringency to the native assembly using BLAT. The alignments were then mapped to the human assembly using the chain and net alignments produced using BLASTZ, which has higher sensitivity than BLAT for diverged organisms. Compared to translated BLAT, TransMap finds fewer paralogs and aligns more UTR bases. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the dog (canFam3) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the dog genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - canFam3.ensembl.transMapV5.bigPsl TransMap RefGene - canFam3.refseq.transMapV5.bigPsl TransMap RNA - canFam3.rna.transMapV5.bigPsl TransMap ESTs - canFam3.est.transMapV5.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/canFam3/transMap/V5/canFam3.refseq.transMapV5.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapRefSeqV5 TransMap RefGene TransMap RefSeq Gene Mappings Version 5 Genes and Gene Predictions Description This track contains RefSeq Gene alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in dog. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the dog (canFam3) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the dog genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - canFam3.ensembl.transMapV4.bigPsl TransMap RefGene - canFam3.refseq.transMapV4.bigPsl TransMap RNA - canFam3.rna.transMapV4.bigPsl TransMap ESTs - canFam3.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/canFam3/transMap/V4/canFam3.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapRnaV5 TransMap RNA TransMap GenBank RNA Mappings Version 5 Genes and Gene Predictions Description This track contains GenBank mRNA alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in dog. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the dog (canFam3) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the dog genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - canFam3.ensembl.transMapV4.bigPsl TransMap RefGene - canFam3.refseq.transMapV4.bigPsl TransMap RNA - canFam3.rna.transMapV4.bigPsl TransMap ESTs - canFam3.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/canFam3/transMap/V4/canFam3.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapEstV5 TransMap ESTs TransMap EST Mappings Version 5 Genes and Gene Predictions Description This track contains GenBank spliced EST alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in dog. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the dog (canFam3) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the dog genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - canFam3.ensembl.transMapV4.bigPsl TransMap RefGene - canFam3.refseq.transMapV4.bigPsl TransMap RNA - canFam3.rna.transMapV4.bigPsl TransMap ESTs - canFam3.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/canFam3/transMap/V4/canFam3.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
gold Assembly Assembly from Fragments Mapping and Sequencing Description This track shows the draft assembly (Sep. 2011, Broad CanFam3.1 (GCA_000002285.2)) of the dog genome. See also NCBI Assembly information: NCBI assembly/GCF_000002285.3 (Broad CanFam3.1) Whole-genome shotgun reads were assembled into contigs. When possible, contigs were grouped into scaffolds (also known as &quot;supercontigs&quot;). The order, orientation and gap sizes between contigs within a scaffold are based on paired-end read evidence. In dense mode, this track depicts the contigs that make up the currently viewed scaffold. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks. All components within this track are of fragment type &quot;W&quot;: Whole Genome Shotgun contig. The mitochondrial sequence &quot;chrM&quot; is type &quot;F&quot; - finished. 
augustusGene AUGUSTUS AUGUSTUS ab initio gene predictions v3.1 Genes and Gene Predictions Description This track shows ab initio predictions from the program AUGUSTUS (version 3.1). The predictions are based on the genome sequence alone. For more information on the different gene tracks, see our Genes FAQ. Methods Statistical signal models were built for splice sites, branch-point patterns, translation start sites, and the poly-A signal. Furthermore, models were built for the sequence content of protein-coding and non-coding regions as well as for the length distributions of different exon and intron types. Detailed descriptions of most of these different models can be found in Mario Stanke's dissertation. This track shows the most likely gene structure according to a Semi-Markov Conditional Random Field model. Alternative splicing transcripts were obtained with a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2). The different models used by Augustus were trained on a number of different species-specific gene sets, which included 1000-2000 training gene structures. The --species option allows one to choose the species used for training the models. Different training species were used for the --species option when generating these predictions for different groups of assemblies. Assembly Group Training Species Fish zebrafish Birds chicken Human and all other vertebrates human Nematodes caenorhabditis Drosophila fly A. mellifera honeybee1 A. gambiae culex S. cerevisiae saccharomyces This table describes which training species was used for a particular group of assemblies. When available, the closest related training species was used. Credits Thanks to the Stanke lab for providing the AUGUSTUS program. The training for the chicken version was done by Stefanie K&ouml;nig and the training for the human and zebrafish versions was done by Mario Stanke. References Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. PMID: 14534192 
cytoBandIdeo Chromosome Band (Ideogram) Ideogram for Orientation Mapping and Sequencing 
est Dog ESTs Dog ESTs Including Unspliced mRNA and EST Description This track shows alignments between dog expressed sequence tags (ESTs) in GenBank and the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only ESTs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display ESTs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most &mdash; but not all &mdash; ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, dog ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
mrna Dog mRNAs Dog mRNAs from GenBank mRNA and EST Description The mRNA track shows alignments between dog mRNAs in GenBank and the genome. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only mRNAs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display mRNAs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods GenBank dog mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
ensGene Ensembl Genes Ensembl Genes Genes and Gene Predictions Description These gene predictions were generated by Ensembl. For more information on the different gene tracks, see our Genes FAQ. Methods For a description of the methods used in Ensembl gene predictions, please refer to Hubbard et al. (2002), also listed in the References section below. Data access Ensembl Gene data can be explored interactively using the Table Browser or the Data Integrator. For local downloads, the genePred format files for canFam3 are available in our downloads directory as ensGene.txt.gz or in our genes download directory in GTF format. For programmatic access, the data can be queried from the REST API or directly from our public MySQL servers. Instructions on this method are available on our MySQL help page and on our blog. Previous versions of this track can be found on our archive download server. Credits We would like to thank Ensembl for providing these gene annotations. For more information, please see Ensembl&#39s genome annotation page. References Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 
evaSnpContainer EVA SNP Short Genetic Variants from European Variant Archive Variation and Repeats Description These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) from the European Variation Archive (EVA) for the dog canFam3 genome. The dbSNP database at NCBI no longer hosts non-human variants. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP variant corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. The display is set to automatically collapse to dense visibility when there are more than 100k variants in the window. When the window size is more than 250k bp, the display is switched to density graph mode. Searching, details, and filtering Navigation to an individual variant can be accomplished by typing or copying the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the Browser. A click on an item in the graphical display displays a page with data about that variant. Data fields include the Reference and Alternate Alleles, the class of the variant as reported by EVA, the source of the data, the amino acid change, if any, and the functional class as determined by UCSC's Variant Annotation Integrator. Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes. Mouse-over Mousing over an item shows the ucscClass, which is the consequence according to the Variant Annotation Integrator, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID separated by spaces describing all possible AA changes. Multiple items may appear due to different variant predictions on multiple gene transcripts. For all organisms the gene models used were the NCBI RefSeq curated when available, if not then ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. Track colors Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below. Color Variant Type Protein-altering variants and splice site variants Synonymous codon variants Non-coding transcript or Untranslated Region (UTR) variants Intergenic and intronic variants Sequence ontology (SO) Variants are classified by EVA into one of the following sequence ontology terms: substitution &mdash; A single nucleotide in the reference is replaced by another, alternate allele deletion &mdash; One or more nucleotides is deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G. insertion &mdash; One or more nucleotides is inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe be represented as Ref = G and Alt = GT delins &mdash; Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. multipleNucleotideVariant &mdash; More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. sequence alteration &mdash; A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. Methods Data were downloaded from the European Variation Archive EVA current_ids.vcf.gz files corresponding to the proper assembly. Chromosome names were converted to UCSC-style and the variants passed through the Variant Annotation Integrator to predict consequence. For every organism the NCBI RefSeq curated models were used when available, followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models were possible. Variants were then colored according to their predicted consequence in the following fashion: Protein-altering variants and splice site variants - exon_loss_variant, frameshift_variant, inframe_deletion, inframe_insertion, initiator_codon_variant, missense_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, stop_gained, stop_lost, coding_sequence_variant, transcript_ablation Synonymous codon variants - synonymous_variant, stop_retained_variant Non-coding transcript or Untranslated Region (UTR) variants - 5_prime_UTR_variant, 3_prime_UTR_variant, complex_transcript_variant, non_coding_transcript_exon_variant Intergenic and intronic variants - upstream_gene_variant, downstream_gene_variant, intron_variant, intergenic_variant, NMD_transcript_variant, no_sequence_alteration Sequence Ontology (&quot;SO:&quot;) terms were converted to the variant classes, then the files were converted to BED, and then bigBed format. No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). Amino-acid substitutions for missense variants are based on RefSeq alignments of mRNA transcripts, which do not always match the amino acids predicted from translating the genomic sequence. Therefore, in some instances, the variant and the genomic nucleotide and associated amino acid may be reversed. E.g., a Pro &gt; Arg change from the perspective of the mRNA would be Arg &gt; Pro from the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. For complete documentation of the processing of these tracks, see the makedoc corresponding to the version of interest. For example, the EVA Release 6 MakeDoc. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from our download server. Use the corresponding version number for the track of interest, e.g. evaSnp6.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/canFam3/bbi/evaSnp6.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits This track was produced from the European Variation Archive release data. Consequences were predicted using UCSC's Variant Annotation Integrator and NCBI's RefSeq as well as ensembl gene models. References Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021 Oct 28:gkab960. doi:10.1093/nar/gkab960. Epub ahead of print. PMID: 34718739. PMID: PMC8728205. Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. PMID: 26740527; PMC: PMC4848401 
evaSnp6 EVA SNP Release 6 Short Genetic Variants from European Variant Archive Release 6 Variation and Repeats Description These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) from the European Variation Archive (EVA) for the dog canFam3 genome. The dbSNP database at NCBI no longer hosts non-human variants. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP variant corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. The display is set to automatically collapse to dense visibility when there are more than 100k variants in the window. When the window size is more than 250k bp, the display is switched to density graph mode. Searching, details, and filtering Navigation to an individual variant can be accomplished by typing or copying the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the Browser. A click on an item in the graphical display displays a page with data about that variant. Data fields include the Reference and Alternate Alleles, the class of the variant as reported by EVA, the source of the data, the amino acid change, if any, and the functional class as determined by UCSC's Variant Annotation Integrator. Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes. Mouse-over Mousing over an item shows the ucscClass, which is the consequence according to the Variant Annotation Integrator, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID separated by spaces describing all possible AA changes. Multiple items may appear due to different variant predictions on multiple gene transcripts. For all organisms the gene models used were the NCBI RefSeq curated when available, if not then ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. Track colors Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below. Color Variant Type Protein-altering variants and splice site variants Synonymous codon variants Non-coding transcript or Untranslated Region (UTR) variants Intergenic and intronic variants Sequence ontology (SO) Variants are classified by EVA into one of the following sequence ontology terms: substitution &mdash; A single nucleotide in the reference is replaced by another, alternate allele deletion &mdash; One or more nucleotides is deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G. insertion &mdash; One or more nucleotides is inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe be represented as Ref = G and Alt = GT delins &mdash; Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. multipleNucleotideVariant &mdash; More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. sequence alteration &mdash; A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. Methods Data were downloaded from the European Variation Archive EVA current_ids.vcf.gz files corresponding to the proper assembly. Chromosome names were converted to UCSC-style and the variants passed through the Variant Annotation Integrator to predict consequence. For every organism the NCBI RefSeq curated models were used when available, followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models were possible. Variants were then colored according to their predicted consequence in the following fashion: Protein-altering variants and splice site variants - exon_loss_variant, frameshift_variant, inframe_deletion, inframe_insertion, initiator_codon_variant, missense_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, stop_gained, stop_lost, coding_sequence_variant, transcript_ablation Synonymous codon variants - synonymous_variant, stop_retained_variant Non-coding transcript or Untranslated Region (UTR) variants - 5_prime_UTR_variant, 3_prime_UTR_variant, complex_transcript_variant, non_coding_transcript_exon_variant Intergenic and intronic variants - upstream_gene_variant, downstream_gene_variant, intron_variant, intergenic_variant, NMD_transcript_variant, no_sequence_alteration Sequence Ontology (&quot;SO:&quot;) terms were converted to the variant classes, then the files were converted to BED, and then bigBed format. No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). Amino-acid substitutions for missense variants are based on RefSeq alignments of mRNA transcripts, which do not always match the amino acids predicted from translating the genomic sequence. Therefore, in some instances, the variant and the genomic nucleotide and associated amino acid may be reversed. E.g., a Pro &gt; Arg change from the perspective of the mRNA would be Arg &gt; Pro from the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. For complete documentation of the processing of these tracks, see the makedoc corresponding to the version of interest. For example, the EVA Release 6 MakeDoc. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from our download server. Use the corresponding version number for the track of interest, e.g. evaSnp6.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/canFam3/bbi/evaSnp6.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits This track was produced from the European Variation Archive release data. Consequences were predicted using UCSC's Variant Annotation Integrator and NCBI's RefSeq as well as ensembl gene models. References Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021 Oct 28:gkab960. doi:10.1093/nar/gkab960. Epub ahead of print. PMID: 34718739. PMID: PMC8728205. Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. PMID: 26740527; PMC: PMC4848401 
evaSnp5 EVA SNP Release 5 Short Genetic Variants from European Variant Archive Release 5 Variation and Repeats Description This track contains mappings of single nucleotide variants and small insertions and deletions (indels) from the European Variation Archive (EVA) Release 5 for the dog canFam3 genome. The dbSNP database at NCBI no longer hosts non-human variants. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP variant corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. The display is set to automatically collapse to dense visibility when there are more than 100k variants in the window. When the window size is more than 250k bp, the display is switched to density graph mode. Searching, details, and filtering Navigation to an individual variant can be accomplished by typing or copying the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the Browser. A click on an item in the graphical display displays a page with data about that variant. Data fields include the Reference and Alternate Alleles, the class of the variant as reported by EVA, the source of the data, the amino acid change, if any, and the functional class as determined by UCSC's Variant Annotation Integrator. Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes. Mouse-over Mousing over an item shows the ucscClass, which is the consequence according to the Variant Annotation Integrator, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID separated by spaces describing all possible AA changes. Multiple items may appear due to different variant predictions on multiple gene transcripts. For all organisms the gene models used were the NCBI RefSeq curated when available, if not then ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. Track colors Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below. Color Variant Type Protein-altering variants and splice site variants Synonymous codon variants Non-coding transcript or Untranslated Region (UTR) variants Intergenic and intronic variants Sequence ontology (SO) Variants are classified by EVA into one of the following sequence ontology terms: substitution &mdash; A single nucleotide in the reference is replaced by another, alternate allele deletion &mdash; One or more nucleotides is deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G. insertion &mdash; One or more nucleotides is inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe be represented as Ref = G and Alt = GT delins &mdash; Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. multipleNucleotideVariant &mdash; More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. sequence alteration &mdash; A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. Methods Data were downloaded from the European Variation Archive EVA release 5 (2023-9-7) current_ids.vcf.gz files corresponding to the proper assembly. Chromosome names were converted to UCSC-style and the variants passed through the Variant Annotation Integrator to predict consequence. For every organism the NCBI RefSeq curated models were used when available, followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models were possible. Variants were then colored according to their predicted consequence in the following fashion: Protein-altering variants and splice site variants - exon_loss_variant, frameshift_variant, inframe_deletion, inframe_insertion, initiator_codon_variant, missense_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, stop_gained, stop_lost, coding_sequence_variant, transcript_ablation Synonymous codon variants - synonymous_variant, stop_retained_variant Non-coding transcript or Untranslated Region (UTR) variants - 5_prime_UTR_variant, 3_prime_UTR_variant, complex_transcript_variant, non_coding_transcript_exon_variant Intergenic and intronic variants - upstream_gene_variant, downstream_gene_variant, intron_variant, intergenic_variant, NMD_transcript_variant, no_sequence_alteration Sequence Ontology (&quot;SO:&quot;) terms were converted to the variant classes, then the files were converted to BED, and then bigBed format. No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). Amino-acid substitutions for missense variants are based on RefSeq alignments of mRNA transcripts, which do not always match the amino acids predicted from translating the genomic sequence. Therefore, in some instances, the variant and the genomic nucleotide and associated amino acid may be reversed. E.g., a Pro &gt; Arg change from the perspective of the mRNA would be Arg &gt; Pro from the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. For complete documentation of the processing of these tracks, read the EVA Release 5 MakeDoc. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called evaSnp5.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/canFam3/bbi/evaSnp5.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits This track was produced from the European Variation Archive release 5 data. Consequences were predicted using UCSC's Variant Annotation Integrator and NCBI's RefSeq as well as ensembl gene models. References Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021 Oct 28:gkab960. doi:10.1093/nar/gkab960. Epub ahead of print. PMID: 34718739. PMID: PMC8728205. Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. PMID: 26740527; PMC: PMC4848401 
evaSnp4 EVA SNP Release 4 Short Genetic Variants from European Variant Archive Release 4 Variation and Repeats Description This track contains mappings of single nucleotide variants and small insertions and deletions (indels) from the European Variation Archive (EVA) Release 4 for the dog canFam3 genome. The dbSNP database at NCBI no longer hosts non-human variants. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP variant corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. The display is set to automatically collapse to dense visibility when there are more than 100k variants in the window. When the window size is more than 250k bp, the display is switched to density graph mode. Searching, details, and filtering Navigation to an individual variant can be accomplished by typing or copying the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the Browser. A click on an item in the graphical display displays a page with data about that variant. Data fields include the Reference and Alternate Alleles, the class of the variant as reported by EVA, the source of the data, the amino acid change, if any, and the functional class as determined by UCSC's Variant Annotation Integrator. Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes. Mouse-over Mousing over an item shows the ucscClass, which is the consequence according to the Variant Annotation Integrator, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID separated by spaces describing all possible AA changes. Multiple items may appear due to different variant predictions on multiple gene transcripts. For all organisms the gene models used were the NCBI RefSeq curated when available, if not then ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. Track colors Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below. Color Variant Type Protein-altering variants and splice site variants Synonymous codon variants Non-coding transcript or Untranslated Region (UTR) variants Intergenic and intronic variants Sequence ontology (SO) Variants are classified by EVA into one of the following sequence ontology terms: substitution &mdash; A single nucleotide in the reference is replaced by another, alternate allele deletion &mdash; One or more nucleotides is deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G. insertion &mdash; One or more nucleotides is inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe be represented as Ref = G and Alt = GT delins &mdash; Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. multipleNucleotideVariant &mdash; More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. sequence alteration &mdash; A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. Methods Data were downloaded from the European Variation Archive EVA release 4 (2022-11-21) current_ids.vcf.gz files corresponding to the proper assembly. Chromosome names were converted to UCSC-style and the variants passed through the Variant Annotation Integrator to predict consequence. For every organism the NCBI RefSeq curated models were used when available, followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models were possible. Variants were then colored according to their predicted consequence in the following fashion: Protein-altering variants and splice site variants - exon_loss_variant, frameshift_variant, inframe_deletion, inframe_insertion, initiator_codon_variant, missense_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, stop_gained, stop_lost, coding_sequence_variant, transcript_ablation Synonymous codon variants - synonymous_variant, stop_retained_variant Non-coding transcript or Untranslated Region (UTR) variants - 5_prime_UTR_variant, 3_prime_UTR_variant, complex_transcript_variant, non_coding_transcript_exon_variant Intergenic and intronic variants - upstream_gene_variant, downstream_gene_variant, intron_variant, intergenic_variant, NMD_transcript_variant, no_sequence_alteration Sequence Ontology (&quot;SO:&quot;) terms were converted to the variant classes, then the files were converted to BED, and then bigBed format. No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). Amino-acid substitutions for missense variants are based on RefSeq alignments of mRNA transcripts, which do not always match the amino acids predicted from translating the genomic sequence. Therefore, in some instances, the variant and the genomic nucleotide and associated amino acid may be reversed. E.g., a Pro &gt; Arg change from the perspective of the mRNA would be Arg &gt; Pro from the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. For complete documentation of the processing of these tracks, read the EVA Release 4 MakeDoc. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called evaSnp4.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/canFam3/bbi/evaSnp4.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits This track was produced from the European Variation Archive release 4 data. Consequences were predicted using UCSC's Variant Annotation Integrator and NCBI's RefSeq as well as ensembl gene models. References Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021 Oct 28:gkab960. doi:10.1093/nar/gkab960. Epub ahead of print. PMID: 34718739. PMID: PMC8728205. Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. PMID: 26740527; PMC: PMC4848401 
evaSnp EVA SNP Release 3 Short Genetic Variants from European Variant Archive Release 3 Variation and Repeats Description This track contains mappings of single nucleotide variants and small insertions and deletions (indels) from the European Variation Archive (EVA) Release 3 for the dog canFam3 genome. The dbSNP database at NCBI no longer hosts non-human variants. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP variant corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. The display is set to automatically collapse to dense visibility when there are more than 100k variants in the window. When the window size is more than 250k bp, the display is switched to density graph mode. Searching, details, and filtering Navigation to an individual variant can be accomplished by typing or copying the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the Browser. A click on an item in the graphical display displays a page with data about that variant. Data fields include the Reference and Alternate Alleles, the class of the variant as reported by EVA, the source of the data, the amino acid change, if any, and the functional class as determined by UCSC's Variant Annotation Integrator. Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes. Mouse-over Mousing over an item shows the ucscClass, which is the consequence according to the Variant Annotation Integrator, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID separated by spaces describing all possible AA changes. Multiple items may appear due to different variant predictions on multiple gene transcripts. For all organisms the gene models used were ncbiRefSeqCurated, except for mm39 which used ncbiRefSeqSelect. Track colors Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below. Color Variant Type Protein-altering variants and splice site variants Synonymous codon variants Non-coding transcript or Untranslated Region (UTR) variants Intergenic and intronic variants Sequence ontology (SO) Variants are classified by EVA into one of the following sequence ontology terms: substitution &mdash; A single nucleotide in the reference is replaced by another, alternate allele deletion &mdash; One or more nucleotides is deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G. insertion &mdash; One or more nucleotides is inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe be represented as Ref = G and Alt = GT delins &mdash; Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. multipleNucleotideVariant &mdash; More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. sequence alteration &mdash; A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. Methods Data were downloaded from the European Variation Archive EVA release 3 (2022-02-24) current_ids.vcf.gz files corresponding to the proper assembly. Chromosome names were converted to UCSC-style, a few problematic variants were removed, and the variants passed through the Variant Annotation Integrator to predict consequence. For every organism the ncbiRefSeqCurated gene models were used to predict the consequences, except for mm39 which used the ncbiRefSeqSelect models. Variants were then colored according to their predicted consequence in the following fashion: Protein-altering variants and splice site variants - exon_loss_variant, frameshift_variant, inframe_deletion, inframe_insertion, initiator_codon_variant, missense_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, stop_gained, stop_lost, coding_sequence_variant, transcript_ablation Synonymous codon variants - synonymous_variant, stop_retained_variant Non-coding transcript or Untranslated Region (UTR) variants - 5_prime_UTR_variant, 3_prime_UTR_variant, complex_transcript_variant, non_coding_transcript_exon_variant Intergenic and intronic variants - upstream_gene_variant, downstream_gene_variant, intron_variant, intergenic_variant, NMD_transcript_variant, no_sequence_alteration Sequence Ontology (&quot;SO:&quot;) terms were converted to the variant classes, then the files were converted to BED, and then bigBed format. No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). Amino-acid substitutions for missense variants are based on RefSeq alignments of mRNA transcripts, which do not always match the amino acids predicted from translating the genomic sequence. Therefore, in some instances, the variant and the genomic nucleotide and associated amino acid may be reversed. E.g., a Pro > Arg change from the perspective of the mRNA would be Arg > Pro from the persepective the genomic sequence. For complete documentation of the processing of these tracks, read the EVA Release 3 MakeDoc. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called evaSnp.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/canFam3/bbi/evaSnp.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits This track was produced from the European Variation Archive release 3 data. Consequences were predicted using UCSC's Variant Annotation Integrator and NCBI's RefSeq gene models. References Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021 Oct 28:gkab960. doi:10.1093/nar/gkab960. Epub ahead of print. PMID: 34718739. PMID: PMC8728205. Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. PMID: 26740527; PMC: PMC4848401 
gap Gap Gap Locations Mapping and Sequencing Description This track depicts gaps in the draft assembly (Sep. 2011, Broad CanFam3.1 (GCA_000002285.2)) of the dog genome. Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap. This assembly contains the following principal types of gaps: Short Arm - 100 bases of Ns marked at the beginning of each chromosome Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. These are represented by varying numbers of Ns in the assembly. In this context, a contig is a set of overlapping sequence reads and a supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads. Fragment gap sizes are usually taken from read pair data. Clone - gaps between supercontigs linked by the physical map. In general, these are represented by 1,000 Ns in the assembly. Other - sequences of Ns in the assembly that were not annotated in the AGP file as gap. Added by UCSC. 
gc5BaseBw GC Percent GC Percent in 5-Base Windows Mapping and Sequencing Description The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the &quot;Graph configuration help&quot; link for an explanation of the configuration options. Credits The data and presentation of this graph were prepared by Hiram Clawson. 
geneid Geneid Genes Geneid Gene Predictions Genes and Gene Predictions Description This track shows gene predictions from the geneid program developed by Roderic Guig&oacute;'s Computational Biology of RNA Processing group which is part of the Centre de Regulaci&oacute; Gen&ograve;mica (CRG) in Barcelona, Catalunya, Spain. Methods Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. Credits Thanks to Computational Biology of RNA Processing for providing these data. References Blanco E, Parra G, Guig&#243; R. Using geneid to identify genes. Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3. PMID: 18428791 Parra G, Blanco E, Guig&#243; R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871 
genscan Genscan Genes Genscan Gene Predictions Genes and Gene Predictions Description This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The track description page offers the following filter and configuration options: Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. Methods For a description of the Genscan program and the model that underlies it, refer to Burge and Karlin (1997) in the References section below. The splice site models used are described in more detail in Burge (1998) below. Credits Thanks to Chris Burge for providing the Genscan program. References Burge C. Modeling Dependencies in Pre-mRNA Splicing Signals. In: Salzberg S, Searls D, Kasif S, editors. Computational Methods in Molecular Biology. Amsterdam: Elsevier Science; 1998. p. 127-163. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997 Apr 25;268(1):78-94. PMID: 9149143 
ucscToINSDC INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration Mapping and Sequencing Description This track associates UCSC Genome Browser chromosome names to accession names from the International Nucleotide Sequence Database Collaboration (INSDC). The data were downloaded from the NCBI assembly database. Credits The data for this track was prepared by Hiram Clawson. 
nestedRepeats Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID Variation and Repeats Description This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program which screens DNA sequences for interspersed repeats and low complexity DNA sequences using the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. The detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output. Display Conventions and Configuration In pack or full mode, each interrupted repeat is displayed as boxes (fragments) joined by horizontal lines, labeled with the repeat name. If all fragments are on the same strand, arrows are added to the horizontal line to indicate the strand. In dense or squish mode, labels and arrows are omitted and in dense mode, all items are collapsed to fit on a single row. Items are shaded according to the average identity score of their fragments. Usually, the shade of an item is similar to the shades of its fragments unless some fragments are much more diverged than others. The score displayed above is the average identity score, clipped to a range of 50% - 100% and then mapped to the range 0 - 1000 for shading in the browser. Methods UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet. Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. See the FAQ for more information. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Repbase Update is described in: Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072 For a discussion of repeats in mammalian genomes, see: Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616 Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846 
microsat Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats Variation and Repeats Description This track displays regions that are likely to be useful as microsatellite markers. These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats and tend to be highly polymorphic in the population. Methods The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. The Simple Repeats track is created using the Tandem Repeats Finder. For more information about this program, see Benson (1999). Credits Tandem Repeats Finder was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
oreganno ORegAnno Regulatory elements from ORegAnno Expression and Regulation Description This track displays literature-curated regulatory regions, transcription factor binding sites, and regulatory polymorphisms from ORegAnno (Open Regulatory Annotation). For more detailed information on a particular regulatory element, follow the link to ORegAnno from the details page. ORegAnno (Open Regulatory Annotation). --> Display Conventions and Configuration The display may be filtered to show only selected region types, such as: regulatory regions (shown in light blue) regulatory polymorphisms (shown in dark blue) transcription factor binding sites (shown in orange) regulatory haplotypes (shown in red) miRNA binding sites (shown in blue-green) To exclude a region type, uncheck the appropriate box in the list at the top of the Track Settings page. Methods An ORegAnno record describes an experimentally proven and published regulatory region (promoter, enhancer, etc.), transcription factor binding site, or regulatory polymorphism. Each annotation must have the following attributes: A stable ORegAnno identifier. A valid taxonomy ID from the NCBI taxonomy database. A valid PubMed reference. A target gene that is either user-defined, in Entrez Gene or in EnsEMBL. A sequence with at least 40 flanking bases (preferably more) to allow the site to be mapped to any release of an associated genome. At least one piece of specific experimental evidence, including the biological technique used to discover the regulatory sequence. (Currently only the evidence subtypes are supplied with the UCSC track.) A positive, neutral or negative outcome based on the experimental results from the primary reference. (Only records with a positive outcome are currently included in the UCSC track.) The following attributes are optionally included: A transcription factor that is either user-defined, in Entrez Gene or in EnsEMBL. A specific cell type for each piece of experimental evidence, using the eVOC cell type ontology. A specific dataset identifier (e.g. the REDfly dataset) that allows external curators to manage particular annotation sets using ORegAnno's curation tools. A &quot;search space&quot; sequence that specifies the region that was assayed, not just the regulatory sequence. A dbSNP identifier and type of variant (germline, somatic or artificial) for regulatory polymorphisms. Mapping to genome coordinates is performed periodically to current genome builds by BLAST sequence alignment. The information provided in this track represents an abbreviated summary of the details for each ORegAnno record. Please visit the official ORegAnno entry (by clicking on the ORegAnno link on the details page of a specific regulatory element) for complete details such as evidence descriptions, comments, validation score history, etc. Credits ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith, and Steven Jones from Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada. The ORegAnno community (please see individual citations for various features): ORegAnno Citation. References Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open Regulatory Annotation Consortium.. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D126-32. PMID: 26578589; PMC: PMC4702855 Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. PMID: 18006570; PMC: PMC2239002 Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 2006 Mar 1;22(5):637-40. PMID: 16397004 
xenoMrna Other mRNAs Non-Dog mRNAs from GenBank mRNA and EST Description This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than dog. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) for this track is in two parts. The first + indicates the orientation of the query sequence whose translated protein produced the match (here always 5' to 3', hence +). The second + or - indicates the orientation of the matching translated genomic sequence. Because the two orientations of a DNA sequence give different predicted protein sequences, there are four combinations. ++ is not the same as --, nor is +- the same as -+. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only mRNAs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display mRNAs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods The mRNAs were aligned against the dog genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
xenoRefGene Other RefSeq Non-Dog RefSeq Genes Genes and Gene Predictions Description This track shows known protein-coding and non-protein-coding genes for organisms other than dog, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods The RNAs were aligned against the dog genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
ucscToRefSeq RefSeq Acc RefSeq Accession Mapping and Sequencing Description This track associates UCSC Genome Browser chromosome names to accession identifiers from the NCBI Reference Sequence Database (RefSeq). The data were downloaded from the NCBI assembly database. Credits The data for this track was prepared by Hiram Clawson. 
simpleRepeat Simple Repeats Simple Tandem Repeats by TRF Variation and Repeats Description This track displays simple tandem repeats (possibly imperfect repeats) located by Tandem Repeats Finder (TRF) which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases. Methods For more information about the TRF program, see Benson (1999). Credits TRF was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
intronEst Spliced ESTs Dog ESTs That Have Been Spliced mRNA and EST Description This track shows alignments between dog expressed sequence tags (ESTs) in GenBank and the genome that show signs of splicing when aligned against the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. To be considered spliced, an EST must show evidence of at least one canonical intron (i.e., the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends). By requiring splicing, the level of contamination in the EST databases is drastically reduced at the expense of eliminating many genuine 3' ESTs. For a display of all ESTs (including unspliced), see the dog EST track. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, darker shading indicates a larger number of aligned ESTs. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only ESTs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display ESTs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most &mdash; but not all &mdash; ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, dog ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence are displayed in this track. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
windowmaskerSdust WM + SDust Genomic Intervals Masked by WindowMasker + SDust Variation and Repeats Description This track depicts masked sequence as determined by WindowMasker. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site. Methods To create this track, WindowMasker was run with the following parameters: windowmasker -mk_counts true -input canFam3.fa -output wm_counts windowmasker -ustat wm_counts -sdust true -input canFam3.fa -output repeats.bed The repeats.bed (BED3) file was loaded into the &quot;windowmaskerSdust&quot; table for this track. References Morgulis A, Gertz EM, Sch&auml;ffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 
chainNetRn6 Rat Chain/Net Rat (Jul. 2014 (RGSC 6.0/rn6)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rat (Jul. 2014 (RGSC 6.0/rn6)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rat assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rat/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rat sequence used in this annotation is from the Jul. 2014 (RGSC 6.0/rn6) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rat/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rat chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRn6Viewnet Net Rat (Jul. 2014 (RGSC 6.0/rn6)), Chain and Net Alignments Comparative Genomics 
netRn6 Rat Net Rat (Jul. 2014 (RGSC 6.0/rn6)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rat (Jul. 2014 (RGSC 6.0/rn6)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rat assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rat/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rat sequence used in this annotation is from the Jul. 2014 (RGSC 6.0/rn6) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rat/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rat chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRn6Viewchain Chain Rat (Jul. 2014 (RGSC 6.0/rn6)), Chain and Net Alignments Comparative Genomics 
chainRn6 Rat Chain Rat (Jul. 2014 (RGSC 6.0/rn6)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rat (Jul. 2014 (RGSC 6.0/rn6)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rat assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rat/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rat sequence used in this annotation is from the Jul. 2014 (RGSC 6.0/rn6) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rat/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rat chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFelCat8 Cat Chain/Net Cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cat and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cat assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cat/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cat sequence used in this annotation is from the Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cat/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cat chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A95-160-43-141 C-160100-121-43 G-43-121100-160 T-141-43-16095 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFelCat8Viewnet Net Cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)), Chain and Net Alignments Comparative Genomics 
netFelCat8 Cat Net Cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cat and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cat assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cat/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cat sequence used in this annotation is from the Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cat/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cat chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A95-160-43-141 C-160100-121-43 G-43-121100-160 T-141-43-16095 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFelCat8Viewchain Chain Cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)), Chain and Net Alignments Comparative Genomics 
chainFelCat8 Cat Chain Cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cat (Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cat and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cat assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cat/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cat sequence used in this annotation is from the Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cat/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cat chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A95-160-43-141 C-160100-121-43 G-43-121100-160 T-141-43-16095 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam4 Dog Chain/Net Dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam4Viewnet Net Dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)), Chain and Net Alignments Comparative Genomics 
netCanFam4 Dog Net Dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam4Viewchain Chain Dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)), Chain and Net Alignments Comparative Genomics 
chainCanFam4 Dog Chain Dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMm10 Mouse Chain/Net Mouse (Dec. 2011 (GRCm38/mm10)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of mouse (Dec. 2011 (GRCm38/mm10)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the mouse assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best mouse/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the Dec. 2011 (GRCm38/mm10) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the mouse/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMm10Viewnet Net Mouse (Dec. 2011 (GRCm38/mm10)), Chain and Net Alignments Comparative Genomics 
netMm10 Mouse Net Mouse (Dec. 2011 (GRCm38/mm10)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of mouse (Dec. 2011 (GRCm38/mm10)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the mouse assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best mouse/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the Dec. 2011 (GRCm38/mm10) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the mouse/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMm10Viewchain Chain Mouse (Dec. 2011 (GRCm38/mm10)), Chain and Net Alignments Comparative Genomics 
chainMm10 Mouse Chain Mouse (Dec. 2011 (GRCm38/mm10)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of mouse (Dec. 2011 (GRCm38/mm10)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the mouse assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best mouse/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the Dec. 2011 (GRCm38/mm10) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the mouse/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetTarSyr2 Tarsier Chain/Net Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both tarsier and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the tarsier assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best tarsier/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The tarsier sequence used in this annotation is from the Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the tarsier/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single tarsier chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetTarSyr2Viewnet Net Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)), Chain and Net Alignments Comparative Genomics 
netTarSyr2 Tarsier Net Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both tarsier and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the tarsier assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best tarsier/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The tarsier sequence used in this annotation is from the Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the tarsier/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single tarsier chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetTarSyr2Viewchain Chain Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)), Chain and Net Alignments Comparative Genomics 
chainTarSyr2 Tarsier Chain Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both tarsier and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the tarsier assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best tarsier/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The tarsier sequence used in this annotation is from the Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the tarsier/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single tarsier chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19 hg19 Chain/Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19Viewnet Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics 
netHg19 hg19 Net Human (Feb. 2009 (GRCh37/hg19)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19Viewchain Chain Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics 
chainHg19 hg19 Chain Human (Feb. 2009 (GRCh37/hg19)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg38 hg38 Chain/Net Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg38Viewnet Net Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments Comparative Genomics 
netHg38 hg38 Net Human (Dec. 2013 (GRCh38/hg38)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg38Viewchain Chain Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments Comparative Genomics 
chainHg38 hg38 Chain Human (Dec. 2013 (GRCh38/hg38)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetXenTro9 X. tropicalis Chain/Net X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both X. tropicalis and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the X. tropicalis assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best X. tropicalis/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The X. tropicalis sequence used in this annotation is from the Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the X. tropicalis/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single X. tropicalis chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetXenTro9Viewnet Net X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)), Chain and Net Alignments Comparative Genomics 
netXenTro9 X. tropicalis Net X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both X. tropicalis and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the X. tropicalis assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best X. tropicalis/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The X. tropicalis sequence used in this annotation is from the Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the X. tropicalis/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single X. tropicalis chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetXenTro9Viewchain Chain X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)), Chain and Net Alignments Comparative Genomics 
chainXenTro9 X. tropicalis Chain X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)) to the dog genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both X. tropicalis and dog simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the X. tropicalis assembly or an insertion in the dog assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the dog genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best X. tropicalis/dog chain for every part of the dog genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The X. tropicalis sequence used in this annotation is from the Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the X. tropicalis/dog split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single X. tropicalis chromosome and a single dog chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961