This directory contains a dump of the UCSC genome annotation database for the Jun. 2020 (GRCm39/mm39) assembly of the mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) from the Mouse Genome Sequencing Consortium. The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: https://www.ncbi.nlm.nih.gov/genome/52 https://www.ncbi.nlm.nih.gov/genome/assembly/7358741 https://www.ncbi.nlm.nih.gov/bioproject/20689 https://www.ncbi.nlm.nih.gov/biosample/n/a Files included in this directory (updated nightly): - *.sql files: the MySQL commands used to create the tables - *.txt.gz files: the database tables in a tab-delimited format compressed with gzip. To see descriptions of the tables underlying Genome Browser annotation tracks, select the table in the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables?db=mm39 and click the "describe table schema" button. There is also a "view table schema" link on the configuration page for each track. --------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.soe.ucsc.edu, then go to the directory goldenPath/mm39/database/. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/gc5Base.txt.gz' -O gc5Base.txt.gz To uncompress the *.txt.gz files: gunzip <table>.txt.gz The tables can be loaded directly from the .txt.gz compressed file. It is not necessary to uncompress them to load into a database, as shown in the example below. To load one of the tables directly into your local mirror database, for example the table chromInfo: ## create table from the sql definition $ hgsql mm39 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql mm39 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- GenBank Data Usage The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. ----------------------------------------------------------------------------- All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - all_est.sql 2020-08-18 00:35 2.1K all_est.txt.gz 2020-08-18 00:35 213M all_mrna.sql 2020-08-17 17:04 2.1K all_mrna.txt.gz 2020-08-17 17:04 41M augustusGene.sql 2020-07-30 12:51 2.0K augustusGene.txt.gz 2020-07-30 12:51 2.3M bigFiles.sql 2024-12-08 03:05 1.4K bigFiles.txt.gz 2024-12-08 03:05 142 bioCycMapDesc.sql 2024-08-15 14:59 1.4K bioCycMapDesc.txt.gz 2024-08-15 14:59 4.9K bioCycPathway.sql 2024-08-15 14:59 1.5K bioCycPathway.txt.gz 2024-08-15 14:59 19K ceBlastTab.sql 2024-08-15 14:59 1.7K ceBlastTab.txt.gz 2024-08-15 14:59 123K chainBosTau9.sql 2020-11-23 18:06 1.7K chainBosTau9.txt.gz 2020-11-23 18:06 67M chainBosTau9Link.sql 2020-11-23 18:10 1.6K chainBosTau9Link.txt.gz 2020-11-23 18:10 498M chainCalJac4.sql 2020-09-04 15:06 1.7K chainCalJac4.txt.gz 2020-09-04 15:06 77M chainCalJac4Link.sql 2020-09-04 15:10 1.6K chainCalJac4Link.txt.gz 2020-09-04 15:10 519M chainCanFam5.sql 2020-08-17 15:44 1.7K chainCanFam5.txt.gz 2020-08-17 15:44 53M chainCanFam5Link.sql 2020-08-17 15:47 1.6K chainCanFam5Link.txt.gz 2020-08-17 15:47 443M chainCanFam6.sql 2021-05-18 12:04 1.7K chainCanFam6.txt.gz 2021-05-18 12:04 49M chainCanFam6Link.sql 2021-05-18 12:07 1.6K chainCanFam6Link.txt.gz 2021-05-18 12:07 418M chainCavPor3.sql 2020-11-25 22:02 1.7K chainCavPor3.txt.gz 2020-11-25 22:02 64M chainCavPor3Link.sql 2020-11-25 22:06 1.6K chainCavPor3Link.txt.gz 2020-11-25 22:06 506M chainDanRer11.sql 2020-11-25 00:58 1.7K chainDanRer11.txt.gz 2020-11-25 00:58 11M chainDanRer11Link.sql 2020-11-25 00:59 1.6K chainDanRer11Link.txt.gz 2020-11-25 00:59 39M chainEchTel2.sql 2020-11-25 00:17 1.7K chainEchTel2.txt.gz 2020-11-25 00:17 57M chainEchTel2Link.sql 2020-11-25 00:20 1.6K chainEchTel2Link.txt.gz 2020-11-25 00:20 340M chainEquCab3.sql 2020-11-24 13:52 1.7K chainEquCab3.txt.gz 2020-11-24 13:52 122M chainEquCab3Link.sql 2020-11-24 13:58 1.6K chainEquCab3Link.txt.gz 2020-11-24 13:58 766M chainEriEur2.sql 2020-11-24 21:40 1.7K chainEriEur2.txt.gz 2020-11-24 21:40 54M chainEriEur2Link.sql 2020-11-24 21:43 1.6K chainEriEur2Link.txt.gz 2020-11-24 21:43 307M chainGalGal6.sql 2020-11-25 00:13 1.7K chainGalGal6.txt.gz 2020-11-25 00:13 4.0M chainGalGal6Link.sql 2020-11-25 00:13 1.6K chainGalGal6Link.txt.gz 2020-11-25 00:13 29M chainGalVar1.sql 2020-11-24 01:32 1.7K chainGalVar1.txt.gz 2020-11-24 01:32 182M chainGalVar1Link.sql 2020-11-24 01:38 1.6K chainGalVar1Link.txt.gz 2020-11-24 01:38 745M chainGorGor6.sql 2020-11-24 05:07 1.7K chainGorGor6.txt.gz 2020-11-24 05:07 98M chainGorGor6Link.sql 2020-11-24 05:11 1.6K chainGorGor6Link.txt.gz 2020-11-24 05:11 525M chainHg38.sql 2020-08-18 09:26 1.7K chainHg38.txt.gz 2020-08-18 09:26 68M chainHg38Link.sql 2020-08-18 09:30 1.6K chainHg38Link.txt.gz 2020-08-18 09:30 541M chainLoxAfr3.sql 2020-11-24 23:55 1.7K chainLoxAfr3.txt.gz 2020-11-24 23:55 93M chainLoxAfr3Link.sql 2020-11-25 00:00 1.6K chainLoxAfr3Link.txt.gz 2020-11-25 00:00 641M chainManPen1.sql 2020-11-24 00:02 1.7K chainManPen1.txt.gz 2020-11-24 00:02 54M chainManPen1Link.sql 2020-11-24 00:05 1.6K chainManPen1Link.txt.gz 2020-11-24 00:05 425M chainMonDom5.sql 2020-11-25 02:13 1.7K chainMonDom5.txt.gz 2020-11-25 02:13 41M chainMonDom5Link.sql 2020-11-25 02:15 1.6K chainMonDom5Link.txt.gz 2020-11-25 02:15 238M chainNeoSch1.sql 2020-11-24 22:03 1.7K chainNeoSch1.txt.gz 2020-11-24 22:03 45M chainNeoSch1Link.sql 2020-11-24 22:06 1.6K chainNeoSch1Link.txt.gz 2020-11-24 22:06 400M chainOchPri3.sql 2020-11-25 19:14 1.7K chainOchPri3.txt.gz 2020-11-25 19:14 39M chainOchPri3Link.sql 2020-11-25 19:16 1.6K chainOchPri3Link.txt.gz 2020-11-25 19:16 290M chainOryCun2.sql 2020-11-24 22:26 1.7K chainOryCun2.txt.gz 2020-11-24 22:26 64M chainOryCun2Link.sql 2020-11-24 22:29 1.6K chainOryCun2Link.txt.gz 2020-11-24 22:29 435M chainOtoGar3.sql 2020-11-24 13:52 1.7K chainOtoGar3.txt.gz 2020-11-24 13:52 50M chainOtoGar3Link.sql 2020-11-24 13:55 1.6K chainOtoGar3Link.txt.gz 2020-11-24 13:55 426M chainOviAri4.sql 2020-11-24 22:34 1.7K chainOviAri4.txt.gz 2020-11-24 22:34 57M chainOviAri4Link.sql 2020-11-24 22:37 1.6K chainOviAri4Link.txt.gz 2020-11-24 22:37 438M chainPanPan3.sql 2020-11-24 05:23 1.7K chainPanPan3.txt.gz 2020-11-24 05:23 94M chainPanPan3Link.sql 2020-11-24 05:27 1.6K chainPanPan3Link.txt.gz 2020-11-24 05:27 539M chainPanTro6.sql 2020-11-24 05:03 1.7K chainPanTro6.txt.gz 2020-11-24 05:03 64M chainPanTro6Link.sql 2020-11-24 05:07 1.6K chainPanTro6Link.txt.gz 2020-11-24 05:07 504M chainPetMar3.sql 2020-11-24 23:03 1.7K chainPetMar3.txt.gz 2020-11-24 23:03 6.3M chainPetMar3Link.sql 2020-11-24 23:03 1.6K chainPetMar3Link.txt.gz 2020-11-24 23:03 18M chainRBestHg38.sql 2020-08-18 15:51 1.7K chainRBestHg38.txt.gz 2020-08-18 15:51 1.4M chainRBestHg38Link.sql 2020-08-18 15:53 1.6K chainRBestHg38Link.txt.gz 2020-08-18 15:53 262M chainRheMac10.sql 2020-10-20 17:03 1.7K chainRheMac10.txt.gz 2020-10-20 17:03 64M chainRheMac10Link.sql 2020-10-20 17:07 1.6K chainRheMac10Link.txt.gz 2020-10-20 17:07 494M chainRn6.sql 2020-10-20 17:26 1.7K chainRn6.txt.gz 2020-10-20 17:26 327M chainRn6Link.sql 2020-10-20 17:51 1.6K chainRn6Link.txt.gz 2020-10-20 17:51 2.4G chainRn7.sql 2021-02-04 18:50 1.7K chainRn7.txt.gz 2021-02-04 18:50 284M chainRn7Link.sql 2021-02-04 19:11 1.6K chainRn7Link.txt.gz 2021-02-04 19:11 1.7G chainSorAra2.sql 2020-11-25 20:26 1.7K chainSorAra2.txt.gz 2020-11-25 20:26 66M chainSorAra2Link.sql 2020-11-25 20:29 1.6K chainSorAra2Link.txt.gz 2020-11-25 20:29 367M chainSpeTri2.sql 2020-11-25 20:45 1.7K chainSpeTri2.txt.gz 2020-11-25 20:45 75M chainSpeTri2Link.sql 2020-11-25 20:49 1.6K chainSpeTri2Link.txt.gz 2020-11-25 20:49 560M chainSusScr3.sql 2020-11-24 13:50 1.7K chainSusScr3.txt.gz 2020-11-24 13:50 52M chainSusScr3Link.sql 2020-11-24 13:53 1.6K chainSusScr3Link.txt.gz 2020-11-24 13:53 469M chainSynHg38.sql 2020-08-18 09:39 1.7K chainSynHg38.txt.gz 2020-08-18 09:39 380K chainSynHg38Link.sql 2020-08-18 09:41 1.6K chainSynHg38Link.txt.gz 2020-08-18 09:41 259M chainTarSyr2.sql 2020-11-23 18:52 1.7K chainTarSyr2.txt.gz 2020-11-23 18:52 63M chainTarSyr2Link.sql 2020-11-23 18:56 1.6K chainTarSyr2Link.txt.gz 2020-11-23 18:56 481M chainTupBel1.sql 2020-11-25 21:44 1.7K chainTupBel1.txt.gz 2020-11-25 21:44 120M chainTupBel1Link.sql 2020-11-25 21:48 1.6K chainTupBel1Link.txt.gz 2020-11-25 21:48 486M chainTurTru2.sql 2020-11-24 13:50 1.7K chainTurTru2.txt.gz 2020-11-24 13:50 22M chainTurTru2Link.sql 2020-11-24 13:52 1.6K chainTurTru2Link.txt.gz 2020-11-24 13:52 295M chainXenTro10.sql 2021-02-23 01:59 1.7K chainXenTro10.txt.gz 2021-02-23 01:59 58M chainXenTro10Link.sql 2021-02-23 02:01 1.6K chainXenTro10Link.txt.gz 2021-02-23 02:01 264M chromAlias.sql 2021-03-12 12:45 1.4K chromAlias.txt.gz 2021-03-12 12:45 1.1K chromInfo.sql 2020-07-27 17:08 1.4K chromInfo.txt.gz 2020-07-27 17:08 583 cpgIslandExt.sql 2020-07-30 09:23 1.7K cpgIslandExt.txt.gz 2020-07-30 09:23 358K cpgIslandExtUnmasked.sql 2020-07-27 15:47 1.7K cpgIslandExtUnmasked.txt.gz 2020-07-27 15:47 527K crisprAllRanges.sql 2020-08-13 01:08 1.5K crisprAllRanges.txt.gz 2020-08-13 01:08 2.8K crisprAllTargets.sql 2020-08-13 01:39 1.3K crisprAllTargets.txt.gz 2020-08-13 01:39 66 cytoBandIdeo.sql 2020-07-27 17:04 1.5K cytoBandIdeo.txt.gz 2020-07-27 17:04 743 dmBlastTab.sql 2024-08-15 14:59 1.7K dmBlastTab.txt.gz 2024-08-15 14:59 156K drBlastTab.sql 2024-08-15 14:59 1.7K drBlastTab.txt.gz 2024-08-15 14:59 350K ensGene.sql 2021-05-25 14:40 1.9K ensGene.txt.gz 2021-05-25 14:40 6.3M estOrientInfo.sql 2020-08-18 00:14 1.8K estOrientInfo.txt.gz 2020-08-18 00:14 57M extFile.sql 2020-12-19 15:17 1.4K extFile.txt.gz 2020-12-19 15:17 795 extNcbiRefSeq.sql 2024-02-14 11:17 1.5K extNcbiRefSeq.txt.gz 2024-02-14 11:17 88 foldUtr3.sql 2024-08-15 14:59 1.4K foldUtr3.txt.gz 2024-08-15 14:59 28M foldUtr5.sql 2024-08-15 14:59 1.4K foldUtr5.txt.gz 2024-08-15 14:59 6.5M gap.sql 2020-07-27 13:01 1.6K gap.txt.gz 2020-07-27 13:01 4.0K gbLoaded.sql 2020-08-18 00:53 1.6K gbLoaded.txt.gz 2020-08-18 00:53 1.5K gc5BaseBw.sql 2020-07-27 17:04 1.3K gc5BaseBw.txt.gz 2020-07-27 17:04 63 genscan.sql 2020-07-30 18:23 1.7K genscan.txt.gz 2020-07-30 18:23 3.0M genscanSubopt.sql 2020-07-30 18:23 1.6K genscanSubopt.txt.gz 2020-07-30 18:23 6.2M gold.sql 2020-07-27 13:01 1.7K gold.txt.gz 2020-07-27 13:01 470K grcIncidentDb.sql 2023-03-06 21:46 1.3K grcIncidentDb.txt.gz 2023-03-06 21:46 77 grp.sql 2020-07-27 17:08 1.4K grp.txt.gz 2020-07-27 17:08 213 hgBlastTab.sql 2024-08-15 14:59 1.7K hgBlastTab.txt.gz 2024-08-15 14:59 1.1M hgFindSpec.sql 2024-11-08 15:28 1.8K hgFindSpec.txt.gz 2024-11-08 15:28 4.0K history.sql 2021-08-24 14:20 1.6K history.txt.gz 2021-08-24 14:20 756 kg12ToKg13.sql 2021-08-17 09:59 1.5K kg12ToKg13.txt.gz 2021-08-17 09:59 2.5M kgAlias.sql 2024-08-15 14:59 1.4K kgAlias.txt.gz 2024-08-15 14:59 9.5M kgColor.sql 2024-08-15 14:59 1.4K kgColor.txt.gz 2024-08-15 14:59 808K kgProtAlias.sql 2024-08-15 14:59 1.5K kgProtAlias.txt.gz 2024-08-15 14:59 2.2M kgSpAlias.sql 2024-08-15 14:59 1.4K kgSpAlias.txt.gz 2024-08-15 14:59 9.9M kgTargetAli.sql 2024-08-15 14:59 2.1K kgTargetAli.txt.gz 2024-08-15 14:59 14M kgVM27ToKgVM30.sql 2022-06-06 17:36 1.6K kgVM27ToKgVM30.txt.gz 2022-06-06 17:36 2.2M kgVM30ToKgVM32.sql 2022-12-30 15:48 1.6K kgVM30ToKgVM32.txt.gz 2022-12-30 15:48 2.3M kgVM32ToKgVM33.sql 2023-08-17 11:08 1.6K kgVM32ToKgVM33.txt.gz 2023-08-17 11:08 2.3M kgVM34ToKgVM35.sql 2024-03-28 19:49 1.6K kgVM34ToKgVM35.txt.gz 2024-03-28 19:49 2.3M kgVM35ToKgVM36.sql 2024-08-15 14:59 1.6K kgVM35ToKgVM36.txt.gz 2024-08-15 14:59 2.3M kgXref.sql 2024-08-15 14:59 1.9K kgXref.txt.gz 2024-08-15 14:59 5.0M knownAlt.sql 2024-08-15 14:59 1.6K knownAlt.txt.gz 2024-08-15 14:59 2.3M knownAttrs.sql 2024-08-15 14:59 1.7K knownAttrs.txt.gz 2024-08-15 14:59 4.2M knownBlastTab.sql 2024-08-15 15:00 1.7K knownBlastTab.txt.gz 2024-08-15 15:00 115M knownCanonical.sql 2024-08-15 15:00 1.6K knownCanonical.txt.gz 2024-08-15 15:00 1.5M knownCds.sql 2024-08-15 15:00 1.5K knownCds.txt.gz 2024-08-15 15:00 1.2M knownGene.sql 2024-08-15 14:59 1.9K knownGene.txt.gz 2024-08-15 14:59 10M knownGeneExt.sql 2024-08-15 14:59 2.0K knownGeneExt.txt.gz 2024-08-15 14:59 10M knownGeneMrna.sql 2024-08-15 14:59 1.4K knownGeneMrna.txt.gz 2024-08-15 14:59 53M knownGenePep.sql 2024-08-15 14:59 1.4K knownGenePep.txt.gz 2024-08-15 14:59 7.7M knownIsoforms.sql 2024-08-15 15:00 1.4K knownIsoforms.txt.gz 2024-08-15 15:00 1.2M knownToEnsembl.sql 2024-08-15 15:00 1.4K knownToEnsembl.txt.gz 2024-08-15 15:00 1.4M knownToGencodeVM27.sql 2021-08-17 10:00 1.4K knownToGencodeVM27.txt.gz 2021-08-17 10:00 755K knownToGencodeVM30.sql 2022-06-06 17:37 1.4K knownToGencodeVM30.txt.gz 2022-06-06 17:37 792K knownToGencodeVM32.sql 2022-12-30 15:49 1.4K knownToGencodeVM32.txt.gz 2022-12-30 15:49 792K knownToGencodeVM33.sql 2023-08-17 11:09 1.4K knownToGencodeVM33.txt.gz 2023-08-17 11:09 792K knownToGencodeVM35.sql 2024-03-28 19:50 1.4K knownToGencodeVM35.txt.gz 2024-03-28 19:50 790K knownToGencodeVM36.sql 2024-08-15 15:00 1.4K knownToGencodeVM36.txt.gz 2024-08-15 15:00 1.4M knownToLocusLink.sql 2024-08-15 15:00 1.4K knownToLocusLink.txt.gz 2024-08-15 15:00 1.0M knownToMrna.sql 2024-08-15 15:01 1.4K knownToMrna.txt.gz 2024-08-15 15:01 6.6M knownToMrnaSingle.sql 2024-08-15 15:01 1.4K knownToMrnaSingle.txt.gz 2024-08-15 15:01 1.0M knownToMupit.sql 2024-08-15 15:01 1.4K knownToMupit.txt.gz 2024-08-15 15:01 1.9K knownToNextProt.sql 2024-08-15 15:01 1.4K knownToNextProt.txt.gz 2024-08-15 15:01 40 knownToPfam.sql 2024-08-15 15:01 1.4K knownToPfam.txt.gz 2024-08-15 15:01 516K knownToRefSeq.sql 2024-08-15 15:01 1.4K knownToRefSeq.txt.gz 2024-08-15 15:01 1.2M knownToSuper.sql 2024-08-15 15:01 1.5K knownToSuper.txt.gz 2024-08-15 15:01 1.9M knownToTag.sql 2024-08-15 15:01 1.4K knownToTag.txt.gz 2024-08-15 15:01 1.8M knownToVisiGene.sql 2024-08-15 15:01 1.4K knownToVisiGene.txt.gz 2024-08-15 15:01 566K knownToWikipedia.sql 2024-08-15 15:01 1.4K knownToWikipedia.txt.gz 2024-08-15 15:01 466 liftOverMm10.sql 2023-03-06 16:10 1.7K liftOverMm10.txt.gz 2023-03-06 16:10 25K liftOverMm10Link.sql 2023-03-06 16:10 1.6K liftOverMm10Link.txt.gz 2023-03-06 16:10 84K microsat.sql 2020-07-27 16:07 1.5K microsat.txt.gz 2020-07-27 16:07 1.9M mrnaOrientInfo.sql 2020-08-18 00:39 1.8K mrnaOrientInfo.txt.gz 2020-08-18 00:39 20M multiz35way.sql 2020-12-19 15:07 1.6K multiz35way.txt.gz 2020-12-19 15:07 595M multiz35wayFrames.sql 2020-12-22 09:27 1.8K multiz35wayFrames.txt.gz 2020-12-22 09:27 65M multiz35waySummary.sql 2020-12-19 15:49 1.6K multiz35waySummary.txt.gz 2020-12-19 15:49 90M ncbiRefSeq.sql 2024-02-20 12:21 1.9K ncbiRefSeq.txt.gz 2024-02-20 12:21 5.5M ncbiRefSeqCds.sql 2024-02-14 11:17 1.4K ncbiRefSeqCds.txt.gz 2024-02-14 11:17 689K ncbiRefSeqCurated.sql 2024-02-20 12:21 2.0K ncbiRefSeqCurated.txt.gz 2024-02-20 12:21 3.2M ncbiRefSeqLink.sql 2024-02-20 12:21 2.0K ncbiRefSeqLink.txt.gz 2024-02-20 12:21 5.9M ncbiRefSeqOther.sql 2024-02-14 11:17 1.3K ncbiRefSeqOther.txt.gz 2024-02-14 11:17 72 ncbiRefSeqPepTable.sql 2024-02-14 11:17 1.4K 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