This directory contains a dump of the UCSC genome annotation database for the
Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) assembly of the X. tropicalis genome
(xenTro9, DOE Joint Genome Institute)
from the X. tropicalis Genome Consortium.
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/80
http://www.ncbi.nlm.nih.gov/genome/assembly/768701
http://www.ncbi.nlm.nih.gov/bioproject/205740
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=xenTro9
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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/xenTro9/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/xenTro9/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/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 xenTro9 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro9 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
chainXenLae2Link.txt.gz 2017-12-05 11:18 3.9G
chainXenLae2.txt.gz 2017-12-05 11:07 1.8G
chainHg38Link.txt.gz 2017-12-05 11:43 1.0G
chainMonDom5Link.txt.gz 2017-12-05 11:34 812M
chainMm10Link.txt.gz 2017-12-05 11:47 401M
chainNanPar1Link.txt.gz 2017-12-05 11:49 293M
chainHg38.txt.gz 2017-12-05 11:41 229M
chainMonDom5.txt.gz 2017-12-05 11:33 224M
chainAnoCar2Link.txt.gz 2017-12-05 11:38 211M
chainCanFam3Link.txt.gz 2017-12-05 11:39 187M
chainMm39Link.txt.gz 2020-11-25 03:45 175M
chainGalGal6Link.txt.gz 2019-01-20 20:26 101M
chainNanPar1.txt.gz 2017-12-05 11:37 97M
netXenLae2.txt.gz 2017-12-05 11:32 89M
chainMm10.txt.gz 2017-12-05 11:47 67M
windowmaskerSdust.txt.gz 2017-12-05 11:51 63M
rmsk.txt.gz 2017-12-05 11:52 58M
multiz11way.txt.gz 2017-12-05 11:50 53M
all_est.txt.gz 2017-12-05 11:32 51M
chainFr3Link.txt.gz 2017-12-05 11:40 49M
chainCanFam3.txt.gz 2017-12-05 11:39 46M
chainAnoCar2.txt.gz 2017-12-05 11:37 45M
chainMm39.txt.gz 2020-11-25 03:44 35M
phastCons11way.txt.gz 2017-12-05 11:51 32M
intronEst.txt.gz 2017-12-05 11:40 32M
phyloP11way.txt.gz 2017-12-05 11:52 32M
chainGalGal5Link.txt.gz 2017-12-05 11:40 25M
chainGalGal6.txt.gz 2019-01-20 20:25 24M
ensPep.txt.gz 2021-05-25 14:10 22M
simpleRepeat.txt.gz 2017-12-05 11:52 19M
xenoRefGene.txt.gz 2020-08-20 19:07 16M
estOrientInfo.txt.gz 2017-12-05 11:40 14M
xenoRefFlat.txt.gz 2020-08-20 19:07 14M
xenoRefSeqAli.txt.gz 2020-08-20 19:13 13M
netNanPar1.txt.gz 2017-12-05 11:51 12M
chainFr3.txt.gz 2017-12-05 11:40 12M
netHg38.txt.gz 2017-12-05 11:51 11M
multiz11wayFrames.txt.gz 2017-12-05 11:51 11M
ncbiRefSeqPepTable.txt.gz 2021-02-11 11:15 10M
netGalGal6.txt.gz 2019-01-20 20:26 9.8M
netMm10.txt.gz 2017-12-05 11:51 9.2M
multiz11waySummary.txt.gz 2017-12-05 11:51 8.9M
netAnoCar2.txt.gz 2017-12-05 11:51 8.2M
netMonDom5.txt.gz 2017-12-05 11:51 7.3M
phastConsElements11way.txt.gz 2017-12-05 11:52 6.8M
chainGalGal5.txt.gz 2017-12-05 11:40 6.7M
netMm39.txt.gz 2020-11-25 03:47 6.5M
netFr3.txt.gz 2017-12-05 11:51 5.8M
netCanFam3.txt.gz 2017-12-05 11:51 5.7M
netGalGal5.txt.gz 2017-12-05 11:51 5.5M
nestedRepeats.txt.gz 2017-12-05 11:51 4.5M
ncbiRefSeqPsl.txt.gz 2021-02-11 09:53 3.5M
ensGene.txt.gz 2021-05-25 14:04 3.4M
ncbiRefSeq.txt.gz 2021-02-11 09:53 2.8M
genscan.txt.gz 2017-12-05 11:50 2.3M
ncbiRefSeqPredicted.txt.gz 2021-02-11 09:53 2.3M
augustusGene.txt.gz 2017-12-05 11:33 2.2M
all_mrna.txt.gz 2020-08-20 18:44 1.8M
ncbiRefSeqLink.txt.gz 2021-02-11 09:53 1.6M
gold.txt.gz 2017-12-05 11:32 1.0M
refSeqAli.txt.gz 2020-08-20 19:13 932K
refGene.txt.gz 2020-08-20 19:07 921K
cpgIslandExtUnmasked.txt.gz 2017-12-05 11:39 888K
ncbiRefSeqCurated.txt.gz 2021-02-11 09:53 877K
refFlat.txt.gz 2020-08-20 19:07 824K
gap.txt.gz 2017-12-05 11:42 714K
seqNcbiRefSeq.txt.gz 2021-02-11 11:15 662K
ensGtp.txt.gz 2021-05-25 14:04 561K
mrnaOrientInfo.txt.gz 2020-08-20 19:13 509K
ensemblToGeneName.txt.gz 2021-05-25 14:04 334K
ncbiRefSeqCds.txt.gz 2021-02-11 11:15 277K
cpgIslandExt.txt.gz 2017-12-05 11:39 274K
ensemblSource.txt.gz 2021-05-25 14:10 155K
microsat.txt.gz 2017-12-05 11:47 145K
chromAlias.txt.gz 2023-01-27 11:27 109K
ucscToRefSeq.txt.gz 2017-12-05 11:52 55K
ucscToINSDC.txt.gz 2017-12-05 11:52 51K
trackDb.txt.gz 2023-12-05 13:52 48K
cytoBandIdeo.txt.gz 2017-12-05 11:40 36K
chromInfo.txt.gz 2017-12-05 11:50 35K
gbLoaded.txt.gz 2020-08-20 19:13 32K
tableDescriptions.txt.gz 2024-11-23 02:04 7.7K
tableList.txt.gz 2024-11-24 03:05 4.9K
xenoRefSeqAli.sql 2020-08-20 19:13 2.1K
ncbiRefSeqPsl.sql 2021-02-11 09:53 2.1K
refSeqAli.sql 2020-08-20 19:13 2.1K
all_mrna.sql 2020-08-20 18:44 2.1K
netMm39.sql 2020-11-25 03:47 2.1K
intronEst.sql 2017-12-05 11:40 2.1K
all_est.sql 2017-12-05 11:32 2.1K
netXenLae2.sql 2017-12-05 11:32 2.1K
netNanPar1.sql 2017-12-05 11:51 2.1K
netMonDom5.sql 2017-12-05 11:51 2.1K
netGalGal6.sql 2019-01-20 20:26 2.1K
netGalGal5.sql 2017-12-05 11:51 2.1K
netCanFam3.sql 2017-12-05 11:51 2.1K
netAnoCar2.sql 2017-12-05 11:51 2.1K
netMm10.sql 2017-12-05 11:51 2.1K
netHg38.sql 2017-12-05 11:51 2.1K
netFr3.sql 2017-12-05 11:51 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
ncbiRefSeqLink.sql 2021-02-11 09:53 2.0K
ncbiRefSeqPredicted.sql 2021-02-11 09:53 2.0K
ncbiRefSeqCurated.sql 2021-02-11 09:53 2.0K
xenoRefGene.sql 2020-08-20 19:07 2.0K
ncbiRefSeq.sql 2021-02-11 09:53 2.0K
refGene.sql 2020-08-20 19:07 1.9K
ensGene.sql 2021-05-25 14:04 1.9K
augustusGene.sql 2017-12-05 11:33 1.9K
nestedRepeats.sql 2017-12-05 11:51 1.9K
simpleRepeat.sql 2017-12-05 11:52 1.9K
rmsk.sql 2017-12-05 11:52 1.9K
mrnaOrientInfo.sql 2020-08-20 19:13 1.8K
phastCons11way.sql 2017-12-05 11:51 1.8K
estOrientInfo.sql 2017-12-05 11:40 1.8K
phyloP11way.sql 2017-12-05 11:52 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-08-20 19:07 1.7K
multiz11wayFrames.sql 2017-12-05 11:51 1.7K
refFlat.sql 2020-08-20 19:07 1.7K
chainMm39.sql 2020-11-25 03:44 1.7K
cpgIslandExtUnmasked.sql 2017-12-05 11:39 1.7K
chainXenLae2.sql 2017-12-05 11:05 1.7K
chainNanPar1.sql 2017-12-05 11:37 1.7K
chainMonDom5.sql 2017-12-05 11:32 1.7K
chainGalGal6.sql 2019-01-20 20:25 1.7K
chainGalGal5.sql 2017-12-05 11:40 1.7K
chainCanFam3.sql 2017-12-05 11:39 1.7K
chainAnoCar2.sql 2017-12-05 11:37 1.7K
chainMm10.sql 2017-12-05 11:47 1.7K
chainHg38.sql 2017-12-05 11:41 1.7K
chainFr3.sql 2017-12-05 11:40 1.7K
cpgIslandExt.sql 2017-12-05 11:39 1.7K
genscan.sql 2017-12-05 11:50 1.7K
gold.sql 2017-12-05 11:32 1.7K
gbLoaded.sql 2020-08-20 19:13 1.6K
gap.sql 2017-12-05 11:42 1.6K
multiz11waySummary.sql 2017-12-05 11:51 1.6K
history.sql 2017-12-05 11:40 1.6K
seqNcbiRefSeq.sql 2021-02-11 11:15 1.6K
tableList.sql 2024-11-24 03:05 1.6K
phastConsElements11way.sql 2017-12-05 11:52 1.6K
chainMm39Link.sql 2020-11-25 03:45 1.6K
chainXenLae2Link.sql 2017-12-05 11:13 1.5K
chainNanPar1Link.sql 2017-12-05 11:49 1.5K
chainMonDom5Link.sql 2017-12-05 11:33 1.5K
chainGalGal6Link.sql 2019-01-20 20:25 1.5K
chainGalGal5Link.sql 2017-12-05 11:40 1.5K
chainCanFam3Link.sql 2017-12-05 11:39 1.5K
chainAnoCar2Link.sql 2017-12-05 11:38 1.5K
chainMm10Link.sql 2017-12-05 11:47 1.5K
chainHg38Link.sql 2017-12-05 11:42 1.5K
chainFr3Link.sql 2017-12-05 11:40 1.5K
multiz11way.sql 2017-12-05 11:50 1.5K
cytoBandIdeo.sql 2017-12-05 11:40 1.5K
windowmaskerSdust.sql 2017-12-05 11:51 1.5K
microsat.sql 2017-12-05 11:47 1.5K
extNcbiRefSeq.sql 2021-02-11 11:15 1.5K
chromAlias.sql 2023-01-27 11:27 1.4K
ensGtp.sql 2021-05-25 14:04 1.4K
ucscToRefSeq.sql 2017-12-05 11:52 1.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
ucscToINSDC.sql 2017-12-05 11:52 1.4K
extFile.sql 2017-12-05 11:40 1.4K
ensemblToGeneName.sql 2021-05-25 14:04 1.4K
chromInfo.sql 2017-12-05 11:50 1.4K
history.txt.gz 2017-12-05 11:40 1.4K
ncbiRefSeqPepTable.sql 2021-02-11 11:15 1.4K
bigFiles.sql 2024-11-24 03:05 1.4K
ensemblSource.sql 2021-05-25 14:10 1.4K
ncbiRefSeqCds.sql 2021-02-11 11:15 1.4K
grp.sql 2017-12-05 11:32 1.3K
ensPep.sql 2021-05-25 14:10 1.3K
ncbiRefSeqOther.sql 2021-02-11 11:15 1.3K
gc5BaseBw.sql 2017-12-05 11:47 1.3K
hgFindSpec.txt.gz 2023-12-05 13:52 1.2K
grp.txt.gz 2017-12-05 11:32 213
bigFiles.txt.gz 2024-11-24 03:05 95
extNcbiRefSeq.txt.gz 2021-02-11 11:15 91
extFile.txt.gz 2017-12-05 11:40 80
ncbiRefSeqOther.txt.gz 2021-02-11 11:15 75
gc5BaseBw.txt.gz 2017-12-05 11:47 66