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 -
gc5BaseBw.txt.gz 2017-12-05 11:47 66
ncbiRefSeqOther.txt.gz 2021-02-11 11:15 75
extFile.txt.gz 2017-12-05 11:40 80
extNcbiRefSeq.txt.gz 2021-02-11 11:15 91
bigFiles.txt.gz 2024-12-29 03:04 95
grp.txt.gz 2017-12-05 11:32 213
hgFindSpec.txt.gz 2023-12-05 13:52 1.2K
gc5BaseBw.sql 2017-12-05 11:47 1.3K
ncbiRefSeqOther.sql 2021-02-11 11:15 1.3K
ensPep.sql 2021-05-25 14:10 1.3K
grp.sql 2017-12-05 11:32 1.3K
ncbiRefSeqCds.sql 2021-02-11 11:15 1.4K
ensemblSource.sql 2021-05-25 14:10 1.4K
ncbiRefSeqPepTable.sql 2021-02-11 11:15 1.4K
history.txt.gz 2017-12-05 11:40 1.4K
chromInfo.sql 2017-12-05 11:50 1.4K
bigFiles.sql 2024-12-29 03:04 1.4K
ensemblToGeneName.sql 2021-05-25 14:04 1.4K
extFile.sql 2017-12-05 11:40 1.4K
ucscToINSDC.sql 2017-12-05 11:52 1.4K
ucscToRefSeq.sql 2017-12-05 11:52 1.4K
ensGtp.sql 2021-05-25 14:04 1.4K
chromAlias.sql 2023-01-27 11:27 1.4K
tableDescriptions.sql 2024-12-28 02:12 1.5K
extNcbiRefSeq.sql 2021-02-11 11:15 1.5K
microsat.sql 2017-12-05 11:47 1.5K
windowmaskerSdust.sql 2017-12-05 11:51 1.5K
cytoBandIdeo.sql 2017-12-05 11:40 1.5K
multiz11way.sql 2017-12-05 11:50 1.5K
chainFr3Link.sql 2017-12-05 11:40 1.5K
chainHg38Link.sql 2017-12-05 11:42 1.5K
chainMm10Link.sql 2017-12-05 11:47 1.5K
chainAnoCar2Link.sql 2017-12-05 11:38 1.5K
chainCanFam3Link.sql 2017-12-05 11:39 1.5K
chainGalGal5Link.sql 2017-12-05 11:40 1.5K
chainGalGal6Link.sql 2019-01-20 20:25 1.5K
chainMonDom5Link.sql 2017-12-05 11:33 1.5K
chainNanPar1Link.sql 2017-12-05 11:49 1.5K
chainXenLae2Link.sql 2017-12-05 11:13 1.5K
chainMm39Link.sql 2020-11-25 03:45 1.6K
phastConsElements11way.sql 2017-12-05 11:52 1.6K
seqNcbiRefSeq.sql 2021-02-11 11:15 1.6K
history.sql 2017-12-05 11:40 1.6K
multiz11waySummary.sql 2017-12-05 11:51 1.6K
tableList.sql 2024-12-29 03:04 1.6K
gap.sql 2017-12-05 11:42 1.6K
gbLoaded.sql 2020-08-20 19:13 1.6K
gold.sql 2017-12-05 11:32 1.7K
genscan.sql 2017-12-05 11:50 1.7K
cpgIslandExt.sql 2017-12-05 11:39 1.7K
chainFr3.sql 2017-12-05 11:40 1.7K
chainHg38.sql 2017-12-05 11:41 1.7K
chainMm10.sql 2017-12-05 11:47 1.7K
chainAnoCar2.sql 2017-12-05 11:37 1.7K
chainCanFam3.sql 2017-12-05 11:39 1.7K
chainGalGal5.sql 2017-12-05 11:40 1.7K
chainGalGal6.sql 2019-01-20 20:25 1.7K
chainMonDom5.sql 2017-12-05 11:32 1.7K
chainNanPar1.sql 2017-12-05 11:37 1.7K
chainXenLae2.sql 2017-12-05 11:05 1.7K
cpgIslandExtUnmasked.sql 2017-12-05 11:39 1.7K
chainMm39.sql 2020-11-25 03:44 1.7K
refFlat.sql 2020-08-20 19:07 1.7K
multiz11wayFrames.sql 2017-12-05 11:51 1.7K
xenoRefFlat.sql 2020-08-20 19:07 1.7K
hgFindSpec.sql 2023-12-05 13:52 1.8K
phyloP11way.sql 2017-12-05 11:52 1.8K
estOrientInfo.sql 2017-12-05 11:40 1.8K
phastCons11way.sql 2017-12-05 11:51 1.8K
mrnaOrientInfo.sql 2020-08-20 19:13 1.8K
rmsk.sql 2017-12-05 11:52 1.9K
simpleRepeat.sql 2017-12-05 11:52 1.9K
nestedRepeats.sql 2017-12-05 11:51 1.9K
augustusGene.sql 2017-12-05 11:33 1.9K
ensGene.sql 2021-05-25 14:04 1.9K
refGene.sql 2020-08-20 19:07 1.9K
ncbiRefSeq.sql 2021-02-11 09:53 2.0K
xenoRefGene.sql 2020-08-20 19:07 2.0K
ncbiRefSeqCurated.sql 2021-02-11 09:53 2.0K
ncbiRefSeqPredicted.sql 2021-02-11 09:53 2.0K
ncbiRefSeqLink.sql 2021-02-11 09:53 2.0K
trackDb.sql 2023-12-05 13:52 2.1K
netFr3.sql 2017-12-05 11:51 2.1K
netHg38.sql 2017-12-05 11:51 2.1K
netMm10.sql 2017-12-05 11:51 2.1K
netAnoCar2.sql 2017-12-05 11:51 2.1K
netCanFam3.sql 2017-12-05 11:51 2.1K
netGalGal5.sql 2017-12-05 11:51 2.1K
netGalGal6.sql 2019-01-20 20:26 2.1K
netMonDom5.sql 2017-12-05 11:51 2.1K
netNanPar1.sql 2017-12-05 11:51 2.1K
netXenLae2.sql 2017-12-05 11:32 2.1K
all_est.sql 2017-12-05 11:32 2.1K
intronEst.sql 2017-12-05 11:40 2.1K
netMm39.sql 2020-11-25 03:47 2.1K
all_mrna.sql 2020-08-20 18:44 2.1K
refSeqAli.sql 2020-08-20 19:13 2.1K
ncbiRefSeqPsl.sql 2021-02-11 09:53 2.1K
xenoRefSeqAli.sql 2020-08-20 19:13 2.1K
tableList.txt.gz 2024-12-29 03:04 4.9K
tableDescriptions.txt.gz 2024-12-28 02:12 7.7K
gbLoaded.txt.gz 2020-08-20 19:13 32K
chromInfo.txt.gz 2017-12-05 11:50 35K
cytoBandIdeo.txt.gz 2017-12-05 11:40 36K
trackDb.txt.gz 2023-12-05 13:52 48K
ucscToINSDC.txt.gz 2017-12-05 11:52 51K
ucscToRefSeq.txt.gz 2017-12-05 11:52 55K
chromAlias.txt.gz 2023-01-27 11:27 109K
microsat.txt.gz 2017-12-05 11:47 145K
ensemblSource.txt.gz 2021-05-25 14:10 155K
cpgIslandExt.txt.gz 2017-12-05 11:39 274K
ncbiRefSeqCds.txt.gz 2021-02-11 11:15 277K
ensemblToGeneName.txt.gz 2021-05-25 14:04 334K
mrnaOrientInfo.txt.gz 2020-08-20 19:13 509K
ensGtp.txt.gz 2021-05-25 14:04 561K
seqNcbiRefSeq.txt.gz 2021-02-11 11:15 662K
gap.txt.gz 2017-12-05 11:42 714K
refFlat.txt.gz 2020-08-20 19:07 824K
ncbiRefSeqCurated.txt.gz 2021-02-11 09:53 877K
cpgIslandExtUnmasked.txt.gz 2017-12-05 11:39 888K
refGene.txt.gz 2020-08-20 19:07 921K
refSeqAli.txt.gz 2020-08-20 19:13 932K
gold.txt.gz 2017-12-05 11:32 1.0M
ncbiRefSeqLink.txt.gz 2021-02-11 09:53 1.6M
all_mrna.txt.gz 2020-08-20 18:44 1.8M
augustusGene.txt.gz 2017-12-05 11:33 2.2M
ncbiRefSeqPredicted.txt.gz 2021-02-11 09:53 2.3M
genscan.txt.gz 2017-12-05 11:50 2.3M
ncbiRefSeq.txt.gz 2021-02-11 09:53 2.8M
ensGene.txt.gz 2021-05-25 14:04 3.4M
ncbiRefSeqPsl.txt.gz 2021-02-11 09:53 3.5M
nestedRepeats.txt.gz 2017-12-05 11:51 4.5M
netGalGal5.txt.gz 2017-12-05 11:51 5.5M
netCanFam3.txt.gz 2017-12-05 11:51 5.7M
netFr3.txt.gz 2017-12-05 11:51 5.8M
netMm39.txt.gz 2020-11-25 03:47 6.5M
chainGalGal5.txt.gz 2017-12-05 11:40 6.7M
phastConsElements11way.txt.gz 2017-12-05 11:52 6.8M
netMonDom5.txt.gz 2017-12-05 11:51 7.3M
netAnoCar2.txt.gz 2017-12-05 11:51 8.2M
multiz11waySummary.txt.gz 2017-12-05 11:51 8.9M
netMm10.txt.gz 2017-12-05 11:51 9.2M
netGalGal6.txt.gz 2019-01-20 20:26 9.8M
ncbiRefSeqPepTable.txt.gz 2021-02-11 11:15 10M
multiz11wayFrames.txt.gz 2017-12-05 11:51 11M
netHg38.txt.gz 2017-12-05 11:51 11M
chainFr3.txt.gz 2017-12-05 11:40 12M
netNanPar1.txt.gz 2017-12-05 11:51 12M
xenoRefSeqAli.txt.gz 2020-08-20 19:13 13M
xenoRefFlat.txt.gz 2020-08-20 19:07 14M
estOrientInfo.txt.gz 2017-12-05 11:40 14M
xenoRefGene.txt.gz 2020-08-20 19:07 16M
simpleRepeat.txt.gz 2017-12-05 11:52 19M
ensPep.txt.gz 2021-05-25 14:10 22M
chainGalGal6.txt.gz 2019-01-20 20:25 24M
chainGalGal5Link.txt.gz 2017-12-05 11:40 25M
phyloP11way.txt.gz 2017-12-05 11:52 32M
intronEst.txt.gz 2017-12-05 11:40 32M
phastCons11way.txt.gz 2017-12-05 11:51 32M
chainMm39.txt.gz 2020-11-25 03:44 35M
chainAnoCar2.txt.gz 2017-12-05 11:37 45M
chainCanFam3.txt.gz 2017-12-05 11:39 46M
chainFr3Link.txt.gz 2017-12-05 11:40 49M
all_est.txt.gz 2017-12-05 11:32 51M
multiz11way.txt.gz 2017-12-05 11:50 53M
rmsk.txt.gz 2017-12-05 11:52 58M
windowmaskerSdust.txt.gz 2017-12-05 11:51 63M
chainMm10.txt.gz 2017-12-05 11:47 67M
netXenLae2.txt.gz 2017-12-05 11:32 89M
chainNanPar1.txt.gz 2017-12-05 11:37 97M
chainGalGal6Link.txt.gz 2019-01-20 20:26 101M
chainMm39Link.txt.gz 2020-11-25 03:45 175M
chainCanFam3Link.txt.gz 2017-12-05 11:39 187M
chainAnoCar2Link.txt.gz 2017-12-05 11:38 211M
chainMonDom5.txt.gz 2017-12-05 11:33 224M
chainHg38.txt.gz 2017-12-05 11:41 229M
chainNanPar1Link.txt.gz 2017-12-05 11:49 293M
chainMm10Link.txt.gz 2017-12-05 11:47 401M
chainMonDom5Link.txt.gz 2017-12-05 11:34 812M
chainHg38Link.txt.gz 2017-12-05 11:43 1.0G
chainXenLae2.txt.gz 2017-12-05 11:07 1.8G
chainXenLae2Link.txt.gz 2017-12-05 11:18 3.9G