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