This directory contains a dump of the UCSC genome annotation database for
the Jul. 2010 (Zv9/danRer7) assembly of the zebrafish genome
(danRer7, Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
Massachusetts..
For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/
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=danRer7
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.cse.ucsc.edu, then go to
the directory goldenPath/danRer7/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.cse.ucsc.edu/goldenPath/danRer7/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer7/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
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 danRer7 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer7 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-21 08:12 22M
xenoRefSeqAli.sql 2020-08-21 08:12 2.1K
xenoRefGene.txt.gz 2020-08-21 08:12 24M
xenoRefGene.sql 2020-08-21 08:12 2.0K
xenoRefFlat.txt.gz 2020-08-21 08:12 22M
xenoRefFlat.sql 2020-08-21 08:12 1.7K
xenoMrna.txt.gz 2020-08-21 07:48 238M
xenoMrna.sql 2020-08-21 07:48 2.1K
ucscToRefSeq.txt.gz 2018-02-18 06:10 9.7K
ucscToRefSeq.sql 2018-02-18 06:10 1.4K
ucscToINSDC.txt.gz 2013-09-15 10:59 9.5K
ucscToINSDC.sql 2013-09-15 10:59 1.4K
trackDb.txt.gz 2024-07-25 09:34 76K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-17 03:41 5.4K
tableList.sql 2024-11-17 03:41 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 8.7K
tableDescriptions.sql 2024-11-16 02:03 1.5K
tRNAs.txt.gz 2012-04-22 21:28 267K
tRNAs.sql 2012-04-22 21:28 1.7K
simpleRepeat.txt.gz 2011-01-19 11:13 26M
simpleRepeat.sql 2011-01-19 11:13 1.9K
rmsk.txt.gz 2011-01-19 10:41 93M
rmsk.sql 2011-01-19 10:39 1.8K
refSeqAli.txt.gz 2020-08-21 08:12 1.7M
refSeqAli.sql 2020-08-21 08:12 2.1K
refGene.txt.gz 2020-08-21 08:12 1.7M
refGene.sql 2020-08-21 08:12 1.9K
refFlat.txt.gz 2020-08-21 08:12 1.5M
refFlat.sql 2020-08-21 08:12 1.7K
pubsBingBlatPsl.txt.gz 2014-01-26 10:26 721K
pubsBingBlatPsl.sql 2014-01-26 10:26 2.2K
pubsBingBlat.txt.gz 2014-01-26 10:26 1.1M
pubsBingBlat.sql 2014-01-26 10:26 2.4K
phyloP8wayFish.txt.gz 2011-10-09 10:35 15M
phyloP8wayFish.sql 2011-10-09 10:35 1.7K
phyloP8way.txt.gz 2011-10-09 10:33 16M
phyloP8way.sql 2011-10-09 10:33 1.7K
phastConsElements8wayFish.txt.gz 2011-10-09 10:33 8.4M
phastConsElements8wayFish.sql 2011-10-09 10:33 1.5K
phastConsElements8way.txt.gz 2011-10-09 10:34 11M
phastConsElements8way.sql 2011-10-09 10:34 1.5K
phastCons8wayFish.txt.gz 2011-10-09 10:33 16M
phastCons8wayFish.sql 2011-10-09 10:33 1.7K
phastCons8way.txt.gz 2011-10-09 10:34 16M
phastCons8way.sql 2011-10-09 10:34 1.7K
netXenTro3.txt.gz 2011-11-06 09:51 9.7M
netXenTro3.sql 2011-11-06 09:51 2.0K
netTetNig2.txt.gz 2011-03-07 08:11 9.5M
netTetNig2.sql 2011-03-07 08:11 2.0K
netPanTro3.txt.gz 2011-03-14 11:10 8.8M
netPanTro3.sql 2011-03-14 11:10 2.0K
netOryLat2.txt.gz 2011-03-07 06:59 14M
netOryLat2.sql 2011-03-07 06:59 2.0K
netMm10.txt.gz 2013-10-27 12:06 8.2M
netMm10.sql 2013-10-27 12:06 2.1K
netMelGal1.txt.gz 2011-11-06 09:58 4.9M
netMelGal1.sql 2011-11-06 09:58 2.0K
netHg19.txt.gz 2011-03-07 08:11 9.1M
netHg19.sql 2011-03-07 08:11 2.0K
netGasAcu1.txt.gz 2011-03-07 08:20 16M
netGasAcu1.sql 2011-03-07 08:20 2.0K
netFr3.txt.gz 2012-06-24 06:38 11M
netFr3.sql 2012-06-24 06:38 2.0K
nestedRepeats.txt.gz 2011-01-19 10:55 8.1M
nestedRepeats.sql 2011-01-19 10:55 1.9K
multiz8waySummary.txt.gz 2011-10-09 10:35 14M
multiz8waySummary.sql 2011-10-09 10:35 1.5K
multiz8wayFrames.txt.gz 2011-10-09 10:36 26M
multiz8wayFrames.sql 2011-10-09 10:35 1.7K
multiz8way.txt.gz 2011-10-09 10:34 44M
multiz8way.sql 2011-10-09 10:34 1.5K
mrnaOrientInfo.txt.gz 2020-08-21 08:12 807K
mrnaOrientInfo.sql 2020-08-21 08:12 1.8K
microsat.txt.gz 2015-08-23 13:32 1.1M
microsat.sql 2015-08-23 13:32 1.5K
mgcGenes.txt.gz 2020-03-01 05:42 1.2M
mgcGenes.sql 2020-03-01 05:42 1.9K
mgcFullMrna.txt.gz 2020-03-01 05:42 1.5M
mgcFullMrna.sql 2020-03-01 05:42 2.1K
locusName.txt.gz 2016-11-06 06:40 4.3M
locusName.sql 2016-11-06 06:40 1.5K
intronEst.txt.gz 2017-11-26 06:48 54M
intronEst.sql 2017-11-26 06:48 2.1K
history.txt.gz 2011-01-19 10:49 249
history.sql 2011-01-19 10:49 1.5K
hgFindSpec.txt.gz 2024-07-25 09:34 1.1K
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2014-03-02 03:40 209
grp.sql 2014-03-02 03:40 1.3K
grcIncidentDb.txt.gz 2018-05-13 05:03 77
grcIncidentDb.sql 2018-05-13 05:03 1.3K
gold.txt.gz 2011-01-19 11:16 692K
gold.sql 2011-01-19 11:16 1.6K
genscan.txt.gz 2013-12-09 21:01 2.5M
genscan.sql 2013-12-09 21:01 1.7K
gc5BaseBw.txt.gz 2011-01-19 11:08 63
gc5BaseBw.sql 2011-01-19 11:08 1.2K
gbLoaded.txt.gz 2020-08-21 08:13 92K
gbLoaded.sql 2020-08-21 08:13 1.6K
gap.txt.gz 2011-01-19 10:54 325K
gap.sql 2011-01-19 10:54 1.5K
extFile.txt.gz 2011-10-09 10:33 80
extFile.sql 2011-10-09 10:33 1.4K
estOrientInfo.txt.gz 2017-11-26 06:47 20M
estOrientInfo.sql 2017-11-26 06:46 1.8K
ensemblToGeneName.txt.gz 2014-04-06 15:46 402K
ensemblToGeneName.sql 2014-04-06 15:46 1.4K
ensemblSource.txt.gz 2014-04-06 15:46 235K
ensemblSource.sql 2014-04-06 15:46 1.4K
ensPep.txt.gz 2014-04-06 15:46 12M
ensPep.sql 2014-04-06 15:46 1.3K
ensGtp.txt.gz 2014-04-06 15:46 540K
ensGtp.sql 2014-04-06 15:46 1.4K
ensGene.txt.gz 2014-04-06 15:50 3.7M
ensGene.sql 2014-04-06 15:50 1.9K
cytoBandIdeo.txt.gz 2013-04-28 12:53 6.4K
cytoBandIdeo.sql 2013-04-28 12:53 1.5K
ctgPos2.txt.gz 2011-01-19 11:12 13K
ctgPos2.sql 2011-01-19 11:12 1.5K
crisprTargets.txt.gz 2016-11-06 06:40 63
crisprTargets.sql 2016-11-06 06:40 1.3K
crisprRanges.txt.gz 2016-11-06 06:40 1.4M
crisprRanges.sql 2016-11-06 06:40 1.4K
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:57 1.0M
cpgIslandExtUnmasked.sql 2014-06-01 10:57 1.7K
cpgIslandExt.txt.gz 2011-08-07 08:02 271K
cpgIslandExt.sql 2011-08-07 08:02 1.6K
chromInfo.txt.gz 2011-01-19 10:55 7.3K
chromInfo.sql 2011-01-19 10:55 1.3K
chromAlias.txt.gz 2018-02-18 06:10 5.7K
chromAlias.sql 2018-02-18 06:10 1.4K
chainXenTro3Link.txt.gz 2011-11-06 09:53 687M
chainXenTro3Link.sql 2011-11-06 09:51 1.5K
chainXenTro3.txt.gz 2011-11-06 09:57 222M
chainXenTro3.sql 2011-11-06 09:57 1.6K
chainTetNig2Link.txt.gz 2011-03-07 07:19 92M
chainTetNig2Link.sql 2011-03-07 07:19 1.5K
chainTetNig2.txt.gz 2011-03-07 06:59 25M
chainTetNig2.sql 2011-03-07 06:59 1.6K
chainPanTro3Link.txt.gz 2011-03-14 11:15 535M
chainPanTro3Link.sql 2011-03-14 11:10 1.5K
chainPanTro3.txt.gz 2011-03-14 11:25 161M
chainPanTro3.sql 2011-03-14 11:24 1.6K
chainOryLat2Link.txt.gz 2011-03-07 07:57 313M
chainOryLat2Link.sql 2011-03-07 07:56 1.5K
chainOryLat2.txt.gz 2011-03-07 08:12 76M
chainOryLat2.sql 2011-03-07 08:11 1.6K
chainMm10Link.txt.gz 2013-10-27 12:05 234M
chainMm10Link.sql 2013-10-27 12:05 1.5K
chainMm10.txt.gz 2013-10-27 12:05 53M
chainMm10.sql 2013-10-27 12:05 1.7K
chainMelGal1Link.txt.gz 2011-11-06 09:51 19M
chainMelGal1Link.sql 2011-11-06 09:51 1.5K
chainMelGal1.txt.gz 2011-11-06 09:51 5.3M
chainMelGal1.sql 2011-11-06 09:51 1.6K
chainHg19Link.txt.gz 2011-03-07 07:05 1.0G
chainHg19Link.sql 2011-03-07 07:00 1.5K
chainHg19.txt.gz 2011-03-07 07:23 317M
chainHg19.sql 2011-03-07 07:21 1.6K
chainGasAcu1Link.txt.gz 2011-03-07 08:05 418M
chainGasAcu1Link.sql 2011-03-07 08:03 1.5K
chainGasAcu1.txt.gz 2011-03-07 07:35 113M
chainGasAcu1.sql 2011-03-07 07:34 1.6K
chainFr3Link.txt.gz 2012-06-24 06:39 115M
chainFr3Link.sql 2012-06-24 06:38 1.5K
chainFr3.txt.gz 2012-06-24 06:38 29M
chainFr3.sql 2012-06-24 06:38 1.6K
blastHg18KG.txt.gz 2011-01-19 11:16 3.1M
blastHg18KG.sql 2011-01-19 11:16 2.1K
bigFiles.txt.gz 2024-11-17 03:41 114
bigFiles.sql 2024-11-17 03:41 1.4K
augustusGene.txt.gz 2015-07-26 11:52 2.8M
augustusGene.sql 2015-07-26 11:52 1.9K
all_mrna.txt.gz 2020-08-21 07:48 2.6M
all_mrna.sql 2020-08-21 07:48 2.1K
all_est.txt.gz 2017-11-26 06:48 83M
all_est.sql 2017-11-26 06:48 2.1K
UMassME3Peak.txt.gz 2011-11-06 09:58 528K
UMassME3Peak.sql 2011-11-06 09:58 1.7K
UMassME3Hotspot.txt.gz 2011-11-06 09:51 389K
UMassME3Hotspot.sql 2011-11-06 09:51 1.5K
UMassME3.txt.gz 2011-11-06 09:58 1.1M
UMassME3.sql 2011-11-06 09:58 1.7K
UMassME1Peak.txt.gz 2011-11-06 09:51 1.1M
UMassME1Peak.sql 2011-11-06 09:51 1.7K
UMassME1Hotspot.txt.gz 2011-11-06 09:51 849K
UMassME1Hotspot.sql 2011-11-06 09:51 1.5K
UMassME1.txt.gz 2011-11-06 09:51 2.4M
UMassME1.sql 2011-11-06 09:51 1.7K
UMassInput.txt.gz 2011-11-06 09:58 2.2M
UMassInput.sql 2011-11-06 09:58 1.7K