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 -
chainHg19Link.txt.gz 2011-03-07 07:05 1.0G
chainXenTro3Link.txt.gz 2011-11-06 09:53 687M
chainPanTro3Link.txt.gz 2011-03-14 11:15 535M
chainGasAcu1Link.txt.gz 2011-03-07 08:05 418M
chainHg19.txt.gz 2011-03-07 07:23 317M
chainOryLat2Link.txt.gz 2011-03-07 07:57 313M
xenoMrna.txt.gz 2020-08-21 07:48 238M
chainMm10Link.txt.gz 2013-10-27 12:05 234M
chainXenTro3.txt.gz 2011-11-06 09:57 222M
chainPanTro3.txt.gz 2011-03-14 11:25 161M
chainFr3Link.txt.gz 2012-06-24 06:39 115M
chainGasAcu1.txt.gz 2011-03-07 07:35 113M
rmsk.txt.gz 2011-01-19 10:41 93M
chainTetNig2Link.txt.gz 2011-03-07 07:19 92M
all_est.txt.gz 2017-11-26 06:48 83M
chainOryLat2.txt.gz 2011-03-07 08:12 76M
intronEst.txt.gz 2017-11-26 06:48 54M
chainMm10.txt.gz 2013-10-27 12:05 53M
multiz8way.txt.gz 2011-10-09 10:34 44M
chainFr3.txt.gz 2012-06-24 06:38 29M
multiz8wayFrames.txt.gz 2011-10-09 10:36 26M
simpleRepeat.txt.gz 2011-01-19 11:13 26M
chainTetNig2.txt.gz 2011-03-07 06:59 25M
xenoRefGene.txt.gz 2020-08-21 08:12 24M
xenoRefSeqAli.txt.gz 2020-08-21 08:12 22M
xenoRefFlat.txt.gz 2020-08-21 08:12 22M
estOrientInfo.txt.gz 2017-11-26 06:47 20M
chainMelGal1Link.txt.gz 2011-11-06 09:51 19M
phastCons8way.txt.gz 2011-10-09 10:34 16M
phyloP8way.txt.gz 2011-10-09 10:33 16M
phastCons8wayFish.txt.gz 2011-10-09 10:33 16M
netGasAcu1.txt.gz 2011-03-07 08:20 16M
phyloP8wayFish.txt.gz 2011-10-09 10:35 15M
netOryLat2.txt.gz 2011-03-07 06:59 14M
multiz8waySummary.txt.gz 2011-10-09 10:35 14M
ensPep.txt.gz 2014-04-06 15:46 12M
phastConsElements8way.txt.gz 2011-10-09 10:34 11M
netFr3.txt.gz 2012-06-24 06:38 11M
netXenTro3.txt.gz 2011-11-06 09:51 9.7M
netTetNig2.txt.gz 2011-03-07 08:11 9.5M
netHg19.txt.gz 2011-03-07 08:11 9.1M
netPanTro3.txt.gz 2011-03-14 11:10 8.8M
phastConsElements8wayFish.txt.gz 2011-10-09 10:33 8.4M
netMm10.txt.gz 2013-10-27 12:06 8.2M
nestedRepeats.txt.gz 2011-01-19 10:55 8.1M
chainMelGal1.txt.gz 2011-11-06 09:51 5.3M
netMelGal1.txt.gz 2011-11-06 09:58 4.9M
locusName.txt.gz 2016-11-06 06:40 4.3M
ensGene.txt.gz 2014-04-06 15:50 3.7M
blastHg18KG.txt.gz 2011-01-19 11:16 3.1M
augustusGene.txt.gz 2015-07-26 11:52 2.8M
all_mrna.txt.gz 2020-08-21 07:48 2.6M
genscan.txt.gz 2013-12-09 21:01 2.5M
UMassME1.txt.gz 2011-11-06 09:51 2.4M
UMassInput.txt.gz 2011-11-06 09:58 2.2M
refGene.txt.gz 2020-08-21 08:12 1.7M
refSeqAli.txt.gz 2020-08-21 08:12 1.7M
mgcFullMrna.txt.gz 2020-03-01 05:42 1.5M
refFlat.txt.gz 2020-08-21 08:12 1.5M
crisprRanges.txt.gz 2016-11-06 06:40 1.4M
mgcGenes.txt.gz 2020-03-01 05:42 1.2M
pubsBingBlat.txt.gz 2014-01-26 10:26 1.1M
microsat.txt.gz 2015-08-23 13:32 1.1M
UMassME1Peak.txt.gz 2011-11-06 09:51 1.1M
UMassME3.txt.gz 2011-11-06 09:58 1.1M
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:57 1.0M
UMassME1Hotspot.txt.gz 2011-11-06 09:51 849K
mrnaOrientInfo.txt.gz 2020-08-21 08:12 807K
pubsBingBlatPsl.txt.gz 2014-01-26 10:26 721K
gold.txt.gz 2011-01-19 11:16 692K
ensGtp.txt.gz 2014-04-06 15:46 540K
UMassME3Peak.txt.gz 2011-11-06 09:58 528K
ensemblToGeneName.txt.gz 2014-04-06 15:46 402K
UMassME3Hotspot.txt.gz 2011-11-06 09:51 389K
gap.txt.gz 2011-01-19 10:54 325K
cpgIslandExt.txt.gz 2011-08-07 08:02 271K
tRNAs.txt.gz 2012-04-22 21:28 267K
ensemblSource.txt.gz 2014-04-06 15:46 235K
gbLoaded.txt.gz 2020-08-21 08:13 92K
trackDb.txt.gz 2023-09-19 16:08 64K
trackDb_pushedout.txt.gz 2023-09-18 17:06 64K
ctgPos2.txt.gz 2011-01-19 11:12 13K
ucscToRefSeq.txt.gz 2018-02-18 06:10 9.7K
ucscToINSDC.txt.gz 2013-09-15 10:59 9.5K
tableDescriptions.txt.gz 2024-04-27 02:03 8.7K
chromInfo.txt.gz 2011-01-19 10:55 7.3K
cytoBandIdeo.txt.gz 2013-04-28 12:53 6.4K
chromAlias.txt.gz 2018-02-18 06:10 5.7K
tableList.txt.gz 2024-04-28 03:33 5.6K
pubsBingBlat.sql 2014-01-26 10:26 2.4K
pubsBingBlatPsl.sql 2014-01-26 10:26 2.2K
xenoRefSeqAli.sql 2020-08-21 08:12 2.1K
refSeqAli.sql 2020-08-21 08:12 2.1K
xenoMrna.sql 2020-08-21 07:48 2.1K
all_mrna.sql 2020-08-21 07:48 2.1K
mgcFullMrna.sql 2020-03-01 05:42 2.1K
intronEst.sql 2017-11-26 06:48 2.1K
all_est.sql 2017-11-26 06:48 2.1K
netMm10.sql 2013-10-27 12:06 2.1K
trackDb_pushedout.sql 2023-09-18 17:06 2.1K
trackDb.sql 2023-09-19 16:08 2.1K
blastHg18KG.sql 2011-01-19 11:16 2.1K
netXenTro3.sql 2011-11-06 09:51 2.0K
netTetNig2.sql 2011-03-07 08:11 2.0K
netPanTro3.sql 2011-03-14 11:10 2.0K
netOryLat2.sql 2011-03-07 06:59 2.0K
netMelGal1.sql 2011-11-06 09:58 2.0K
netGasAcu1.sql 2011-03-07 08:20 2.0K
netHg19.sql 2011-03-07 08:11 2.0K
netFr3.sql 2012-06-24 06:38 2.0K
xenoRefGene.sql 2020-08-21 08:12 2.0K
refGene.sql 2020-08-21 08:12 1.9K
augustusGene.sql 2015-07-26 11:52 1.9K
mgcGenes.sql 2020-03-01 05:42 1.9K
ensGene.sql 2014-04-06 15:50 1.9K
nestedRepeats.sql 2011-01-19 10:55 1.9K
simpleRepeat.sql 2011-01-19 11:13 1.9K
mrnaOrientInfo.sql 2020-08-21 08:12 1.8K
rmsk.sql 2011-01-19 10:39 1.8K
hgFindSpec_pushedout.sql 2023-09-18 17:06 1.8K
estOrientInfo.sql 2017-11-26 06:46 1.8K
hgFindSpec.sql 2023-09-19 16:08 1.8K
xenoRefFlat.sql 2020-08-21 08:12 1.7K
refFlat.sql 2020-08-21 08:12 1.7K
phastCons8wayFish.sql 2011-10-09 10:33 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 10:57 1.7K
phyloP8wayFish.sql 2011-10-09 10:35 1.7K
chainMm10.sql 2013-10-27 12:05 1.7K
phastCons8way.sql 2011-10-09 10:34 1.7K
UMassME3Peak.sql 2011-11-06 09:58 1.7K
UMassME1Peak.sql 2011-11-06 09:51 1.7K
phyloP8way.sql 2011-10-09 10:33 1.7K
UMassInput.sql 2011-11-06 09:58 1.7K
UMassME3.sql 2011-11-06 09:58 1.7K
UMassME1.sql 2011-11-06 09:51 1.7K
tRNAs.sql 2012-04-22 21:28 1.7K
genscan.sql 2013-12-09 21:01 1.7K
multiz8wayFrames.sql 2011-10-09 10:35 1.7K
chainXenTro3.sql 2011-11-06 09:57 1.6K
chainTetNig2.sql 2011-03-07 06:59 1.6K
chainPanTro3.sql 2011-03-14 11:24 1.6K
chainOryLat2.sql 2011-03-07 08:11 1.6K
chainMelGal1.sql 2011-11-06 09:51 1.6K
chainGasAcu1.sql 2011-03-07 07:34 1.6K
chainHg19.sql 2011-03-07 07:21 1.6K
chainFr3.sql 2012-06-24 06:38 1.6K
cpgIslandExt.sql 2011-08-07 08:02 1.6K
gbLoaded.sql 2020-08-21 08:13 1.6K
gold.sql 2011-01-19 11:16 1.6K
tableList.sql 2024-04-28 03:33 1.6K
chainMm10Link.sql 2013-10-27 12:05 1.5K
gap.sql 2011-01-19 10:54 1.5K
cytoBandIdeo.sql 2013-04-28 12:53 1.5K
multiz8waySummary.sql 2011-10-09 10:35 1.5K
history.sql 2011-01-19 10:49 1.5K
phastConsElements8wayFish.sql 2011-10-09 10:33 1.5K
phastConsElements8way.sql 2011-10-09 10:34 1.5K
locusName.sql 2016-11-06 06:40 1.5K
microsat.sql 2015-08-23 13:32 1.5K
chainXenTro3Link.sql 2011-11-06 09:51 1.5K
chainTetNig2Link.sql 2011-03-07 07:19 1.5K
chainPanTro3Link.sql 2011-03-14 11:10 1.5K
chainOryLat2Link.sql 2011-03-07 07:56 1.5K
chainMelGal1Link.sql 2011-11-06 09:51 1.5K
chainGasAcu1Link.sql 2011-03-07 08:03 1.5K
UMassME3Hotspot.sql 2011-11-06 09:51 1.5K
UMassME1Hotspot.sql 2011-11-06 09:51 1.5K
ctgPos2.sql 2011-01-19 11:12 1.5K
chainHg19Link.sql 2011-03-07 07:00 1.5K
chainFr3Link.sql 2012-06-24 06:38 1.5K
multiz8way.sql 2011-10-09 10:34 1.5K
tableDescriptions.sql 2024-04-27 02:03 1.5K
crisprRanges.sql 2016-11-06 06:40 1.4K
ensGtp.sql 2014-04-06 15:46 1.4K
ucscToRefSeq.sql 2018-02-18 06:10 1.4K
ucscToINSDC.sql 2013-09-15 10:59 1.4K
chromAlias.sql 2018-02-18 06:10 1.4K
bigFiles.sql 2024-04-28 03:33 1.4K
ensemblToGeneName.sql 2014-04-06 15:46 1.4K
ensemblSource.sql 2014-04-06 15:46 1.4K
extFile.sql 2011-10-09 10:33 1.4K
grp.sql 2014-03-02 03:40 1.3K
ensPep.sql 2014-04-06 15:46 1.3K
chromInfo.sql 2011-01-19 10:55 1.3K
grcIncidentDb.sql 2018-05-13 05:03 1.3K
crisprTargets.sql 2016-11-06 06:40 1.3K
gc5BaseBw.sql 2011-01-19 11:08 1.2K
hgFindSpec_pushedout.txt.gz 2023-09-18 17:06 1.1K
hgFindSpec.txt.gz 2023-09-19 16:08 1.1K
history.txt.gz 2011-01-19 10:49 249
grp.txt.gz 2014-03-02 03:40 209
bigFiles.txt.gz 2024-04-28 03:33 114
extFile.txt.gz 2011-10-09 10:33 80
grcIncidentDb.txt.gz 2018-05-13 05:03 77
gc5BaseBw.txt.gz 2011-01-19 11:08 63
crisprTargets.txt.gz 2016-11-06 06:40 63