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