This directory contains a dump of the UCSC genome annotation database for
the Jul. 2007 Zv7 assembly of the zebrafish genome (danRer5) obtained from
the Wellcome Trust Sanger Institute. 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=danRer5
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.cse.ucsc.edu, then go to
the directory goldenPath/danRer5/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/danRer5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/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 danRer5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer5 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Zv7 zebrafish sequence data were produced by the Zebrafish Sequencing
Group at the Sanger Institute and can be obtained directly from
ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release/. All sequence
data are made available before scientific publication with the understanding
that the groups involved in generating the data intend to publish the
initial large-scale analyses of the dataset. This will include a summary
detailing the data that have beeen generated and key features of the
genome identified from genomic assembly and clone mapping/sequencing. Any
redistribution of the data should carry this notice.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
bigFiles.txt.gz 2024-11-17 03:26 33
extFile.txt.gz 2007-10-15 10:28 129
grp.txt.gz 2014-03-02 03:40 208
history.txt.gz 2007-10-15 10:34 907
vegaPep.sql 2007-10-15 10:47 1.1K
chromInfo.sql 2007-10-15 10:27 1.2K
vegaToCloneId.sql 2007-10-15 10:47 1.2K
ensPep.sql 2009-09-27 08:01 1.3K
extFile.sql 2007-10-15 10:28 1.3K
bigFiles.sql 2024-11-17 03:26 1.4K
hgFindSpec.txt.gz 2023-03-28 13:48 1.4K
grp.sql 2014-03-02 03:40 1.4K
ensGtp.sql 2009-09-27 08:00 1.4K
history.sql 2007-10-15 10:34 1.4K
chainFr2Link.sql 2007-10-15 10:01 1.4K
chainMm9Link.sql 2007-10-15 10:05 1.4K
ctgPos2.sql 2007-10-15 10:27 1.4K
seq.sql 2007-10-15 10:45 1.4K
chainOryLat2Link.sql 2008-11-16 07:52 1.4K
chainTetNig1Link.sql 2007-10-15 10:25 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
UMassME1Hotspot.sql 2011-11-06 09:43 1.5K
UMassME3Hotspot.sql 2011-11-06 09:43 1.5K
vegaInfoZfish.sql 2007-10-15 10:47 1.5K
microsat.sql 2015-08-23 13:18 1.5K
gap.sql 2007-10-15 10:28 1.5K
chainHg19Link.sql 2009-10-04 07:34 1.5K
chainMonDom5Link.sql 2009-09-27 08:01 1.5K
tableList.sql 2024-11-17 03:26 1.6K
gold.sql 2007-10-15 10:34 1.6K
gbLoaded.sql 2020-08-21 09:14 1.6K
chainFr2.sql 2007-10-15 10:00 1.6K
chainMm9.sql 2007-10-15 10:05 1.6K
chainOryLat2.sql 2008-11-16 07:51 1.7K
chainTetNig1.sql 2007-10-15 10:25 1.7K
tRNAs.sql 2012-04-22 21:08 1.7K
UMassME1.sql 2011-11-06 09:43 1.7K
UMassME3.sql 2011-11-06 09:43 1.7K
UMassInput.sql 2011-11-06 09:43 1.7K
UMassME1Peak.sql 2011-11-06 09:43 1.7K
UMassME3Peak.sql 2011-11-06 09:43 1.7K
gc5Base.sql 2007-10-15 10:34 1.7K
refFlat.sql 2020-08-21 08:59 1.7K
xenoRefFlat.sql 2020-08-21 08:59 1.7K
hgFindSpec.sql 2023-03-28 13:48 1.8K
estOrientInfo.sql 2017-11-26 06:44 1.8K
chainHg19.sql 2009-10-04 07:34 1.8K
chainMonDom5.sql 2009-09-27 08:01 1.8K
mrnaOrientInfo.sql 2020-08-21 09:12 1.8K
affyZonWildType.sql 2007-10-15 09:57 1.8K
rmsk.sql 2007-10-15 10:41 1.9K
affyTargetZonWildType.sql 2007-10-15 09:56 1.9K
nestedRepeats.sql 2007-10-15 10:37 1.9K
vegaGene.sql 2007-10-15 10:46 1.9K
simpleRepeat.sql 2007-10-15 10:45 1.9K
mgcGenes.sql 2020-03-01 05:36 1.9K
vegaPseudoGene.sql 2007-10-15 10:47 1.9K
augustusGene.sql 2015-07-26 11:52 1.9K
refGene.sql 2020-08-21 08:56 1.9K
xenoRefGene.sql 2020-08-21 08:59 2.0K
ensGene.sql 2009-09-27 08:00 2.0K
trackDb.sql 2023-03-28 13:48 2.1K
all_est.sql 2017-11-26 06:44 2.1K
xenoMrna.sql 2016-02-21 12:56 2.1K
intronEst.sql 2017-11-26 06:44 2.1K
mgcFullMrna.sql 2020-03-01 05:36 2.1K
all_mrna.sql 2020-08-21 08:49 2.1K
refSeqAli.sql 2020-08-21 09:12 2.1K
xenoRefSeqAli.sql 2020-08-21 09:14 2.1K
affyZebrafishTarget.sql 2007-10-15 09:56 2.2K
affyZebrafishConsensus.sql 2007-10-15 09:56 2.2K
netFr2.sql 2007-10-15 10:38 2.2K
netMm9.sql 2007-10-15 10:39 2.2K
netOryLat2.sql 2008-11-16 07:56 2.2K
netTetNig1.sql 2007-10-15 10:40 2.2K
blastHg18KG.sql 2009-12-20 10:59 2.3K
netHg19.sql 2009-10-04 07:34 2.3K
netMonDom5.sql 2009-09-27 08:01 2.3K
vegaPseudoGene.txt.gz 2007-10-15 10:47 3.5K
tableList.txt.gz 2024-11-17 03:26 4.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.6K
chromInfo.txt.gz 2007-10-15 10:27 28K
trackDb.txt.gz 2023-03-28 13:48 36K
gbLoaded.txt.gz 2020-08-21 09:14 43K
vegaToCloneId.txt.gz 2007-10-15 10:47 56K
gold.txt.gz 2007-10-15 10:34 86K
tRNAs.txt.gz 2012-04-22 21:08 268K
vegaInfoZfish.txt.gz 2007-10-15 10:47 339K
ensGtp.txt.gz 2009-09-27 08:00 364K
seq.txt.gz 2007-10-15 10:45 365K
UMassME3Hotspot.txt.gz 2011-11-06 09:43 408K
gap.txt.gz 2007-10-15 10:28 538K
UMassME1Hotspot.txt.gz 2011-11-06 09:43 560K
UMassME3Peak.txt.gz 2011-11-06 09:43 565K
affyZebrafishTarget.txt.gz 2007-10-15 09:57 717K
UMassME1Peak.txt.gz 2011-11-06 09:43 750K
mrnaOrientInfo.txt.gz 2020-08-21 09:12 827K
ctgPos2.txt.gz 2007-10-15 10:27 835K
vegaGene.txt.gz 2007-10-15 10:46 1.0M
affyZebrafishConsensus.txt.gz 2007-10-15 09:56 1.1M
microsat.txt.gz 2015-08-23 13:18 1.1M
mgcGenes.txt.gz 2020-03-01 05:36 1.2M
UMassME3.txt.gz 2011-11-06 09:43 1.5M
refFlat.txt.gz 2020-08-21 08:59 1.5M
mgcFullMrna.txt.gz 2020-03-01 05:36 1.5M
affyTargetZonWildType.txt.gz 2007-10-15 09:56 1.7M
refSeqAli.txt.gz 2020-08-21 09:12 1.7M
refGene.txt.gz 2020-08-21 08:56 1.7M
affyZonWildType.txt.gz 2007-10-15 09:57 1.9M
vegaPep.txt.gz 2007-10-15 10:47 2.1M
UMassInput.txt.gz 2011-11-06 09:43 2.4M
ensGene.txt.gz 2009-09-27 08:00 2.5M
all_mrna.txt.gz 2020-08-21 08:49 2.6M
UMassME1.txt.gz 2011-11-06 09:43 2.6M
augustusGene.txt.gz 2015-07-26 11:52 2.8M
blastHg18KG.txt.gz 2009-12-20 11:00 3.0M
gc5Base.txt.gz 2007-10-15 10:34 5.6M
ensPep.txt.gz 2009-09-27 08:01 7.4M
netMm9.txt.gz 2007-10-15 10:39 7.5M
netHg19.txt.gz 2009-10-04 07:34 8.2M
netMonDom5.txt.gz 2009-09-27 08:01 8.3M
chainMm9.txt.gz 2007-10-15 10:05 9.1M
netTetNig1.txt.gz 2007-10-15 10:40 10M
chainHg19.txt.gz 2009-10-04 07:34 10M
chainTetNig1.txt.gz 2007-10-15 10:25 11M
netFr2.txt.gz 2007-10-15 10:38 11M
nestedRepeats.txt.gz 2007-10-15 10:38 11M
chainFr2.txt.gz 2007-10-15 10:00 15M
netOryLat2.txt.gz 2008-11-16 07:56 16M
xenoRefSeqAli.txt.gz 2020-08-21 09:14 19M
chainMonDom5.txt.gz 2009-09-27 08:01 19M
xenoRefFlat.txt.gz 2020-08-21 08:59 20M
estOrientInfo.txt.gz 2017-11-26 06:44 20M
xenoRefGene.txt.gz 2020-08-21 08:59 22M
simpleRepeat.txt.gz 2007-10-15 10:46 25M
intronEst.txt.gz 2017-11-26 06:44 54M
chainOryLat2.txt.gz 2008-11-16 07:52 62M
chainTetNig1Link.txt.gz 2007-10-15 10:26 63M
chainHg19Link.txt.gz 2009-10-04 07:34 65M
chainMm9Link.txt.gz 2007-10-15 10:07 67M
all_est.txt.gz 2017-11-26 06:44 85M
rmsk.txt.gz 2007-10-15 10:43 87M
chainFr2Link.txt.gz 2007-10-15 10:03 93M
chainMonDom5Link.txt.gz 2009-09-27 08:01 95M
xenoMrna.txt.gz 2016-02-21 12:56 213M
chainOryLat2Link.txt.gz 2008-11-16 07:54 317M