This directory contains a dump of the UCSC genome annotation database for the
May 2017 (GRCz11/danRer11) assembly of the zebrafish genome
(danRer11, Genome Reference 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/50
http://www.ncbi.nlm.nih.gov/genome/assembly/1104621
http://www.ncbi.nlm.nih.gov/bioproject/11776
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=danRer11
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/danRer11/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/danRer11/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11/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 danRer11 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer11 --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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2017-11-01 13:04 67
crisprAllTargets.txt.gz 2023-11-06 10:50 70
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 76
grcIncidentDb.txt.gz 2019-09-22 03:19 78
extNcbiRefSeq.txt.gz 2020-05-10 03:27 92
bigFiles.txt.gz 2024-11-17 03:14 145
grp.txt.gz 2017-11-01 13:04 213
history.txt.gz 2017-11-01 13:05 606
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
gc5BaseBw.sql 2017-11-01 13:04 1.3K
grcIncidentDb.sql 2019-09-22 03:19 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ensPep.sql 2019-02-10 03:41 1.3K
crisprAllTargets.sql 2023-11-06 10:50 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
grp.sql 2017-11-01 13:04 1.3K
ensemblLift.sql 2019-01-13 04:04 1.4K
ensemblSource.sql 2019-02-10 03:41 1.4K
ucscToEnsembl.sql 2019-01-13 04:04 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
chromInfo.sql 2017-11-01 13:03 1.4K
bigFiles.sql 2024-11-17 03:14 1.4K
ensGtp.sql 2019-02-10 03:41 1.4K
chromAlias.sql 2018-08-05 06:11 1.4K
ucscToINSDC.sql 2017-11-01 13:03 1.4K
ucscToRefSeq.sql 2017-11-01 13:03 1.4K
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.5K
microsat.sql 2017-11-01 13:02 1.5K
windowmaskerSdust.sql 2017-11-01 13:03 1.5K
cytoBandIdeo.sql 2017-11-01 13:03 1.5K
chainHg38Link.sql 2017-11-01 13:00 1.5K
chainMm10Link.sql 2017-11-01 13:03 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
chainGalGal6Link.sql 2019-01-20 08:06 1.6K
chainMm39Link.sql 2020-11-25 02:49 1.6K
genscanSubopt.sql 2017-11-01 13:04 1.6K
history.sql 2017-11-01 13:05 1.6K
tableList.sql 2024-11-17 03:14 1.6K
gap.sql 2017-11-01 13:03 1.6K
gbLoaded.sql 2020-08-18 22:17 1.6K
gold.sql 2017-11-01 13:03 1.7K
genscan.sql 2017-11-01 13:04 1.7K
cpgIslandExt.sql 2017-11-01 13:03 1.7K
hgBlastTab.sql 2022-07-12 17:02 1.7K
mmBlastTab.sql 2022-07-12 17:09 1.7K
chainHg38.sql 2017-11-01 12:59 1.7K
chainMm10.sql 2017-11-01 13:02 1.7K
chainGalGal6.sql 2019-01-20 08:06 1.7K
cpgIslandExtUnmasked.sql 2017-11-01 13:03 1.7K
chainMm39.sql 2020-11-25 02:48 1.7K
refFlat.sql 2020-08-18 21:59 1.7K
xenoRefFlat.sql 2020-08-18 21:59 1.7K
estOrientInfo.sql 2017-11-26 06:41 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
mrnaOrientInfo.sql 2020-08-18 22:14 1.8K
rmsk.sql 2017-11-01 12:58 1.9K
ensGene.sql 2019-02-10 03:41 1.9K
simpleRepeat.sql 2017-11-01 12:59 1.9K
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
nestedRepeats.sql 2017-11-01 13:03 1.9K
augustusGene.sql 2017-11-01 12:58 1.9K
refGene.sql 2020-08-18 21:59 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
xenoRefGene.sql 2020-08-18 21:59 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
trackDb.sql 2024-07-25 09:34 2.1K
netHg38.sql 2017-11-01 13:03 2.1K
netMm10.sql 2017-11-01 13:03 2.1K
netGalGal6.sql 2019-01-20 08:07 2.1K
all_est.sql 2017-11-26 06:40 2.1K
intronEst.sql 2017-11-26 06:40 2.1K
netMm39.sql 2020-11-25 02:50 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
all_mrna.sql 2020-08-18 21:59 2.1K
xenoMrna.sql 2020-08-18 21:59 2.1K
refSeqAli.sql 2020-08-18 22:14 2.1K
xenoRefSeqAli.sql 2020-08-18 22:14 2.2K
tableList.txt.gz 2024-11-17 03:14 3.9K
ensemblLift.txt.gz 2019-01-13 04:04 6.8K
tableDescriptions.txt.gz 2024-11-16 02:03 6.9K
ucscToEnsembl.txt.gz 2019-01-13 04:04 9.7K
cytoBandIdeo.txt.gz 2017-11-01 13:03 13K
chromInfo.txt.gz 2017-11-01 13:03 14K
ucscToINSDC.txt.gz 2017-11-01 13:03 17K
ucscToRefSeq.txt.gz 2017-11-01 13:03 18K
chromAlias.txt.gz 2018-08-05 06:11 20K
gbLoaded.txt.gz 2020-08-18 22:17 28K
trackDb.txt.gz 2024-07-25 09:34 76K
gap.txt.gz 2017-11-01 13:03 196K
ensemblSource.txt.gz 2019-02-10 03:41 200K
cpgIslandExt.txt.gz 2017-11-01 13:03 287K
mmBlastTab.txt.gz 2022-07-12 17:09 348K
hgBlastTab.txt.gz 2022-07-12 17:02 356K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 370K
ensemblToGeneName.txt.gz 2019-02-10 03:41 451K
gold.txt.gz 2017-11-01 13:03 657K
ensGtp.txt.gz 2019-02-10 03:41 687K
mrnaOrientInfo.txt.gz 2020-08-18 22:14 869K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 922K
cpgIslandExtUnmasked.txt.gz 2017-11-01 13:03 1.1M
microsat.txt.gz 2017-11-01 13:02 1.2M
refFlat.txt.gz 2020-08-18 21:59 1.7M
refSeqAli.txt.gz 2020-08-18 22:14 1.8M
refGene.txt.gz 2020-08-18 21:59 1.9M
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 1.9M
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 2.4M
genscan.txt.gz 2017-11-01 13:04 2.5M
all_mrna.txt.gz 2020-08-18 21:59 2.8M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.0M
augustusGene.txt.gz 2017-11-01 12:58 3.3M
ensGene.txt.gz 2019-02-10 03:41 3.8M
genscanSubopt.txt.gz 2017-11-01 13:04 3.9M
ncbiRefSeq.txt.gz 2020-05-10 03:27 4.4M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.5M
netMm10.txt.gz 2017-11-01 13:03 6.4M
netHg38.txt.gz 2017-11-01 13:03 6.6M
netMm39.txt.gz 2020-11-25 02:50 6.8M
nestedRepeats.txt.gz 2017-11-01 13:03 9.8M
chainMm39.txt.gz 2020-11-25 02:48 11M
netGalGal6.txt.gz 2019-01-20 08:07 11M
xenoRefSeqAli.txt.gz 2020-08-18 22:14 13M
xenoRefFlat.txt.gz 2020-08-18 21:59 14M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 14M
ensPep.txt.gz 2019-02-10 03:41 15M
xenoRefGene.txt.gz 2020-08-18 21:59 16M
estOrientInfo.txt.gz 2017-11-26 06:41 20M
chainGalGal6.txt.gz 2019-01-20 08:06 26M
simpleRepeat.txt.gz 2017-11-01 12:59 29M
chainMm10.txt.gz 2017-11-01 13:02 33M
chainMm39Link.txt.gz 2020-11-25 02:49 41M
intronEst.txt.gz 2017-11-26 06:40 59M
chainMm10Link.txt.gz 2017-11-01 13:03 83M
all_est.txt.gz 2017-11-26 06:40 84M
chainGalGal6Link.txt.gz 2019-01-20 08:06 96M
windowmaskerSdust.txt.gz 2017-11-01 13:03 99M
rmsk.txt.gz 2017-11-01 12:58 113M
xenoMrna.txt.gz 2020-08-18 21:59 153M
chainHg38.txt.gz 2017-11-01 12:59 239M
chainHg38Link.txt.gz 2017-11-01 13:01 554M