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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
rmsk.sql 2017-11-01 12:58 1.9K
rmsk.txt.gz 2017-11-01 12:58 113M
augustusGene.sql 2017-11-01 12:58 1.9K
augustusGene.txt.gz 2017-11-01 12:58 3.3M
simpleRepeat.sql 2017-11-01 12:59 1.9K
simpleRepeat.txt.gz 2017-11-01 12:59 29M
chainHg38.sql 2017-11-01 12:59 1.7K
chainHg38.txt.gz 2017-11-01 12:59 239M
chainHg38Link.sql 2017-11-01 13:00 1.5K
chainHg38Link.txt.gz 2017-11-01 13:01 554M
microsat.sql 2017-11-01 13:02 1.5K
chainMm10.sql 2017-11-01 13:02 1.7K
microsat.txt.gz 2017-11-01 13:02 1.2M
chainMm10.txt.gz 2017-11-01 13:02 33M
chainMm10Link.sql 2017-11-01 13:03 1.5K
chainMm10Link.txt.gz 2017-11-01 13:03 83M
nestedRepeats.sql 2017-11-01 13:03 1.9K
nestedRepeats.txt.gz 2017-11-01 13:03 9.8M
chromInfo.sql 2017-11-01 13:03 1.4K
chromInfo.txt.gz 2017-11-01 13:03 14K
cpgIslandExt.sql 2017-11-01 13:03 1.7K
cpgIslandExt.txt.gz 2017-11-01 13:03 287K
netHg38.sql 2017-11-01 13:03 2.1K
netHg38.txt.gz 2017-11-01 13:03 6.6M
cpgIslandExtUnmasked.sql 2017-11-01 13:03 1.7K
cpgIslandExtUnmasked.txt.gz 2017-11-01 13:03 1.1M
cytoBandIdeo.sql 2017-11-01 13:03 1.5K
cytoBandIdeo.txt.gz 2017-11-01 13:03 13K
gold.sql 2017-11-01 13:03 1.7K
gold.txt.gz 2017-11-01 13:03 657K
netMm10.sql 2017-11-01 13:03 2.1K
netMm10.txt.gz 2017-11-01 13:03 6.4M
ucscToINSDC.sql 2017-11-01 13:03 1.4K
ucscToINSDC.txt.gz 2017-11-01 13:03 17K
gap.sql 2017-11-01 13:03 1.6K
gap.txt.gz 2017-11-01 13:03 196K
ucscToRefSeq.sql 2017-11-01 13:03 1.4K
ucscToRefSeq.txt.gz 2017-11-01 13:03 18K
windowmaskerSdust.sql 2017-11-01 13:03 1.5K
windowmaskerSdust.txt.gz 2017-11-01 13:03 99M
gc5BaseBw.sql 2017-11-01 13:04 1.3K
gc5BaseBw.txt.gz 2017-11-01 13:04 67
genscan.sql 2017-11-01 13:04 1.7K
genscan.txt.gz 2017-11-01 13:04 2.5M
genscanSubopt.sql 2017-11-01 13:04 1.6K
genscanSubopt.txt.gz 2017-11-01 13:04 3.9M
grp.sql 2017-11-01 13:04 1.3K
grp.txt.gz 2017-11-01 13:04 213
history.sql 2017-11-01 13:05 1.6K
history.txt.gz 2017-11-01 13:05 606
all_est.sql 2017-11-26 06:40 2.1K
all_est.txt.gz 2017-11-26 06:40 84M
intronEst.sql 2017-11-26 06:40 2.1K
intronEst.txt.gz 2017-11-26 06:40 59M
estOrientInfo.sql 2017-11-26 06:41 1.8K
estOrientInfo.txt.gz 2017-11-26 06:41 20M
chromAlias.sql 2018-08-05 06:11 1.4K
chromAlias.txt.gz 2018-08-05 06:11 20K
ensemblLift.sql 2019-01-13 04:04 1.4K
ensemblLift.txt.gz 2019-01-13 04:04 6.8K
ucscToEnsembl.sql 2019-01-13 04:04 1.4K
ucscToEnsembl.txt.gz 2019-01-13 04:04 9.7K
chainGalGal6.sql 2019-01-20 08:06 1.7K
chainGalGal6.txt.gz 2019-01-20 08:06 26M
chainGalGal6Link.sql 2019-01-20 08:06 1.6K
chainGalGal6Link.txt.gz 2019-01-20 08:06 96M
netGalGal6.sql 2019-01-20 08:07 2.1K
netGalGal6.txt.gz 2019-01-20 08:07 11M
ensPep.sql 2019-02-10 03:41 1.3K
ensPep.txt.gz 2019-02-10 03:41 15M
ensGene.sql 2019-02-10 03:41 1.9K
ensGtp.sql 2019-02-10 03:41 1.4K
ensGtp.txt.gz 2019-02-10 03:41 687K
ensGene.txt.gz 2019-02-10 03:41 3.8M
ensemblSource.sql 2019-02-10 03:41 1.4K
ensemblSource.txt.gz 2019-02-10 03:41 200K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
ensemblToGeneName.txt.gz 2019-02-10 03:41 451K
grcIncidentDb.sql 2019-09-22 03:19 1.3K
grcIncidentDb.txt.gz 2019-09-22 03:19 78
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:27 4.4M
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 92
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 370K
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.5M
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 922K
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 2.4M
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 76
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 14M
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.0M
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 1.9M
all_mrna.sql 2020-08-18 21:59 2.1K
all_mrna.txt.gz 2020-08-18 21:59 2.8M
xenoMrna.sql 2020-08-18 21:59 2.1K
xenoMrna.txt.gz 2020-08-18 21:59 153M
refGene.sql 2020-08-18 21:59 1.9K
refGene.txt.gz 2020-08-18 21:59 1.9M
refFlat.sql 2020-08-18 21:59 1.7K
refFlat.txt.gz 2020-08-18 21:59 1.7M
xenoRefGene.sql 2020-08-18 21:59 2.0K
xenoRefGene.txt.gz 2020-08-18 21:59 16M
xenoRefFlat.sql 2020-08-18 21:59 1.7K
xenoRefFlat.txt.gz 2020-08-18 21:59 14M
mrnaOrientInfo.sql 2020-08-18 22:14 1.8K
mrnaOrientInfo.txt.gz 2020-08-18 22:14 869K
refSeqAli.sql 2020-08-18 22:14 2.1K
refSeqAli.txt.gz 2020-08-18 22:14 1.8M
xenoRefSeqAli.sql 2020-08-18 22:14 2.2K
xenoRefSeqAli.txt.gz 2020-08-18 22:14 13M
gbLoaded.sql 2020-08-18 22:17 1.6K
gbLoaded.txt.gz 2020-08-18 22:17 28K
chainMm39.sql 2020-11-25 02:48 1.7K
chainMm39.txt.gz 2020-11-25 02:48 11M
chainMm39Link.sql 2020-11-25 02:49 1.6K
chainMm39Link.txt.gz 2020-11-25 02:49 41M
netMm39.sql 2020-11-25 02:50 2.1K
netMm39.txt.gz 2020-11-25 02:50 6.8M
hgBlastTab.sql 2022-07-12 17:02 1.7K
hgBlastTab.txt.gz 2022-07-12 17:02 356K
mmBlastTab.sql 2022-07-12 17:09 1.7K
mmBlastTab.txt.gz 2022-07-12 17:09 348K
crisprAllTargets.sql 2023-11-06 10:50 1.3K
crisprAllTargets.txt.gz 2023-11-06 10:50 70
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 76K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
tableDescriptions.sql 2024-11-16 02:03 1.5K
tableDescriptions.txt.gz 2024-11-16 02:03 6.9K
tableList.sql 2024-11-17 03:14 1.6K
tableList.txt.gz 2024-11-17 03:14 3.9K
bigFiles.sql 2024-11-17 03:14 1.4K
bigFiles.txt.gz 2024-11-17 03:14 145