This directory contains a dump of the UCSC genome annotation database for the
Sep. 2014 (GRCz10/danRer10) assembly of the zebrafish genome
(danRer10, Genome Reference Consortium Zebrafish Build 10) .
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/210611
http://www.ncbi.nlm.nih.gov/bioproject/13922
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=danRer10
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/danRer10/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/danRer10/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/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 danRer10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer10 --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 -
xenoRefSeqAli.txt.gz 2020-08-18 21:59 11M
xenoRefSeqAli.sql 2020-08-18 21:59 2.2K
xenoRefGene.txt.gz 2020-08-18 21:59 13M
xenoRefGene.sql 2020-08-18 21:59 2.0K
xenoRefFlat.txt.gz 2020-08-18 21:59 12M
xenoRefFlat.sql 2020-08-18 21:59 1.7K
xenoMrna.txt.gz 2020-08-18 21:22 131M
xenoMrna.sql 2020-08-18 21:22 2.1K
windowmaskerSdust.txt.gz 2015-04-01 15:09 80M
windowmaskerSdust.sql 2015-04-01 15:09 1.5K
ucscToRefSeq.txt.gz 2018-02-18 06:01 9.7K
ucscToRefSeq.sql 2018-02-18 06:01 1.4K
ucscToINSDC.txt.gz 2015-04-01 15:09 8.6K
ucscToINSDC.sql 2015-04-01 15:09 1.4K
trackDb.txt.gz 2024-07-25 09:34 76K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-12-08 03:06 3.9K
tableList.sql 2024-12-08 03:06 1.6K
tableDescriptions.txt.gz 2024-12-07 02:03 6.9K
tableDescriptions.sql 2024-12-07 02:03 1.5K
simpleRepeat.txt.gz 2015-04-01 15:09 25M
simpleRepeat.sql 2015-04-01 15:09 1.9K
seqNcbiRefSeq.txt.gz 2018-04-08 05:49 844K
seqNcbiRefSeq.sql 2018-04-08 05:49 1.5K
rmsk.txt.gz 2015-04-01 15:09 93M
rmsk.sql 2015-04-01 15:09 1.9K
refSeqAli.txt.gz 2020-08-18 21:59 1.6M
refSeqAli.sql 2020-08-18 21:59 2.1K
refGene.txt.gz 2020-08-18 21:59 1.7M
refGene.sql 2020-08-18 21:59 1.9K
refFlat.txt.gz 2020-08-18 21:59 1.5M
refFlat.sql 2020-08-18 21:59 1.7K
netRn6.txt.gz 2017-03-26 19:16 9.4M
netRn6.sql 2017-03-26 19:16 2.1K
netMelGal5.txt.gz 2017-03-19 16:57 4.8M
netMelGal5.sql 2017-03-19 16:57 2.1K
netHg38.txt.gz 2015-04-01 15:07 10M
netHg38.sql 2015-04-01 15:07 2.1K
netGalGal5.txt.gz 2016-09-18 07:35 6.3M
netGalGal5.sql 2016-09-18 07:35 2.1K
nestedRepeats.txt.gz 2015-04-01 15:06 8.1M
nestedRepeats.sql 2015-04-01 15:06 1.9K
ncbiRefSeqPsl.txt.gz 2018-04-08 05:49 4.5M
ncbiRefSeqPsl.sql 2018-04-08 05:49 2.1K
ncbiRefSeqPredicted.txt.gz 2018-04-08 05:49 2.6M
ncbiRefSeqPredicted.sql 2018-04-08 05:49 2.0K
ncbiRefSeqPepTable.txt.gz 2018-04-08 05:49 13M
ncbiRefSeqPepTable.sql 2018-04-08 05:49 1.4K
ncbiRefSeqOther.txt.gz 2018-04-08 05:49 76
ncbiRefSeqOther.sql 2018-04-08 05:49 1.3K
ncbiRefSeqLink.txt.gz 2018-04-08 05:49 1.9M
ncbiRefSeqLink.sql 2018-04-08 05:49 2.0K
ncbiRefSeqCurated.txt.gz 2018-04-08 05:49 1.5M
ncbiRefSeqCurated.sql 2018-04-08 05:49 2.0K
ncbiRefSeqCds.txt.gz 2018-04-08 05:49 324K
ncbiRefSeqCds.sql 2018-04-08 05:49 1.3K
ncbiRefSeq.txt.gz 2018-04-08 05:49 3.7M
ncbiRefSeq.sql 2018-04-08 05:49 1.9K
mrnaOrientInfo.txt.gz 2020-08-18 21:59 764K
mrnaOrientInfo.sql 2020-08-18 21:59 1.8K
mmBlastTab.txt.gz 2018-05-21 16:02 339K
mmBlastTab.sql 2018-05-21 16:02 1.7K
microsat.txt.gz 2015-08-23 12:56 1.0M
microsat.sql 2015-08-23 12:56 1.5K
mgcGenes.txt.gz 2020-03-01 05:32 1.2M
mgcGenes.sql 2020-03-01 05:32 1.9K
mgcFullMrna.txt.gz 2020-03-01 05:32 1.5M
mgcFullMrna.sql 2020-03-01 05:32 2.1K
intronEst.txt.gz 2017-11-26 06:39 51M
intronEst.sql 2017-11-26 06:39 2.1K
history.txt.gz 2015-04-01 15:06 441
history.sql 2015-04-01 15:06 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2015-04-01 15:06 213
grp.sql 2015-04-01 15:06 1.3K
grcIncidentDb.txt.gz 2018-05-13 04:55 78
grcIncidentDb.sql 2018-05-13 04:55 1.3K
gold.txt.gz 2015-04-01 15:06 641K
gold.sql 2015-04-01 15:06 1.7K
genscan.txt.gz 2015-04-01 15:06 2.4M
genscan.sql 2015-04-01 15:06 1.7K
gc5BaseBw.txt.gz 2015-04-01 15:08 67
gc5BaseBw.sql 2015-04-01 15:08 1.3K
gbLoaded.txt.gz 2020-08-18 21:59 42K
gbLoaded.sql 2020-08-18 21:59 1.6K
gap.txt.gz 2015-04-01 15:06 244K
gap.sql 2015-04-01 15:06 1.6K
extNcbiRefSeq.txt.gz 2018-04-08 05:49 92
extNcbiRefSeq.sql 2018-04-08 05:49 1.4K
estOrientInfo.txt.gz 2017-11-26 06:40 17M
estOrientInfo.sql 2017-11-26 06:39 1.8K
ensemblToGeneName.txt.gz 2018-02-04 06:19 458K
ensemblToGeneName.sql 2018-02-04 06:19 1.4K
ensemblSource.txt.gz 2018-02-04 06:19 207K
ensemblSource.sql 2018-02-04 06:19 1.4K
ensPep.txt.gz 2018-02-04 06:19 13M
ensPep.sql 2018-02-04 06:19 1.3K
ensGtp.txt.gz 2018-02-04 06:19 706K
ensGtp.sql 2018-02-04 06:19 1.4K
ensGene.txt.gz 2018-02-04 06:19 4.0M
ensGene.sql 2018-02-04 06:19 1.9K
cytoBandIdeo.txt.gz 2015-04-01 15:06 6.3K
cytoBandIdeo.sql 2015-04-01 15:06 1.5K
crisprAllTargets.txt.gz 2023-11-06 10:50 70
crisprAllTargets.sql 2023-11-06 10:50 1.3K
cpgIslandExtUnmasked.txt.gz 2015-04-01 15:06 957K
cpgIslandExtUnmasked.sql 2015-04-01 15:06 1.7K
cpgIslandExt.txt.gz 2015-04-01 15:06 250K
cpgIslandExt.sql 2015-04-01 15:06 1.7K
chromInfo.txt.gz 2015-04-01 15:06 6.8K
chromInfo.sql 2015-04-01 15:06 1.4K
chromAlias.txt.gz 2017-09-03 05:24 12K
chromAlias.sql 2017-09-03 05:24 1.4K
chainRn6Link.txt.gz 2017-03-26 19:07 291M
chainRn6Link.sql 2017-03-26 19:04 1.5K
chainRn6.txt.gz 2017-03-26 19:02 60M
chainRn6.sql 2017-03-26 19:02 1.7K
chainMelGal5Link.txt.gz 2017-03-19 16:58 20M
chainMelGal5Link.sql 2017-03-19 16:58 1.6K
chainMelGal5.txt.gz 2017-03-19 16:57 5.9M
chainMelGal5.sql 2017-03-19 16:57 1.7K
chainHg38Link.txt.gz 2015-04-01 15:03 734M
chainHg38Link.sql 2015-04-01 15:02 1.5K
chainHg38.txt.gz 2015-04-01 15:00 200M
chainHg38.sql 2015-04-01 15:00 1.7K
chainGalGal5Link.txt.gz 2016-09-18 07:35 55M
chainGalGal5Link.sql 2016-09-18 07:35 1.6K
chainGalGal5.txt.gz 2016-09-18 07:35 12M
chainGalGal5.sql 2016-09-18 07:35 1.7K
bigFiles.txt.gz 2024-12-08 03:06 145
bigFiles.sql 2024-12-08 03:06 1.4K
augustusGene.txt.gz 2015-07-26 11:52 2.7M
augustusGene.sql 2015-07-26 11:52 1.9K
all_mrna.txt.gz 2020-08-18 21:22 2.4M
all_mrna.sql 2020-08-18 21:22 2.1K
all_est.txt.gz 2017-11-26 06:40 73M
all_est.sql 2017-11-26 06:40 2.1K