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.

---------------------------------------------------------------
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;'

-----------------------------------------------------------------------------
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 - all_est.sql 2017-11-26 06:40 2.1K all_est.txt.gz 2017-11-26 06:40 73M all_mrna.sql 2020-08-18 21:22 2.1K all_mrna.txt.gz 2020-08-18 21:22 2.4M augustusGene.sql 2015-07-26 11:52 1.9K augustusGene.txt.gz 2015-07-26 11:52 2.7M bigFiles.sql 2022-06-26 03:04 1.4K bigFiles.txt.gz 2022-06-26 03:04 121 chainGalGal5.sql 2016-09-18 07:35 1.7K chainGalGal5.txt.gz 2016-09-18 07:35 12M chainGalGal5Link.sql 2016-09-18 07:35 1.6K chainGalGal5Link.txt.gz 2016-09-18 07:35 55M chainHg38.sql 2015-04-01 15:00 1.7K chainHg38.txt.gz 2015-04-01 15:00 200M chainHg38Link.sql 2015-04-01 15:02 1.5K chainHg38Link.txt.gz 2015-04-01 15:03 734M chainMelGal5.sql 2017-03-19 16:57 1.7K chainMelGal5.txt.gz 2017-03-19 16:57 5.9M chainMelGal5Link.sql 2017-03-19 16:58 1.6K chainMelGal5Link.txt.gz 2017-03-19 16:58 20M chainRn6.sql 2017-03-26 19:02 1.7K chainRn6.txt.gz 2017-03-26 19:02 60M chainRn6Link.sql 2017-03-26 19:04 1.5K chainRn6Link.txt.gz 2017-03-26 19:07 291M chromAlias.sql 2017-09-03 05:24 1.4K chromAlias.txt.gz 2017-09-03 05:24 12K chromInfo.sql 2015-04-01 15:06 1.4K chromInfo.txt.gz 2015-04-01 15:06 6.8K cpgIslandExt.sql 2015-04-01 15:06 1.7K cpgIslandExt.txt.gz 2015-04-01 15:06 250K cpgIslandExtUnmasked.sql 2015-04-01 15:06 1.7K cpgIslandExtUnmasked.txt.gz 2015-04-01 15:06 957K cytoBandIdeo.sql 2015-04-01 15:06 1.5K cytoBandIdeo.txt.gz 2015-04-01 15:06 6.3K ensGene.sql 2018-02-04 06:19 1.9K ensGene.txt.gz 2018-02-04 06:19 4.0M ensGtp.sql 2018-02-04 06:19 1.4K ensGtp.txt.gz 2018-02-04 06:19 706K ensPep.sql 2018-02-04 06:19 1.3K ensPep.txt.gz 2018-02-04 06:19 13M ensemblSource.sql 2018-02-04 06:19 1.4K ensemblSource.txt.gz 2018-02-04 06:19 207K ensemblToGeneName.sql 2018-02-04 06:19 1.4K ensemblToGeneName.txt.gz 2018-02-04 06:19 458K estOrientInfo.sql 2017-11-26 06:39 1.8K estOrientInfo.txt.gz 2017-11-26 06:40 17M extNcbiRefSeq.sql 2018-04-08 05:49 1.4K extNcbiRefSeq.txt.gz 2018-04-08 05:49 92 gap.sql 2015-04-01 15:06 1.6K gap.txt.gz 2015-04-01 15:06 244K gbLoaded.sql 2020-08-18 21:59 1.6K gbLoaded.txt.gz 2020-08-18 21:59 42K gc5BaseBw.sql 2015-04-01 15:08 1.3K gc5BaseBw.txt.gz 2015-04-01 15:08 67 genscan.sql 2015-04-01 15:06 1.7K genscan.txt.gz 2015-04-01 15:06 2.4M gold.sql 2015-04-01 15:06 1.7K gold.txt.gz 2015-04-01 15:06 641K grcIncidentDb.sql 2018-05-13 04:55 1.3K grcIncidentDb.txt.gz 2018-05-13 04:55 78 grp.sql 2015-04-01 15:06 1.3K grp.txt.gz 2015-04-01 15:06 213 hgFindSpec.sql 2022-05-06 12:33 1.8K hgFindSpec.txt.gz 2022-05-06 12:33 1.3K hgFindSpec_pushedout.sql 2022-04-26 10:29 1.8K hgFindSpec_pushedout.txt.gz 2022-04-26 10:29 1.3K history.sql 2015-04-01 15:06 1.6K history.txt.gz 2015-04-01 15:06 441 intronEst.sql 2017-11-26 06:39 2.1K intronEst.txt.gz 2017-11-26 06:39 51M mgcFullMrna.sql 2020-03-01 05:32 2.1K mgcFullMrna.txt.gz 2020-03-01 05:32 1.5M mgcGenes.sql 2020-03-01 05:32 1.9K mgcGenes.txt.gz 2020-03-01 05:32 1.2M microsat.sql 2015-08-23 12:56 1.5K microsat.txt.gz 2015-08-23 12:56 1.0M mmBlastTab.sql 2018-05-21 16:02 1.7K mmBlastTab.txt.gz 2018-05-21 16:02 339K mrnaOrientInfo.sql 2020-08-18 21:59 1.8K mrnaOrientInfo.txt.gz 2020-08-18 21:59 764K ncbiRefSeq.sql 2018-04-08 05:49 1.9K ncbiRefSeq.txt.gz 2018-04-08 05:49 3.7M ncbiRefSeqCds.sql 2018-04-08 05:49 1.3K ncbiRefSeqCds.txt.gz 2018-04-08 05:49 324K ncbiRefSeqCurated.sql 2018-04-08 05:49 2.0K ncbiRefSeqCurated.txt.gz 2018-04-08 05:49 1.5M ncbiRefSeqLink.sql 2018-04-08 05:49 2.0K ncbiRefSeqLink.txt.gz 2018-04-08 05:49 1.9M ncbiRefSeqOther.sql 2018-04-08 05:49 1.3K ncbiRefSeqOther.txt.gz 2018-04-08 05:49 76 ncbiRefSeqPepTable.sql 2018-04-08 05:49 1.4K ncbiRefSeqPepTable.txt.gz 2018-04-08 05:49 13M ncbiRefSeqPredicted.sql 2018-04-08 05:49 2.0K ncbiRefSeqPredicted.txt.gz 2018-04-08 05:49 2.6M ncbiRefSeqPsl.sql 2018-04-08 05:49 2.1K ncbiRefSeqPsl.txt.gz 2018-04-08 05:49 4.5M nestedRepeats.sql 2015-04-01 15:06 1.9K nestedRepeats.txt.gz 2015-04-01 15:06 8.1M netGalGal5.sql 2016-09-18 07:35 2.1K netGalGal5.txt.gz 2016-09-18 07:35 6.3M netHg38.sql 2015-04-01 15:07 2.1K netHg38.txt.gz 2015-04-01 15:07 10M netMelGal5.sql 2017-03-19 16:57 2.1K netMelGal5.txt.gz 2017-03-19 16:57 4.8M netRn6.sql 2017-03-26 19:16 2.1K netRn6.txt.gz 2017-03-26 19:16 9.4M refFlat.sql 2020-08-18 21:59 1.7K refFlat.txt.gz 2020-08-18 21:59 1.5M refGene.sql 2020-08-18 21:59 1.9K refGene.txt.gz 2020-08-18 21:59 1.7M refSeqAli.sql 2020-08-18 21:59 2.1K refSeqAli.txt.gz 2020-08-18 21:59 1.6M rmsk.sql 2015-04-01 15:09 1.9K rmsk.txt.gz 2015-04-01 15:09 93M seqNcbiRefSeq.sql 2018-04-08 05:49 1.5K seqNcbiRefSeq.txt.gz 2018-04-08 05:49 844K simpleRepeat.sql 2015-04-01 15:09 1.9K simpleRepeat.txt.gz 2015-04-01 15:09 25M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 6.8K tableList.sql 2022-06-26 03:04 1.6K tableList.txt.gz 2022-06-26 03:04 4.1K trackDb.sql 2022-05-06 12:33 2.1K trackDb.txt.gz 2022-05-06 12:33 52K trackDb_pushedout.sql 2022-04-26 10:29 2.1K trackDb_pushedout.txt.gz 2022-04-26 10:29 52K ucscToINSDC.sql 2015-04-01 15:09 1.4K ucscToINSDC.txt.gz 2015-04-01 15:09 8.6K ucscToRefSeq.sql 2018-02-18 06:01 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:01 9.7K windowmaskerSdust.sql 2015-04-01 15:09 1.5K windowmaskerSdust.txt.gz 2015-04-01 15:09 80M xenoMrna.sql 2020-08-18 21:22 2.1K xenoMrna.txt.gz 2020-08-18 21:22 131M xenoRefFlat.sql 2020-08-18 21:59 1.7K xenoRefFlat.txt.gz 2020-08-18 21:59 12M xenoRefGene.sql 2020-08-18 21:59 1.9K xenoRefGene.txt.gz 2020-08-18 21:59 13M xenoRefSeqAli.sql 2020-08-18 21:59 2.1K xenoRefSeqAli.txt.gz 2020-08-18 21:59 11M