This directory contains a dump of the UCSC genome annotation database for the
    Jul. 2014 (RGSC 6.0/rn6) assembly of the rat genome
    (rn6, RGSC Rnor_6.0) 
from the Rat Genome Sequencing 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/73
    http://www.ncbi.nlm.nih.gov/assembly/GCA_000001895.4/
    http://www.ncbi.nlm.nih.gov/bioproject/10629

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=rn6
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/rn6/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/rn6/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6/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 rn6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rn6 --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 - xenoRefSeqAli.txt.gz 2020-08-20 09:02 25M xenoRefSeqAli.sql 2020-08-20 09:02 2.1K xenoRefGene.txt.gz 2020-08-20 08:47 25M xenoRefGene.sql 2020-08-20 08:47 1.9K xenoRefFlat.txt.gz 2020-08-20 08:59 22M xenoRefFlat.sql 2020-08-20 08:59 1.7K xenoMrna.txt.gz 2020-08-20 08:47 243M xenoMrna.sql 2020-08-20 08:47 2.1K windowmaskerSdust.txt.gz 2014-07-31 16:17 133M windowmaskerSdust.sql 2014-07-31 16:17 1.5K ucscToRefSeq.txt.gz 2017-03-21 05:02 8.4K ucscToRefSeq.sql 2017-03-21 05:02 1.4K ucscToINSDC.txt.gz 2014-07-31 16:17 8.4K ucscToINSDC.sql 2014-07-31 16:17 1.4K trackDb.txt.gz 2021-03-26 09:06 67K trackDb.sql 2021-03-26 09:06 2.1K tableList.txt.gz 2021-06-06 11:29 7.1K tableList.sql 2021-06-06 11:29 1.6K tableDescriptions.txt.gz 2021-03-13 06:37 9.8K tableDescriptions.sql 2021-03-13 06:37 1.4K simpleRepeat.txt.gz 2014-07-31 16:17 40M simpleRepeat.sql 2014-07-31 16:17 1.9K sgpGene.txt.gz 2015-08-31 07:00 2.5M sgpGene.sql 2015-08-31 07:00 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:29 1.0M seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K rmsk.txt.gz 2014-07-31 16:17 132M rmsk.sql 2014-07-31 16:16 1.9K refSeqAli.txt.gz 2020-08-20 08:59 1.9M refSeqAli.sql 2020-08-20 08:59 2.1K refGene.txt.gz 2020-08-20 08:47 2.0M refGene.sql 2020-08-20 08:47 1.9K refFlat.txt.gz 2020-08-20 08:47 1.7M refFlat.sql 2020-08-20 08:47 1.7K phyloP20way.txt.gz 2017-03-21 05:00 74M phyloP20way.sql 2017-03-21 04:59 1.8K phastConsElements20way.txt.gz 2017-03-21 04:58 24M phastConsElements20way.sql 2017-03-21 04:58 1.6K phastCons20way.txt.gz 2017-03-21 04:56 65M phastCons20way.sql 2017-03-21 04:56 1.8K netXenTro7.txt.gz 2017-03-21 04:55 13M netXenTro7.sql 2017-03-21 04:55 2.1K netTarSyr2.txt.gz 2017-03-21 04:54 60M netTarSyr2.sql 2017-03-21 04:54 2.1K netRheMac8.txt.gz 2017-03-21 04:52 58M netRheMac8.sql 2017-03-21 04:51 2.1K netPanTro5.txt.gz 2017-03-21 04:50 59M netPanTro5.sql 2017-03-21 04:48 2.1K netOryCun2.txt.gz 2017-03-21 04:47 46M netOryCun2.sql 2017-03-21 04:46 2.1K netOrnAna2.txt.gz 2017-03-21 04:46 18M netOrnAna2.sql 2017-03-21 04:46 2.1K netMonDom5.txt.gz 2017-03-21 04:45 22M netMonDom5.sql 2017-03-21 04:45 2.1K netMm39.txt.gz 2020-10-21 10:12 64M netMm39.sql 2020-10-21 10:12 2.1K netMm10.txt.gz 2017-03-21 04:43 64M netMm10.sql 2017-03-21 04:42 2.1K netMelGal5.txt.gz 2017-03-21 04:42 7.4M netMelGal5.sql 2017-03-21 04:42 2.1K netHg38.txt.gz 2017-03-21 04:41 53M netHg38.sql 2017-03-21 04:41 2.1K netGalGal5.txt.gz 2016-09-18 11:10 10M netGalGal5.sql 2016-09-18 11:10 2.1K netFelCat8.txt.gz 2017-03-21 04:40 49M netFelCat8.sql 2017-03-21 04:39 2.1K netDanRer10.txt.gz 2017-03-21 04:39 10M netDanRer10.sql 2017-03-21 04:39 2.1K netCavPor3.txt.gz 2017-03-21 04:37 53M netCavPor3.sql 2017-03-21 04:37 2.1K netCanFam3.txt.gz 2017-03-21 04:36 46M netCanFam3.sql 2017-03-21 04:35 2.1K netCalMil1.txt.gz 2017-03-21 04:35 6.0M netCalMil1.sql 2017-03-21 04:35 2.1K netBosTau8.txt.gz 2017-03-21 04:35 44M netBosTau8.sql 2017-03-21 04:34 2.1K netAilMel1.txt.gz 2017-03-21 04:33 49M netAilMel1.sql 2017-03-21 04:32 2.1K nestedRepeats.txt.gz 2014-07-31 16:14 12M nestedRepeats.sql 2014-07-31 16:14 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 5.0M ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.7M ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 13M ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:29 71 ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:29 2.7M ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 1.8M ncbiRefSeqCurated.sql 2020-05-10 03:29 1.9K ncbiRefSeqCds.txt.gz 2020-05-10 03:29 390K ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:29 3.7M ncbiRefSeq.sql 2020-05-10 03:29 1.9K multiz20waySummary.txt.gz 2017-03-21 04:31 48M multiz20waySummary.sql 2017-03-21 04:31 1.6K multiz20wayFrames.txt.gz 2017-03-21 04:30 26M multiz20wayFrames.sql 2017-03-21 04:30 1.7K multiz20way.txt.gz 2017-03-21 04:18 339M multiz20way.sql 2017-03-21 04:16 1.5K mrnaOrientInfo.txt.gz 2020-08-20 08:59 3.0M mrnaOrientInfo.sql 2020-08-20 08:59 1.8K mmBlastTab.txt.gz 2019-04-14 03:23 628K mmBlastTab.sql 2019-04-14 03:23 1.7K microsat.txt.gz 2015-08-24 01:23 2.3M microsat.sql 2015-08-24 01:23 1.5K mgcGenes.txt.gz 2020-03-01 08:53 620K mgcGenes.sql 2020-03-01 08:53 1.9K mgcFullMrna.txt.gz 2020-03-01 08:53 672K mgcFullMrna.sql 2020-03-01 08:53 2.1K intronEst.txt.gz 2016-07-10 09:33 25M intronEst.sql 2016-07-10 09:33 2.1K history.txt.gz 2014-07-31 16:14 413 history.sql 2014-07-31 16:14 1.6K hgFindSpec.txt.gz 2021-03-26 09:06 1.6K hgFindSpec.sql 2021-03-26 09:06 1.8K hgBlastTab.txt.gz 2019-10-13 03:46 620K hgBlastTab.sql 2019-10-13 03:45 1.7K grp.txt.gz 2014-08-03 13:05 200 grp.sql 2014-08-03 13:05 1.3K gold.txt.gz 2014-07-31 16:13 1.4M gold.sql 2014-07-31 16:13 1.7K genscanSubopt.txt.gz 2014-07-31 16:13 6.9M genscanSubopt.sql 2014-07-31 16:13 1.6K genscan.txt.gz 2014-07-31 16:16 3.2M genscan.sql 2014-07-31 16:16 1.7K geneid.txt.gz 2015-11-22 21:02 2.5M geneid.sql 2015-11-22 21:02 1.9K gc5BaseBw.txt.gz 2014-07-31 16:16 62 gc5BaseBw.sql 2014-07-31 16:16 1.3K gbLoaded.txt.gz 2020-08-20 09:02 41K gbLoaded.sql 2020-08-20 09:02 1.6K gap.txt.gz 2014-07-31 16:14 1.7M gap.sql 2014-07-31 16:14 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:29 87 extNcbiRefSeq.sql 2020-05-10 03:29 1.4K extFile.txt.gz 2017-03-21 04:16 77 extFile.sql 2017-03-21 04:16 1.4K estOrientInfo.txt.gz 2016-07-10 09:33 15M estOrientInfo.sql 2016-07-10 09:33 1.8K ensemblToGeneName.txt.gz 2019-02-10 03:42 320K ensemblToGeneName.sql 2019-02-10 03:42 1.4K ensemblSource.txt.gz 2019-02-10 03:42 139K ensemblSource.sql 2019-02-10 03:42 1.3K ensToRgd.txt.gz 2016-08-28 08:08 205K ensToRgd.sql 2016-08-28 08:08 1.4K ensPep.txt.gz 2019-02-10 03:42 8.6M ensPep.sql 2019-02-10 03:42 1.3K ensGtp.txt.gz 2019-02-10 03:42 446K ensGtp.sql 2019-02-10 03:42 1.4K ensGene.txt.gz 2019-02-10 03:42 2.9M ensGene.sql 2019-02-10 03:42 1.9K cytoBandIdeo.txt.gz 2017-03-20 14:10 8.4K cytoBandIdeo.sql 2017-03-20 14:10 1.4K cytoBand.txt.gz 2017-03-21 04:16 8.4K cytoBand.sql 2017-03-21 04:16 1.5K cpgIslandExtUnmasked.txt.gz 2014-07-31 16:13 503K cpgIslandExtUnmasked.sql 2014-07-31 16:13 1.7K cpgIslandExt.txt.gz 2014-07-31 16:12 411K cpgIslandExt.sql 2014-07-31 16:12 1.7K cloneEndmultipleMaps.txt.gz 2016-07-10 09:33 163K cloneEndmultipleMaps.sql 2016-07-10 09:33 1.8K cloneEndcoverageReverse.txt.gz 2016-07-10 09:33 89 cloneEndcoverageReverse.sql 2016-07-10 09:33 1.3K cloneEndcoverageForward.txt.gz 2016-07-10 09:33 90 cloneEndcoverageForward.sql 2016-07-10 09:33 1.3K cloneEndbadEnds.txt.gz 2016-07-10 09:33 573K cloneEndbadEnds.sql 2016-07-10 09:33 1.8K cloneEndRP32.txt.gz 2016-07-10 09:33 2.9K cloneEndRP32.sql 2016-07-10 09:33 1.8K cloneEndRNB2.txt.gz 2016-07-10 09:33 2.3M cloneEndRNB2.sql 2016-07-10 09:33 1.8K cloneEndRNB1.txt.gz 2016-07-10 09:33 3.1M cloneEndRNB1.sql 2016-07-10 09:33 1.8K cloneEndCH230.txt.gz 2016-07-10 09:33 2.0M cloneEndCH230.sql 2016-07-10 09:33 1.8K chromInfo.txt.gz 2014-07-31 16:12 6.8K chromInfo.sql 2014-07-31 16:12 1.4K chromAlias.txt.gz 2018-08-05 09:15 11K chromAlias.sql 2018-08-05 09:15 1.4K chainXenTro7Link.txt.gz 2017-03-21 03:35 1.4G chainXenTro7Link.sql 2017-03-21 03:19 1.5K chainXenTro7.txt.gz 2017-03-21 03:15 311M chainXenTro7.sql 2017-03-21 03:11 1.7K chainTarSyr2Link.txt.gz 2017-03-21 02:01 1.7G chainTarSyr2Link.sql 2017-03-21 01:52 1.5K chainTarSyr2.txt.gz 2017-03-21 01:39 374M chainTarSyr2.sql 2017-03-21 01:38 1.7K chainRheMac8Link.txt.gz 2017-03-20 23:59 2.2G chainRheMac8Link.sql 2017-03-20 23:31 1.5K chainRheMac8.txt.gz 2017-03-20 23:20 610M chainRheMac8.sql 2017-03-20 23:17 1.7K chainPanTro5Link.txt.gz 2017-03-20 21:51 2.9G chainPanTro5Link.sql 2017-03-20 21:35 1.5K chainPanTro5.txt.gz 2017-03-20 21:10 949M chainPanTro5.sql 2017-03-20 21:02 1.7K chainOryCun2Link.txt.gz 2017-03-20 20:41 505M chainOryCun2Link.sql 2017-03-20 20:38 1.5K chainOryCun2.txt.gz 2017-03-20 20:36 82M chainOryCun2.sql 2017-03-20 20:36 1.7K chainOrnAna2Link.txt.gz 2017-03-20 20:18 619M chainOrnAna2Link.sql 2017-03-20 20:12 1.5K chainOrnAna2.txt.gz 2017-03-20 20:10 130M chainOrnAna2.sql 2017-03-20 20:10 1.7K chainMonDom5Link.txt.gz 2017-03-20 19:41 743M chainMonDom5Link.sql 2017-03-20 19:38 1.5K chainMonDom5.txt.gz 2017-03-20 19:34 102M chainMonDom5.sql 2017-03-20 19:34 1.7K chainMm39Link.txt.gz 2020-10-21 10:09 2.3G chainMm39Link.sql 2020-10-21 10:09 1.6K chainMm39.txt.gz 2020-10-21 09:46 318M chainMm39.sql 2020-10-21 09:46 1.7K chainMm10Link.txt.gz 2017-03-20 18:10 2.3G chainMm10Link.sql 2017-03-20 17:57 1.5K chainMm10.txt.gz 2017-03-20 17:48 298M chainMm10.sql 2017-03-20 17:46 1.7K chainMelGal5Link.txt.gz 2017-03-20 17:46 26M chainMelGal5Link.sql 2017-03-20 17:46 1.5K chainMelGal5.txt.gz 2017-03-20 17:46 5.6M chainMelGal5.sql 2017-03-20 17:46 1.7K chainHg38Link.txt.gz 2017-03-20 17:06 1.1G chainHg38Link.sql 2017-03-20 16:59 1.5K chainHg38.txt.gz 2017-03-20 16:55 319M chainHg38.sql 2017-03-20 16:53 1.7K chainGalGal5Link.txt.gz 2016-09-18 11:10 95M chainGalGal5Link.sql 2016-09-18 11:10 1.5K chainGalGal5.txt.gz 2016-09-18 11:10 14M chainGalGal5.sql 2016-09-18 11:10 1.7K chainFelCat8Link.txt.gz 2017-03-20 16:36 626M chainFelCat8Link.sql 2017-03-20 16:30 1.5K chainFelCat8.txt.gz 2017-03-20 16:28 124M chainFelCat8.sql 2017-03-20 16:28 1.7K chainDanRer10Link.txt.gz 2017-03-20 16:20 287M chainDanRer10Link.sql 2017-03-20 16:16 1.5K chainDanRer10.txt.gz 2017-03-20 16:16 59M chainDanRer10.sql 2017-03-20 16:15 1.7K chainCavPor3Link.txt.gz 2017-03-20 15:54 611M chainCavPor3Link.sql 2017-03-20 15:50 1.5K chainCavPor3.txt.gz 2017-03-20 15:48 86M chainCavPor3.sql 2017-03-20 15:47 1.7K chainCanFam3Link.txt.gz 2017-03-20 15:30 487M chainCanFam3Link.sql 2017-03-20 15:27 1.5K chainCanFam3.txt.gz 2017-03-20 15:26 61M chainCanFam3.sql 2017-03-20 15:25 1.7K chainCalMil1Link.txt.gz 2017-03-20 15:13 309M chainCalMil1Link.sql 2017-03-20 15:11 1.5K chainCalMil1.txt.gz 2017-03-20 15:09 79M chainCalMil1.sql 2017-03-20 15:09 1.7K chainBosTau8Link.txt.gz 2017-03-20 14:47 656M chainBosTau8Link.sql 2017-03-20 14:43 1.5K chainBosTau8.txt.gz 2017-03-20 14:42 115M chainBosTau8.sql 2017-03-20 14:41 1.7K chainAilMel1Link.txt.gz 2017-03-20 14:24 462M chainAilMel1Link.sql 2017-03-20 14:22 1.5K chainAilMel1.txt.gz 2017-03-20 14:21 53M chainAilMel1.sql 2017-03-20 14:21 1.7K bigFiles.txt.gz 2021-06-06 11:29 139 bigFiles.sql 2021-06-06 11:29 1.4K augustusGene.txt.gz 2015-07-26 17:28 2.4M augustusGene.sql 2015-07-26 17:28 1.9K all_mrna.txt.gz 2020-08-20 08:47 6.5M all_mrna.sql 2020-08-20 08:47 2.1K all_est.txt.gz 2016-07-10 09:32 50M all_est.sql 2016-07-10 09:32 2.1K