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