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 - gc5BaseBw.txt.gz 2014-07-31 16:16 62 ncbiRefSeqOther.txt.gz 2020-05-10 03:29 71 extFile.txt.gz 2017-03-21 04:16 77 extNcbiRefSeq.txt.gz 2020-05-10 03:29 87 cloneEndcoverageReverse.txt.gz 2016-07-10 09:33 89 cloneEndcoverageForward.txt.gz 2016-07-10 09:33 90 bigFiles.txt.gz 2021-06-13 03:16 139 grp.txt.gz 2014-08-03 13:05 200 history.txt.gz 2014-07-31 16:14 413 gc5BaseBw.sql 2014-07-31 16:16 1.3K ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K cloneEndcoverageForward.sql 2016-07-10 09:33 1.3K cloneEndcoverageReverse.sql 2016-07-10 09:33 1.3K ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K ensPep.sql 2021-05-25 14:49 1.3K grp.sql 2014-08-03 13:05 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K ensToRgd.sql 2016-08-28 08:08 1.4K bigFiles.sql 2021-06-13 03:16 1.4K ensemblSource.sql 2021-05-25 14:49 1.4K chromInfo.sql 2014-07-31 16:12 1.4K ensemblToGeneName.sql 2021-05-25 14:47 1.4K extFile.sql 2017-03-21 04:16 1.4K chromAlias.sql 2018-08-05 09:15 1.4K tableDescriptions.sql 2021-03-13 06:37 1.4K ucscToINSDC.sql 2014-07-31 16:17 1.4K ucscToRefSeq.sql 2017-03-21 05:02 1.4K cytoBandIdeo.sql 2017-03-20 14:10 1.4K extNcbiRefSeq.sql 2020-05-10 03:29 1.4K ensGtp.sql 2021-05-25 14:47 1.4K microsat.sql 2015-08-24 01:23 1.5K cytoBand.sql 2017-03-21 04:16 1.5K windowmaskerSdust.sql 2014-07-31 16:17 1.5K multiz20way.sql 2017-03-21 04:16 1.5K chainHg38Link.sql 2017-03-20 16:59 1.5K chainMm10Link.sql 2017-03-20 17:57 1.5K seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K chainAilMel1Link.sql 2017-03-20 14:22 1.5K chainBosTau8Link.sql 2017-03-20 14:43 1.5K chainCalMil1Link.sql 2017-03-20 15:11 1.5K chainCanFam3Link.sql 2017-03-20 15:27 1.5K chainCavPor3Link.sql 2017-03-20 15:50 1.5K chainFelCat8Link.sql 2017-03-20 16:30 1.5K chainGalGal5Link.sql 2016-09-18 11:10 1.5K chainMelGal5Link.sql 2017-03-20 17:46 1.5K chainMonDom5Link.sql 2017-03-20 19:38 1.5K chainOrnAna2Link.sql 2017-03-20 20:12 1.5K chainOryCun2Link.sql 2017-03-20 20:38 1.5K chainPanTro5Link.sql 2017-03-20 21:35 1.5K chainRheMac8Link.sql 2017-03-20 23:31 1.5K chainTarSyr2Link.sql 2017-03-21 01:52 1.5K chainXenTro7Link.sql 2017-03-21 03:19 1.5K chainDanRer10Link.sql 2017-03-20 16:16 1.5K chainMm39Link.sql 2020-10-21 10:09 1.6K tableList.sql 2021-06-13 03:16 1.6K phastConsElements20way.sql 2017-03-21 04:58 1.6K genscanSubopt.sql 2014-07-31 16:13 1.6K history.sql 2014-07-31 16:14 1.6K gbLoaded.sql 2020-08-20 09:02 1.6K multiz20waySummary.sql 2017-03-21 04:31 1.6K gap.sql 2014-07-31 16:14 1.6K hgFindSpec.txt.gz 2021-06-10 16:48 1.6K gold.sql 2014-07-31 16:13 1.7K genscan.sql 2014-07-31 16:16 1.7K hgBlastTab.sql 2019-10-13 03:45 1.7K mmBlastTab.sql 2019-04-14 03:23 1.7K cpgIslandExt.sql 2014-07-31 16:12 1.7K chainHg38.sql 2017-03-20 16:53 1.7K chainMm10.sql 2017-03-20 17:46 1.7K refFlat.sql 2020-08-20 08:47 1.7K chainAilMel1.sql 2017-03-20 14:21 1.7K chainBosTau8.sql 2017-03-20 14:41 1.7K chainCalMil1.sql 2017-03-20 15:09 1.7K chainCanFam3.sql 2017-03-20 15:25 1.7K chainCavPor3.sql 2017-03-20 15:47 1.7K chainFelCat8.sql 2017-03-20 16:28 1.7K chainGalGal5.sql 2016-09-18 11:10 1.7K chainMelGal5.sql 2017-03-20 17:46 1.7K chainMonDom5.sql 2017-03-20 19:34 1.7K chainOrnAna2.sql 2017-03-20 20:10 1.7K chainOryCun2.sql 2017-03-20 20:36 1.7K chainPanTro5.sql 2017-03-20 21:02 1.7K chainRheMac8.sql 2017-03-20 23:17 1.7K chainTarSyr2.sql 2017-03-21 01:38 1.7K chainXenTro7.sql 2017-03-21 03:11 1.7K cpgIslandExtUnmasked.sql 2014-07-31 16:13 1.7K chainDanRer10.sql 2017-03-20 16:15 1.7K xenoRefFlat.sql 2020-08-20 08:59 1.7K chainMm39.sql 2020-10-21 09:46 1.7K multiz20wayFrames.sql 2017-03-21 04:30 1.7K hgFindSpec.sql 2021-06-10 16:48 1.8K phyloP20way.sql 2017-03-21 04:59 1.8K estOrientInfo.sql 2016-07-10 09:33 1.8K mrnaOrientInfo.sql 2020-08-20 08:59 1.8K phastCons20way.sql 2017-03-21 04:56 1.8K cloneEndRNB1.sql 2016-07-10 09:33 1.8K cloneEndRNB2.sql 2016-07-10 09:33 1.8K cloneEndRP32.sql 2016-07-10 09:33 1.8K cloneEndCH230.sql 2016-07-10 09:33 1.8K cloneEndbadEnds.sql 2016-07-10 09:33 1.8K cloneEndmultipleMaps.sql 2016-07-10 09:33 1.8K rmsk.sql 2014-07-31 16:16 1.9K geneid.sql 2015-11-22 21:02 1.9K refGene.sql 2020-08-20 08:47 1.9K sgpGene.sql 2015-08-31 07:00 1.9K mgcGenes.sql 2020-03-01 08:53 1.9K simpleRepeat.sql 2014-07-31 16:17 1.9K ncbiRefSeq.sql 2020-05-10 03:29 1.9K nestedRepeats.sql 2014-07-31 16:14 1.9K xenoRefGene.sql 2020-08-20 08:47 1.9K augustusGene.sql 2015-07-26 17:28 1.9K ensGene.sql 2021-05-25 14:47 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:29 1.9K ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K trackDb.sql 2021-06-10 16:48 2.1K netHg38.sql 2017-03-21 04:41 2.1K netMm10.sql 2017-03-21 04:42 2.1K netAilMel1.sql 2017-03-21 04:32 2.1K netBosTau8.sql 2017-03-21 04:34 2.1K netCalMil1.sql 2017-03-21 04:35 2.1K netCanFam3.sql 2017-03-21 04:35 2.1K netCavPor3.sql 2017-03-21 04:37 2.1K netFelCat8.sql 2017-03-21 04:39 2.1K netGalGal5.sql 2016-09-18 11:10 2.1K netMelGal5.sql 2017-03-21 04:42 2.1K netMonDom5.sql 2017-03-21 04:45 2.1K netOrnAna2.sql 2017-03-21 04:46 2.1K netOryCun2.sql 2017-03-21 04:46 2.1K netPanTro5.sql 2017-03-21 04:48 2.1K netRheMac8.sql 2017-03-21 04:51 2.1K netTarSyr2.sql 2017-03-21 04:54 2.1K netXenTro7.sql 2017-03-21 04:55 2.1K netDanRer10.sql 2017-03-21 04:39 2.1K all_est.sql 2016-07-10 09:32 2.1K all_mrna.sql 2020-08-20 08:47 2.1K xenoMrna.sql 2020-08-20 08:47 2.1K intronEst.sql 2016-07-10 09:33 2.1K refSeqAli.sql 2020-08-20 08:59 2.1K netMm39.sql 2020-10-21 10:12 2.1K mgcFullMrna.sql 2020-03-01 08:53 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K xenoRefSeqAli.sql 2020-08-20 09:02 2.1K cloneEndRP32.txt.gz 2016-07-10 09:33 2.9K chromInfo.txt.gz 2014-07-31 16:12 6.8K tableList.txt.gz 2021-06-13 03:16 7.1K ucscToRefSeq.txt.gz 2017-03-21 05:02 8.4K ucscToINSDC.txt.gz 2014-07-31 16:17 8.4K cytoBand.txt.gz 2017-03-21 04:16 8.4K cytoBandIdeo.txt.gz 2017-03-20 14:10 8.4K tableDescriptions.txt.gz 2021-03-13 06:37 9.8K chromAlias.txt.gz 2018-08-05 09:15 11K gbLoaded.txt.gz 2020-08-20 09:02 41K trackDb.txt.gz 2021-06-10 16:48 67K ensemblSource.txt.gz 2021-05-25 14:49 139K cloneEndmultipleMaps.txt.gz 2016-07-10 09:33 163K ensToRgd.txt.gz 2016-08-28 08:08 205K ensemblToGeneName.txt.gz 2021-05-25 14:47 324K ncbiRefSeqCds.txt.gz 2020-05-10 03:29 390K cpgIslandExt.txt.gz 2014-07-31 16:12 411K ensGtp.txt.gz 2021-05-25 14:47 454K cpgIslandExtUnmasked.txt.gz 2014-07-31 16:13 503K cloneEndbadEnds.txt.gz 2016-07-10 09:33 573K hgBlastTab.txt.gz 2019-10-13 03:46 620K mgcGenes.txt.gz 2020-03-01 08:53 620K mmBlastTab.txt.gz 2019-04-14 03:23 628K mgcFullMrna.txt.gz 2020-03-01 08:53 672K seqNcbiRefSeq.txt.gz 2020-05-10 03:29 1.0M gold.txt.gz 2014-07-31 16:13 1.4M gap.txt.gz 2014-07-31 16:14 1.7M refFlat.txt.gz 2020-08-20 08:47 1.7M ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 1.8M refSeqAli.txt.gz 2020-08-20 08:59 1.9M refGene.txt.gz 2020-08-20 08:47 2.0M cloneEndCH230.txt.gz 2016-07-10 09:33 2.0M cloneEndRNB2.txt.gz 2016-07-10 09:33 2.3M microsat.txt.gz 2015-08-24 01:23 2.3M augustusGene.txt.gz 2015-07-26 17:28 2.4M sgpGene.txt.gz 2015-08-31 07:00 2.5M geneid.txt.gz 2015-11-22 21:02 2.5M ncbiRefSeqLink.txt.gz 2020-05-10 03:29 2.7M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.7M ensGene.txt.gz 2021-05-25 14:47 2.9M mrnaOrientInfo.txt.gz 2020-08-20 08:59 3.0M cloneEndRNB1.txt.gz 2016-07-10 09:33 3.1M genscan.txt.gz 2014-07-31 16:16 3.2M ncbiRefSeq.txt.gz 2020-05-10 03:29 3.7M ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 5.0M chainMelGal5.txt.gz 2017-03-20 17:46 5.6M netCalMil1.txt.gz 2017-03-21 04:35 6.0M all_mrna.txt.gz 2020-08-20 08:47 6.5M genscanSubopt.txt.gz 2014-07-31 16:13 6.9M netMelGal5.txt.gz 2017-03-21 04:42 7.4M ensPep.txt.gz 2021-05-25 14:49 8.6M netGalGal5.txt.gz 2016-09-18 11:10 10M netDanRer10.txt.gz 2017-03-21 04:39 10M nestedRepeats.txt.gz 2014-07-31 16:14 12M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 13M netXenTro7.txt.gz 2017-03-21 04:55 13M chainGalGal5.txt.gz 2016-09-18 11:10 14M estOrientInfo.txt.gz 2016-07-10 09:33 15M netOrnAna2.txt.gz 2017-03-21 04:46 18M netMonDom5.txt.gz 2017-03-21 04:45 22M xenoRefFlat.txt.gz 2020-08-20 08:59 22M phastConsElements20way.txt.gz 2017-03-21 04:58 24M intronEst.txt.gz 2016-07-10 09:33 25M xenoRefGene.txt.gz 2020-08-20 08:47 25M xenoRefSeqAli.txt.gz 2020-08-20 09:02 25M multiz20wayFrames.txt.gz 2017-03-21 04:30 26M chainMelGal5Link.txt.gz 2017-03-20 17:46 26M simpleRepeat.txt.gz 2014-07-31 16:17 40M netBosTau8.txt.gz 2017-03-21 04:35 44M netCanFam3.txt.gz 2017-03-21 04:36 46M netOryCun2.txt.gz 2017-03-21 04:47 46M multiz20waySummary.txt.gz 2017-03-21 04:31 48M netAilMel1.txt.gz 2017-03-21 04:33 49M netFelCat8.txt.gz 2017-03-21 04:40 49M all_est.txt.gz 2016-07-10 09:32 50M chainAilMel1.txt.gz 2017-03-20 14:21 53M netHg38.txt.gz 2017-03-21 04:41 53M netCavPor3.txt.gz 2017-03-21 04:37 53M netRheMac8.txt.gz 2017-03-21 04:52 58M netPanTro5.txt.gz 2017-03-21 04:50 59M chainDanRer10.txt.gz 2017-03-20 16:16 59M netTarSyr2.txt.gz 2017-03-21 04:54 60M chainCanFam3.txt.gz 2017-03-20 15:26 61M netMm10.txt.gz 2017-03-21 04:43 64M netMm39.txt.gz 2020-10-21 10:12 64M phastCons20way.txt.gz 2017-03-21 04:56 65M phyloP20way.txt.gz 2017-03-21 05:00 74M chainCalMil1.txt.gz 2017-03-20 15:09 79M chainOryCun2.txt.gz 2017-03-20 20:36 82M chainCavPor3.txt.gz 2017-03-20 15:48 86M chainGalGal5Link.txt.gz 2016-09-18 11:10 95M chainMonDom5.txt.gz 2017-03-20 19:34 102M chainBosTau8.txt.gz 2017-03-20 14:42 115M chainFelCat8.txt.gz 2017-03-20 16:28 124M chainOrnAna2.txt.gz 2017-03-20 20:10 130M rmsk.txt.gz 2014-07-31 16:17 132M windowmaskerSdust.txt.gz 2014-07-31 16:17 133M xenoMrna.txt.gz 2020-08-20 08:47 243M chainDanRer10Link.txt.gz 2017-03-20 16:20 287M chainMm10.txt.gz 2017-03-20 17:48 298M chainCalMil1Link.txt.gz 2017-03-20 15:13 309M chainXenTro7.txt.gz 2017-03-21 03:15 311M chainMm39.txt.gz 2020-10-21 09:46 318M chainHg38.txt.gz 2017-03-20 16:55 319M multiz20way.txt.gz 2017-03-21 04:18 339M chainTarSyr2.txt.gz 2017-03-21 01:39 374M chainAilMel1Link.txt.gz 2017-03-20 14:24 462M chainCanFam3Link.txt.gz 2017-03-20 15:30 487M chainOryCun2Link.txt.gz 2017-03-20 20:41 505M chainRheMac8.txt.gz 2017-03-20 23:20 610M chainCavPor3Link.txt.gz 2017-03-20 15:54 611M chainOrnAna2Link.txt.gz 2017-03-20 20:18 619M chainFelCat8Link.txt.gz 2017-03-20 16:36 626M chainBosTau8Link.txt.gz 2017-03-20 14:47 656M chainMonDom5Link.txt.gz 2017-03-20 19:41 743M chainPanTro5.txt.gz 2017-03-20 21:10 949M chainHg38Link.txt.gz 2017-03-20 17:06 1.1G chainXenTro7Link.txt.gz 2017-03-21 03:35 1.4G chainTarSyr2Link.txt.gz 2017-03-21 02:01 1.7G chainRheMac8Link.txt.gz 2017-03-20 23:59 2.2G chainMm10Link.txt.gz 2017-03-20 18:10 2.3G chainMm39Link.txt.gz 2020-10-21 10:09 2.3G chainPanTro5Link.txt.gz 2017-03-20 21:51 2.9G