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 2024-04-21 03:38 139
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
ensemblSource.sql 2021-05-25 14:49 1.4K
chromInfo.sql 2014-07-31 16:12 1.4K
bigFiles.sql 2024-04-21 03:38 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
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
tableDescriptions.sql 2024-04-20 02:04 1.5K
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
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
multiz20waySummary.sql 2017-03-21 04:31 1.6K
tableList.sql 2024-04-21 03:38 1.6K
gap.sql 2014-07-31 16:14 1.6K
gbLoaded.sql 2020-08-20 09:02 1.6K
gold.sql 2014-07-31 16:13 1.7K
genscan.sql 2014-07-31 16:16 1.7K
cpgIslandExt.sql 2014-07-31 16:12 1.7K
hgBlastTab.sql 2022-07-13 01:39 1.7K
mmBlastTab.sql 2022-07-13 01:39 1.7K
chainHg38.sql 2017-03-20 16:53 1.7K
chainMm10.sql 2017-03-20 17:46 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
hgFindSpec.txt.gz 2024-01-31 15:13 1.7K
chainMm39.sql 2020-10-21 09:46 1.7K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.7K
refFlat.sql 2020-08-20 08:47 1.7K
multiz20wayFrames.sql 2017-03-21 04:30 1.7K
xenoRefFlat.sql 2020-08-20 08:59 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
phyloP20way.sql 2017-03-21 04:59 1.8K
estOrientInfo.sql 2016-07-10 09:33 1.8K
phastCons20way.sql 2017-03-21 04:56 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:52 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
mrnaOrientInfo.sql 2020-08-20 08:59 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
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
augustusGene.sql 2015-07-26 17:28 1.9K
ensGene.sql 2021-05-25 14:47 1.9K
refGene.sql 2020-08-20 08:47 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:29 1.9K
xenoRefGene.sql 2020-08-20 08:47 1.9K
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb_pushedout.sql 2023-12-05 13:52 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
intronEst.sql 2016-07-10 09:33 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
all_mrna.sql 2020-08-20 08:47 2.1K
xenoMrna.sql 2020-08-20 08:47 2.1K
refSeqAli.sql 2020-08-20 08:59 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 2024-04-21 03:38 7.3K
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 2024-04-20 02:04 9.8K
chromAlias.txt.gz 2018-08-05 09:15 11K
gbLoaded.txt.gz 2020-08-20 09:02 41K
trackDb_pushedout.txt.gz 2023-12-05 13:52 55K
trackDb.txt.gz 2024-01-31 15:13 92K
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 2022-07-13 01:39 617K
mgcGenes.txt.gz 2020-03-01 08:53 620K
mmBlastTab.txt.gz 2022-07-13 01:39 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