This directory contains a dump of the UCSC genome annotation database for the
Nov. 2020 (mRatBN7.2/rn7) assembly of the rat genome
(rn7, Wellcome Sanger Institute)
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:
https://www.ncbi.nlm.nih.gov/genome/73
https://www.ncbi.nlm.nih.gov/genome/assembly/9079111
https://www.ncbi.nlm.nih.gov/bioproject/662791
https://www.ncbi.nlm.nih.gov/biosample/SAMN16261960
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=rn7
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.soe.ucsc.edu, then go to
the directory goldenPath/rn7/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.soe.ucsc.edu/goldenPath/rn7/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 rn7 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rn7 --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 -
bigFiles.txt.gz 2024-11-24 03:04 115
bigFiles.sql 2024-11-24 03:04 1.4K
tableList.txt.gz 2024-11-24 03:04 3.5K
tableList.sql 2024-11-24 03:04 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.3K
tableDescriptions.sql 2024-11-23 02:04 1.4K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
hgFindSpec.sql 2024-07-25 09:34 1.8K
trackDb.txt.gz 2024-07-25 09:34 68K
trackDb.sql 2024-07-25 09:34 2.1K
ncbiRefSeqPepTable.txt.gz 2021-03-31 12:00 15M
ncbiRefSeqPepTable.sql 2021-03-31 12:00 1.4K
history.txt.gz 2021-03-31 12:00 1.0K
history.sql 2021-03-31 12:00 1.6K
ncbiRefSeqLink.txt.gz 2021-03-31 09:31 3.4M
ncbiRefSeqLink.sql 2021-03-31 09:31 2.0K
mrnaOrientInfo.txt.gz 2021-03-25 15:56 2.8M
mrnaOrientInfo.sql 2021-03-25 15:56 1.8K
intronEst.txt.gz 2021-03-25 15:56 24M
intronEst.sql 2021-03-25 15:56 2.1K
gbLoaded.txt.gz 2021-03-25 15:56 1.4K
gbLoaded.sql 2021-03-25 15:56 1.6K
estOrientInfo.txt.gz 2021-03-25 15:56 14M
estOrientInfo.sql 2021-03-25 15:56 1.8K
all_est.txt.gz 2021-03-25 15:56 48M
all_est.sql 2021-03-25 15:56 2.1K
xenoRefSeqAli.txt.gz 2021-03-24 17:17 20M
xenoRefSeqAli.sql 2021-03-24 17:17 2.1K
refSeqAli.txt.gz 2021-03-24 17:17 1.8M
refSeqAli.sql 2021-03-24 17:17 2.1K
xenoRefFlat.txt.gz 2021-03-24 17:17 9.7M
xenoRefFlat.sql 2021-03-24 17:17 1.7K
xenoRefGene.txt.gz 2021-03-24 17:17 11M
xenoRefGene.sql 2021-03-24 17:17 1.9K
refFlat.txt.gz 2021-03-24 17:16 1.6M
refFlat.sql 2021-03-24 17:16 1.7K
refGene.txt.gz 2021-03-24 17:16 1.8M
refGene.sql 2021-03-24 17:16 1.9K
xenoMrna.txt.gz 2021-03-24 16:37 217M
xenoMrna.sql 2021-03-24 16:37 2.1K
all_mrna.txt.gz 2021-03-24 16:36 6.0M
all_mrna.sql 2021-03-24 16:36 2.1K
mgcFullMrna.txt.gz 2021-03-24 16:36 655K
mgcFullMrna.sql 2021-03-24 16:36 2.1K
mgcGenes.txt.gz 2021-03-24 16:36 650K
mgcGenes.sql 2021-03-24 16:36 1.9K
netMm10.txt.gz 2021-02-15 16:19 58M
netMm10.sql 2021-02-15 16:19 2.1K
chainMm10Link.txt.gz 2021-02-15 16:17 1.6G
chainMm10Link.sql 2021-02-15 16:17 1.6K
chainMm10.txt.gz 2021-02-15 15:58 252M
chainMm10.sql 2021-02-15 15:58 1.7K
genscan.txt.gz 2021-02-15 14:59 3.0M
genscan.sql 2021-02-15 14:59 1.7K
crisprAllTargets.txt.gz 2021-02-11 17:21 65
crisprAllTargets.sql 2021-02-11 17:21 1.3K
netMm39.txt.gz 2021-02-04 19:17 58M
netMm39.sql 2021-02-04 19:17 2.1K
chainMm39Link.txt.gz 2021-02-04 19:15 1.7G
chainMm39Link.sql 2021-02-04 19:15 1.6K
chainMm39.txt.gz 2021-02-04 18:54 281M
chainMm39.sql 2021-02-04 18:54 1.7K
netHg38.txt.gz 2021-02-04 18:42 51M
netHg38.sql 2021-02-04 18:42 2.1K
chainHg38Link.txt.gz 2021-02-04 18:40 1.1G
chainHg38Link.sql 2021-02-04 18:40 1.6K
chainHg38.txt.gz 2021-02-04 18:27 329M
chainHg38.sql 2021-02-04 18:27 1.7K
augustusGene.txt.gz 2021-02-04 11:46 2.3M
augustusGene.sql 2021-02-04 11:46 2.0K
extNcbiRefSeq.txt.gz 2021-02-04 10:33 87
extNcbiRefSeq.sql 2021-02-04 10:33 1.5K
ncbiRefSeqOther.txt.gz 2021-02-04 10:33 71
ncbiRefSeqOther.sql 2021-02-04 10:33 1.3K
ncbiRefSeqCds.txt.gz 2021-02-04 10:33 519K
ncbiRefSeqCds.sql 2021-02-04 10:33 1.4K
seqNcbiRefSeq.txt.gz 2021-02-04 10:33 1.5M
seqNcbiRefSeq.sql 2021-02-04 10:33 1.6K
ncbiRefSeqPsl.txt.gz 2021-02-04 09:54 6.6M
ncbiRefSeqPsl.sql 2021-02-04 09:54 2.1K
ncbiRefSeqPredicted.txt.gz 2021-02-04 09:54 3.6M
ncbiRefSeqPredicted.sql 2021-02-04 09:54 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-04 09:54 1.8M
ncbiRefSeqCurated.sql 2021-02-04 09:54 2.0K
ncbiRefSeq.txt.gz 2021-02-04 09:54 4.5M
ncbiRefSeq.sql 2021-02-04 09:54 1.9K
cpgIslandExt.txt.gz 2021-02-04 09:28 362K
cpgIslandExt.sql 2021-02-04 09:28 1.7K
windowmaskerSdust.txt.gz 2021-02-03 23:39 123M
windowmaskerSdust.sql 2021-02-03 23:39 1.5K
nestedRepeats.txt.gz 2021-02-03 22:50 12M
nestedRepeats.sql 2021-02-03 22:50 1.9K
rmsk.txt.gz 2021-02-03 22:49 124M
rmsk.sql 2021-02-03 22:49 1.9K
microsat.txt.gz 2021-02-03 22:00 2.3M
microsat.sql 2021-02-03 22:00 1.5K
simpleRepeat.txt.gz 2021-02-03 21:17 34M
simpleRepeat.sql 2021-02-03 21:17 1.9K
ucscToRefSeq.txt.gz 2021-02-03 16:59 1.6K
ucscToRefSeq.sql 2021-02-03 16:59 1.4K
ucscToINSDC.txt.gz 2021-02-03 16:59 1.7K
ucscToINSDC.sql 2021-02-03 16:59 1.4K
chromAlias.txt.gz 2021-02-03 16:54 2.8K
chromAlias.sql 2021-02-03 16:54 1.4K
cpgIslandExtUnmasked.txt.gz 2021-02-03 16:43 432K
cpgIslandExtUnmasked.sql 2021-02-03 16:43 1.7K
cytoBandIdeo.txt.gz 2021-02-03 16:33 1.3K
cytoBandIdeo.sql 2021-02-03 16:33 1.5K
gc5BaseBw.txt.gz 2021-02-03 16:22 62
gc5BaseBw.sql 2021-02-03 16:22 1.3K
grp.txt.gz 2021-02-03 16:22 213
grp.sql 2021-02-03 16:22 1.4K
chromInfo.txt.gz 2021-02-03 16:22 1.3K
chromInfo.sql 2021-02-03 16:22 1.4K
gap.txt.gz 2021-02-03 16:22 8.8K
gap.sql 2021-02-03 16:22 1.6K
gold.txt.gz 2021-02-03 16:22 14K
gold.sql 2021-02-03 16:22 1.7K