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;'

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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 - all_est.sql 2021-03-25 15:56 2.1K all_est.txt.gz 2021-03-25 15:56 48M all_mrna.sql 2021-03-24 16:36 2.1K all_mrna.txt.gz 2021-03-24 16:36 6.0M augustusGene.sql 2021-02-04 11:46 2.0K augustusGene.txt.gz 2021-02-04 11:46 2.3M bigFiles.sql 2021-05-09 03:03 1.4K bigFiles.txt.gz 2021-05-09 03:03 115 chainHg38.sql 2021-02-04 18:27 1.7K chainHg38.txt.gz 2021-02-04 18:27 329M chainHg38Link.sql 2021-02-04 18:40 1.6K chainHg38Link.txt.gz 2021-02-04 18:40 1.1G chainMm10.sql 2021-02-15 15:58 1.7K chainMm10.txt.gz 2021-02-15 15:58 252M chainMm10Link.sql 2021-02-15 16:17 1.6K chainMm10Link.txt.gz 2021-02-15 16:17 1.6G chainMm39.sql 2021-02-04 18:54 1.7K chainMm39.txt.gz 2021-02-04 18:54 281M chainMm39Link.sql 2021-02-04 19:15 1.6K chainMm39Link.txt.gz 2021-02-04 19:15 1.7G chromAlias.sql 2021-02-03 16:54 1.4K chromAlias.txt.gz 2021-02-03 16:54 2.8K chromInfo.sql 2021-02-03 16:22 1.4K chromInfo.txt.gz 2021-02-03 16:22 1.3K cpgIslandExt.sql 2021-02-04 09:28 1.7K cpgIslandExt.txt.gz 2021-02-04 09:28 362K cpgIslandExtUnmasked.sql 2021-02-03 16:43 1.7K cpgIslandExtUnmasked.txt.gz 2021-02-03 16:43 432K crisprAllTargets.sql 2021-02-11 17:21 1.3K crisprAllTargets.txt.gz 2021-02-11 17:21 65 cytoBandIdeo.sql 2021-02-03 16:33 1.5K cytoBandIdeo.txt.gz 2021-02-03 16:33 1.3K estOrientInfo.sql 2021-03-25 15:56 1.8K estOrientInfo.txt.gz 2021-03-25 15:56 14M extNcbiRefSeq.sql 2021-02-04 10:33 1.5K extNcbiRefSeq.txt.gz 2021-02-04 10:33 87 gap.sql 2021-02-03 16:22 1.6K gap.txt.gz 2021-02-03 16:22 8.8K gbLoaded.sql 2021-03-25 15:56 1.6K gbLoaded.txt.gz 2021-03-25 15:56 1.4K gc5BaseBw.sql 2021-02-03 16:22 1.3K gc5BaseBw.txt.gz 2021-02-03 16:22 62 genscan.sql 2021-02-15 14:59 1.7K genscan.txt.gz 2021-02-15 14:59 3.0M gold.sql 2021-02-03 16:22 1.7K gold.txt.gz 2021-02-03 16:22 14K grp.sql 2021-02-03 16:22 1.4K grp.txt.gz 2021-02-03 16:22 213 hgFindSpec.sql 2021-04-26 05:22 1.8K hgFindSpec.txt.gz 2021-04-26 05:22 1.1K history.sql 2021-03-31 12:00 1.6K history.txt.gz 2021-03-31 12:00 1.0K intronEst.sql 2021-03-25 15:56 2.1K intronEst.txt.gz 2021-03-25 15:56 24M mgcFullMrna.sql 2021-03-24 16:36 2.1K mgcFullMrna.txt.gz 2021-03-24 16:36 655K mgcGenes.sql 2021-03-24 16:36 1.9K mgcGenes.txt.gz 2021-03-24 16:36 650K microsat.sql 2021-02-03 22:00 1.5K microsat.txt.gz 2021-02-03 22:00 2.3M mrnaOrientInfo.sql 2021-03-25 15:56 1.8K mrnaOrientInfo.txt.gz 2021-03-25 15:56 2.8M ncbiRefSeq.sql 2021-02-04 09:54 1.9K ncbiRefSeq.txt.gz 2021-02-04 09:54 4.5M ncbiRefSeqCds.sql 2021-02-04 10:33 1.4K ncbiRefSeqCds.txt.gz 2021-02-04 10:33 519K ncbiRefSeqCurated.sql 2021-02-04 09:54 2.0K ncbiRefSeqCurated.txt.gz 2021-02-04 09:54 1.8M ncbiRefSeqLink.sql 2021-03-31 09:31 2.0K ncbiRefSeqLink.txt.gz 2021-03-31 09:31 3.4M ncbiRefSeqOther.sql 2021-02-04 10:33 1.3K ncbiRefSeqOther.txt.gz 2021-02-04 10:33 71 ncbiRefSeqPepTable.sql 2021-03-31 12:00 1.4K ncbiRefSeqPepTable.txt.gz 2021-03-31 12:00 15M ncbiRefSeqPredicted.sql 2021-02-04 09:54 2.0K ncbiRefSeqPredicted.txt.gz 2021-02-04 09:54 3.6M ncbiRefSeqPsl.sql 2021-02-04 09:54 2.1K ncbiRefSeqPsl.txt.gz 2021-02-04 09:54 6.6M nestedRepeats.sql 2021-02-03 22:50 1.9K nestedRepeats.txt.gz 2021-02-03 22:50 12M netHg38.sql 2021-02-04 18:42 2.1K netHg38.txt.gz 2021-02-04 18:42 51M netMm10.sql 2021-02-15 16:19 2.1K netMm10.txt.gz 2021-02-15 16:19 58M netMm39.sql 2021-02-04 19:17 2.1K netMm39.txt.gz 2021-02-04 19:17 58M refFlat.sql 2021-03-24 17:16 1.7K refFlat.txt.gz 2021-03-24 17:16 1.6M refGene.sql 2021-03-24 17:16 1.9K refGene.txt.gz 2021-03-24 17:16 1.8M refSeqAli.sql 2021-03-24 17:17 2.1K refSeqAli.txt.gz 2021-03-24 17:17 1.8M rmsk.sql 2021-02-03 22:49 1.9K rmsk.txt.gz 2021-02-03 22:49 124M seqNcbiRefSeq.sql 2021-02-04 10:33 1.6K seqNcbiRefSeq.txt.gz 2021-02-04 10:33 1.5M simpleRepeat.sql 2021-02-03 21:17 1.9K simpleRepeat.txt.gz 2021-02-03 21:17 34M tableDescriptions.sql 2021-04-21 06:33 1.4K tableDescriptions.txt.gz 2021-04-21 06:33 6.2K tableList.sql 2021-05-09 03:03 1.6K tableList.txt.gz 2021-05-09 03:03 3.5K trackDb.sql 2021-04-26 05:22 2.1K trackDb.txt.gz 2021-04-26 05:22 37K ucscToINSDC.sql 2021-02-03 16:59 1.4K ucscToINSDC.txt.gz 2021-02-03 16:59 1.7K ucscToRefSeq.sql 2021-02-03 16:59 1.4K ucscToRefSeq.txt.gz 2021-02-03 16:59 1.6K windowmaskerSdust.sql 2021-02-03 23:39 1.5K windowmaskerSdust.txt.gz 2021-02-03 23:39 123M xenoMrna.sql 2021-03-24 16:37 2.1K xenoMrna.txt.gz 2021-03-24 16:37 217M xenoRefFlat.sql 2021-03-24 17:17 1.7K xenoRefFlat.txt.gz 2021-03-24 17:17 9.7M xenoRefGene.sql 2021-03-24 17:17 1.9K xenoRefGene.txt.gz 2021-03-24 17:17 11M xenoRefSeqAli.sql 2021-03-24 17:17 2.1K xenoRefSeqAli.txt.gz 2021-03-24 17:17 20M