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 - xenoRefSeqAli.txt.gz 2021-03-24 17:17 20M xenoRefSeqAli.sql 2021-03-24 17:17 2.1K xenoRefGene.txt.gz 2021-03-24 17:17 11M xenoRefGene.sql 2021-03-24 17:17 1.9K xenoRefFlat.txt.gz 2021-03-24 17:17 9.7M xenoRefFlat.sql 2021-03-24 17:17 1.7K xenoMrna.txt.gz 2021-03-24 16:37 217M xenoMrna.sql 2021-03-24 16:37 2.1K windowmaskerSdust.txt.gz 2021-02-03 23:39 123M windowmaskerSdust.sql 2021-02-03 23:39 1.5K 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 trackDb_pushedout.txt.gz 2022-04-26 10:29 48K trackDb_pushedout.sql 2022-04-26 10:29 2.1K trackDb.txt.gz 2022-05-06 12:33 48K trackDb.sql 2022-05-06 12:33 2.1K tableList.txt.gz 2022-08-14 03:03 3.6K tableList.sql 2022-08-14 03:03 1.6K tableDescriptions.txt.gz 2021-04-21 06:33 6.2K tableDescriptions.sql 2021-04-21 06:33 1.4K simpleRepeat.txt.gz 2021-02-03 21:17 34M simpleRepeat.sql 2021-02-03 21:17 1.9K seqNcbiRefSeq.txt.gz 2021-02-04 10:33 1.5M seqNcbiRefSeq.sql 2021-02-04 10:33 1.6K rmsk.txt.gz 2021-02-03 22:49 124M rmsk.sql 2021-02-03 22:49 1.9K refSeqAli.txt.gz 2021-03-24 17:17 1.8M refSeqAli.sql 2021-03-24 17:17 2.1K refGene.txt.gz 2021-03-24 17:16 1.8M refGene.sql 2021-03-24 17:16 1.9K refFlat.txt.gz 2021-03-24 17:16 1.6M refFlat.sql 2021-03-24 17:16 1.7K netMm39.txt.gz 2021-02-04 19:17 58M netMm39.sql 2021-02-04 19:17 2.1K netMm10.txt.gz 2021-02-15 16:19 58M netMm10.sql 2021-02-15 16:19 2.1K netHg38.txt.gz 2021-02-04 18:42 51M netHg38.sql 2021-02-04 18:42 2.1K nestedRepeats.txt.gz 2021-02-03 22:50 12M nestedRepeats.sql 2021-02-03 22:50 1.9K 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 ncbiRefSeqPepTable.txt.gz 2021-03-31 12:00 15M ncbiRefSeqPepTable.sql 2021-03-31 12:00 1.4K ncbiRefSeqOther.txt.gz 2021-02-04 10:33 71 ncbiRefSeqOther.sql 2021-02-04 10:33 1.3K ncbiRefSeqLink.txt.gz 2021-03-31 09:31 3.4M ncbiRefSeqLink.sql 2021-03-31 09:31 2.0K ncbiRefSeqCurated.txt.gz 2021-02-04 09:54 1.8M ncbiRefSeqCurated.sql 2021-02-04 09:54 2.0K ncbiRefSeqCds.txt.gz 2021-02-04 10:33 519K ncbiRefSeqCds.sql 2021-02-04 10:33 1.4K ncbiRefSeq.txt.gz 2021-02-04 09:54 4.5M ncbiRefSeq.sql 2021-02-04 09:54 1.9K mrnaOrientInfo.txt.gz 2021-03-25 15:56 2.8M mrnaOrientInfo.sql 2021-03-25 15:56 1.8K microsat.txt.gz 2021-02-03 22:00 2.3M microsat.sql 2021-02-03 22:00 1.5K mgcGenes.txt.gz 2021-03-24 16:36 650K mgcGenes.sql 2021-03-24 16:36 1.9K mgcFullMrna.txt.gz 2021-03-24 16:36 655K mgcFullMrna.sql 2021-03-24 16:36 2.1K intronEst.txt.gz 2021-03-25 15:56 24M intronEst.sql 2021-03-25 15:56 2.1K history.txt.gz 2021-03-31 12:00 1.0K history.sql 2021-03-31 12:00 1.6K hgFindSpec_pushedout.txt.gz 2022-04-26 10:29 1.2K hgFindSpec_pushedout.sql 2022-04-26 10:29 1.8K hgFindSpec.txt.gz 2022-05-06 12:33 1.1K hgFindSpec.sql 2022-05-06 12:33 1.8K grp.txt.gz 2021-02-03 16:22 213 grp.sql 2021-02-03 16:22 1.4K gold.txt.gz 2021-02-03 16:22 14K gold.sql 2021-02-03 16:22 1.7K genscan.txt.gz 2021-02-15 14:59 3.0M genscan.sql 2021-02-15 14:59 1.7K gc5BaseBw.txt.gz 2021-02-03 16:22 62 gc5BaseBw.sql 2021-02-03 16:22 1.3K gbLoaded.txt.gz 2021-03-25 15:56 1.4K gbLoaded.sql 2021-03-25 15:56 1.6K gap.txt.gz 2021-02-03 16:22 8.8K gap.sql 2021-02-03 16:22 1.6K extNcbiRefSeq.txt.gz 2021-02-04 10:33 87 extNcbiRefSeq.sql 2021-02-04 10:33 1.5K estOrientInfo.txt.gz 2021-03-25 15:56 14M estOrientInfo.sql 2021-03-25 15:56 1.8K cytoBandIdeo.txt.gz 2021-02-03 16:33 1.3K cytoBandIdeo.sql 2021-02-03 16:33 1.5K crisprAllTargets.txt.gz 2021-02-11 17:21 65 crisprAllTargets.sql 2021-02-11 17:21 1.3K cpgIslandExtUnmasked.txt.gz 2021-02-03 16:43 432K cpgIslandExtUnmasked.sql 2021-02-03 16:43 1.7K cpgIslandExt.txt.gz 2021-02-04 09:28 362K cpgIslandExt.sql 2021-02-04 09:28 1.7K chromInfo.txt.gz 2021-02-03 16:22 1.3K chromInfo.sql 2021-02-03 16:22 1.4K chromAlias.txt.gz 2021-02-03 16:54 2.8K chromAlias.sql 2021-02-03 16:54 1.4K 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 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 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 bigFiles.txt.gz 2022-08-14 03:03 115 bigFiles.sql 2022-08-14 03:03 1.4K augustusGene.txt.gz 2021-02-04 11:46 2.3M augustusGene.sql 2021-02-04 11:46 2.0K all_mrna.txt.gz 2021-03-24 16:36 6.0M all_mrna.sql 2021-03-24 16:36 2.1K all_est.txt.gz 2021-03-25 15:56 48M all_est.sql 2021-03-25 15:56 2.1K