This directory contains a dump of the UCSC genome annotation database for the
    Jun. 2020 (GRCm39/mm39) assembly of the mouse genome
    (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) 
from the Mouse 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/52
    https://www.ncbi.nlm.nih.gov/genome/assembly/7358741
    https://www.ncbi.nlm.nih.gov/bioproject/20689
    https://www.ncbi.nlm.nih.gov/biosample/n/a

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=mm39
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/mm39/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/mm39/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/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 mm39 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql mm39 --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 2020-08-18 00:35 2.1K all_est.txt.gz 2020-08-18 00:35 213M all_mrna.sql 2020-08-17 17:04 2.1K all_mrna.txt.gz 2020-08-17 17:04 41M augustusGene.sql 2020-07-30 12:51 1.9K augustusGene.txt.gz 2020-07-30 12:51 2.3M bigFiles.sql 2021-01-24 03:03 1.4K bigFiles.txt.gz 2021-01-24 03:03 92 chainCanFam5.sql 2020-08-17 15:44 1.7K chainCanFam5.txt.gz 2020-08-17 15:44 53M chainCanFam5Link.sql 2020-08-17 15:47 1.6K chainCanFam5Link.txt.gz 2020-08-17 15:47 443M chainHg38.sql 2020-08-18 09:26 1.7K chainHg38.txt.gz 2020-08-18 09:26 68M chainHg38Link.sql 2020-08-18 09:30 1.5K chainHg38Link.txt.gz 2020-08-18 09:30 541M chainRBestHg38.sql 2020-08-18 15:51 1.7K chainRBestHg38.txt.gz 2020-08-18 15:51 1.4M chainRBestHg38Link.sql 2020-08-18 15:53 1.6K chainRBestHg38Link.txt.gz 2020-08-18 15:53 262M chainSynHg38.sql 2020-08-18 09:39 1.7K chainSynHg38.txt.gz 2020-08-18 09:39 380K chainSynHg38Link.sql 2020-08-18 09:41 1.5K chainSynHg38Link.txt.gz 2020-08-18 09:41 259M chromAlias.sql 2020-07-27 15:48 1.4K chromAlias.txt.gz 2020-07-27 15:48 779 chromInfo.sql 2020-07-27 17:08 1.4K chromInfo.txt.gz 2020-07-27 17:08 583 cpgIslandExt.sql 2020-07-30 09:23 1.7K cpgIslandExt.txt.gz 2020-07-30 09:23 358K cpgIslandExtUnmasked.sql 2020-07-27 15:47 1.7K cpgIslandExtUnmasked.txt.gz 2020-07-27 15:47 527K crisprAllRanges.sql 2020-08-13 01:08 1.5K crisprAllRanges.txt.gz 2020-08-13 01:08 2.8K crisprAllTargets.sql 2020-08-13 01:39 1.3K crisprAllTargets.txt.gz 2020-08-13 01:39 66 cytoBandIdeo.sql 2020-07-27 17:04 1.5K cytoBandIdeo.txt.gz 2020-07-27 17:04 743 estOrientInfo.sql 2020-08-18 00:14 1.8K estOrientInfo.txt.gz 2020-08-18 00:14 57M gap.sql 2020-07-27 13:01 1.6K gap.txt.gz 2020-07-27 13:01 4.0K gbLoaded.sql 2020-08-18 00:53 1.6K gbLoaded.txt.gz 2020-08-18 00:53 1.5K gc5BaseBw.sql 2020-07-27 17:04 1.3K gc5BaseBw.txt.gz 2020-07-27 17:04 63 genscan.sql 2020-07-30 18:23 1.7K genscan.txt.gz 2020-07-30 18:23 3.0M genscanSubopt.sql 2020-07-30 18:23 1.6K genscanSubopt.txt.gz 2020-07-30 18:23 6.2M gold.sql 2020-07-27 13:01 1.7K gold.txt.gz 2020-07-27 13:01 470K grp.sql 2020-07-27 17:08 1.3K grp.txt.gz 2020-07-27 17:08 213 hgFindSpec.sql 2021-01-21 09:35 1.8K hgFindSpec.txt.gz 2021-01-21 09:35 665 history.sql 2020-09-08 17:07 1.6K history.txt.gz 2020-09-08 17:07 818 microsat.sql 2020-07-27 16:07 1.5K microsat.txt.gz 2020-07-27 16:07 1.9M mrnaOrientInfo.sql 2020-08-18 00:39 1.8K mrnaOrientInfo.txt.gz 2020-08-18 00:39 20M nestedRepeats.sql 2020-07-30 08:39 1.9K nestedRepeats.txt.gz 2020-07-30 08:39 14M netCanFam5.sql 2020-08-17 15:49 2.1K netCanFam5.txt.gz 2020-08-17 15:49 47M netHg38.sql 2020-08-18 09:32 2.1K netHg38.txt.gz 2020-08-18 09:32 52M netRBestHg38.sql 2020-08-18 15:55 2.1K netRBestHg38.txt.gz 2020-08-18 15:55 52M netSynHg38.sql 2020-08-18 09:41 2.1K netSynHg38.txt.gz 2020-08-18 09:41 47M refFlat.sql 2020-08-17 18:26 1.7K refFlat.txt.gz 2020-08-17 18:26 2.7M refGene.sql 2020-08-17 18:26 1.9K refGene.txt.gz 2020-08-17 18:26 3.0M refSeqAli.sql 2020-08-17 18:26 2.1K refSeqAli.txt.gz 2020-08-17 18:26 3.4M rmsk.sql 2020-07-30 08:37 1.9K rmsk.txt.gz 2020-07-30 08:37 135M simpleRepeat.sql 2020-07-27 16:07 1.9K simpleRepeat.txt.gz 2020-07-27 16:07 38M tableDescriptions.sql 2021-01-23 06:34 1.4K tableDescriptions.txt.gz 2021-01-23 06:34 5.5K tableList.sql 2021-01-24 03:03 1.6K tableList.txt.gz 2021-01-24 03:03 3.0K tandemDups.sql 2020-07-30 09:22 1.8K tandemDups.txt.gz 2020-07-30 09:22 18M trackDb.sql 2021-01-21 09:35 2.1K trackDb.txt.gz 2021-01-21 09:35 25K ucscToINSDC.sql 2020-07-27 17:04 1.4K ucscToINSDC.txt.gz 2020-07-27 17:04 688 windowmaskerSdust.sql 2020-07-28 09:18 1.5K windowmaskerSdust.txt.gz 2020-07-28 09:18 116M xenoMrna.sql 2020-08-17 17:05 2.1K xenoMrna.txt.gz 2020-08-17 17:05 193M xenoRefFlat.sql 2020-08-17 18:26 1.7K xenoRefFlat.txt.gz 2020-08-17 18:26 8.5M xenoRefGene.sql 2020-08-17 18:26 1.9K xenoRefGene.txt.gz 2020-08-17 18:26 9.5M xenoRefSeqAli.sql 2020-08-17 18:26 2.1K xenoRefSeqAli.txt.gz 2020-08-17 18:26 17M