This directory contains a dump of the UCSC genome annotation database for
the Apr. 2011 (SacCer_Apr2011/sacCer3) assembly of the S. cerevisiae genome
(sacCer3, Saccharomyces cerevisiae S288c assembly from
Saccharomyces Genome Database (GCA_000146055.2)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly is based on sequence dated April 2011 in the Saccharomyces Genome
Database (http://www.yeastgenome.org/) and was obtained from the site
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/fungi/Saccharomyces_cerevisiae/SacCer_Apr2011/
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=sacCer3
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/sacCer3/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/sacCer3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/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 sacCer3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql sacCer3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
chrV_intronEst.sql 2011-10-06 16:15 2.0K
chrV_intronEst.txt.gz 2011-10-06 16:15 3.4K
phastConsElements7way.sql 2011-10-06 16:15 1.5K
phastConsElements7way.txt.gz 2011-10-06 16:15 503K
ceBlastTab.sql 2011-10-06 16:15 1.6K
ceBlastTab.txt.gz 2011-10-06 16:15 87K
pslChainAWRI1631.sql 2011-10-06 16:15 2.1K
pslChainAWRI1631.txt.gz 2011-10-06 16:15 3.3M
multiz7waySummary.sql 2011-10-06 16:15 1.5K
multiz7waySummary.txt.gz 2011-10-06 16:15 33K
sgdOther.sql 2011-10-06 16:15 1.5K
sgdOther.txt.gz 2011-10-06 16:15 41K
transRegCode.sql 2011-10-06 16:15 1.5K
transRegCode.txt.gz 2011-10-06 16:15 1.4M
phastCons7way.sql 2011-10-06 16:15 1.7K
phastCons7way.txt.gz 2011-10-06 16:15 305K
chrIX_intronEst.sql 2011-10-06 16:15 2.1K
chrIX_intronEst.txt.gz 2011-10-06 16:15 2.6K
multiz7way.sql 2011-10-06 16:15 1.5K
multiz7way.txt.gz 2011-10-06 16:15 669K
chrXV_intronEst.sql 2011-10-06 16:15 2.1K
chrXV_intronEst.txt.gz 2011-10-06 16:15 5.3K
blastHg18KG.sql 2011-10-06 16:15 2.1K
blastHg18KG.txt.gz 2011-10-06 16:15 350K
sgdPep.sql 2011-10-06 16:15 1.3K
sgdPep.txt.gz 2011-10-06 16:15 1.7M
transRegCodeProbe.sql 2011-10-06 16:15 1.5K
transRegCodeProbe.txt.gz 2011-10-06 16:15 143K
sgdBlastTab.sql 2011-10-06 16:15 1.6K
sgdBlastTab.txt.gz 2011-10-06 16:15 943K
esRegMotif.sql 2011-10-06 16:15 1.4K
esRegMotif.txt.gz 2011-10-06 16:15 17K
chrM_est.sql 2011-10-06 16:16 2.0K
chrM_est.txt.gz 2011-10-06 16:16 33
choExpDistance.sql 2011-10-06 16:16 1.3K
choExpDistance.txt.gz 2011-10-06 16:16 34M
gold.sql 2011-10-06 16:17 1.6K
gold.txt.gz 2011-10-06 16:17 287
chrII_intronEst.sql 2011-10-06 16:17 2.1K
chrII_intronEst.txt.gz 2011-10-06 16:17 9.4K
chrXIV_intronEst.sql 2011-10-06 16:17 2.1K
chrXIV_intronEst.txt.gz 2011-10-06 16:17 2.5K
chromInfo.sql 2011-10-06 16:17 1.3K
chromInfo.txt.gz 2011-10-06 16:17 193
extFile.sql 2011-10-06 16:17 1.4K
extFile.txt.gz 2011-10-06 16:17 265
chrVIII_intronEst.sql 2011-10-06 16:17 2.1K
chrVIII_intronEst.txt.gz 2011-10-06 16:17 3.7K
chrM_intronEst.sql 2011-10-06 16:17 2.0K
chrM_intronEst.txt.gz 2011-10-06 16:17 39
sgdDescription.sql 2011-10-06 16:17 1.3K
sgdDescription.txt.gz 2011-10-06 16:17 337K
gap.sql 2011-10-06 16:17 1.5K
gap.txt.gz 2011-10-06 16:17 28
dmBlastTab.sql 2011-10-06 16:17 1.6K
dmBlastTab.txt.gz 2011-10-06 16:17 85K
sgdOtherDescription.sql 2011-10-06 16:17 1.3K
sgdOtherDescription.txt.gz 2011-10-06 16:17 12K
gc5BaseBw.sql 2011-10-06 16:17 1.2K
gc5BaseBw.txt.gz 2011-10-06 16:17 63
chrI_intronEst.sql 2011-10-06 16:18 2.0K
chrI_intronEst.txt.gz 2011-10-06 16:18 1.1K
chrXIII_intronEst.sql 2011-10-06 16:18 2.1K
chrXIII_intronEst.txt.gz 2011-10-06 16:18 5.6K
sgdCanonical.sql 2011-10-06 16:18 1.5K
sgdCanonical.txt.gz 2011-10-06 16:18 102K
sgdIsoforms.sql 2011-10-06 16:18 1.3K
sgdIsoforms.txt.gz 2011-10-06 16:18 31K
esRegUpstreamRegion.sql 2011-10-06 16:18 1.6K
esRegUpstreamRegion.txt.gz 2011-10-06 16:18 19K
simpleRepeat.sql 2011-10-06 16:18 1.9K
simpleRepeat.txt.gz 2011-10-06 16:18 54K
chrXI_intronEst.sql 2011-10-06 16:18 2.1K
chrXI_intronEst.txt.gz 2011-10-06 16:18 3.2K
esRegGeneToMotif.sql 2011-10-06 16:18 1.6K
esRegGeneToMotif.txt.gz 2011-10-06 16:18 38K
chrIII_intronEst.sql 2011-10-06 16:18 2.1K
chrIII_intronEst.txt.gz 2011-10-06 16:18 1.5K
multiz7wayFrames.sql 2011-10-06 16:18 1.7K
multiz7wayFrames.txt.gz 2011-10-06 16:18 83K
esRegGeneToModule.sql 2011-10-06 16:18 1.3K
esRegGeneToModule.txt.gz 2011-10-06 16:18 9.1K
sgdGene.sql 2011-10-06 16:18 1.7K
sgdGene.txt.gz 2011-10-06 16:18 131K
chrVII_intronEst.sql 2011-10-06 16:18 2.1K
chrVII_intronEst.txt.gz 2011-10-06 16:18 8.4K
transRegCodeCondition.sql 2011-10-06 16:18 1.4K
transRegCodeCondition.txt.gz 2011-10-06 16:18 1.2K
sgdToSwissProt.sql 2011-10-06 16:18 1.3K
sgdToSwissProt.txt.gz 2011-10-06 16:18 31K
sgdClone.sql 2011-10-06 16:18 1.5K
sgdClone.txt.gz 2011-10-06 16:18 16K
sgdToName.sql 2011-10-06 16:18 1.3K
sgdToName.txt.gz 2011-10-06 16:18 36K
transRegCodeMotif.sql 2011-10-06 16:18 1.4K
transRegCodeMotif.txt.gz 2011-10-06 16:18 6.5K
rnBlastTab.sql 2012-02-26 05:30 1.6K
rnBlastTab.txt.gz 2012-02-26 05:30 42K
chrVIII_est.sql 2012-05-28 14:19 2.0K
chrVIII_est.txt.gz 2012-05-28 14:19 32K
chrVII_est.sql 2012-05-28 14:19 2.0K
chrVII_est.txt.gz 2012-05-28 14:19 84K
chrV_est.sql 2012-05-28 14:19 2.0K
chrV_est.txt.gz 2012-05-28 14:19 52K
chrXIV_est.sql 2012-05-28 14:19 2.0K
chrXIV_est.txt.gz 2012-05-28 14:19 46K
chrX_intronEst.sql 2012-05-28 14:19 2.0K
chrX_intronEst.txt.gz 2012-05-28 14:19 3.3K
all_est.sql 2012-05-28 14:19 2.0K
all_est.txt.gz 2012-05-28 14:19 962K
chrIV_intronEst.sql 2012-05-28 14:19 2.1K
chrIV_intronEst.txt.gz 2012-05-28 14:19 12K
chrXII_est.sql 2012-05-28 14:19 2.0K
chrXII_est.txt.gz 2012-05-28 14:19 81K
chrX_est.sql 2012-05-28 14:19 2.0K
chrX_est.txt.gz 2012-05-28 14:19 49K
chrI_est.sql 2012-05-28 14:19 2.0K
chrI_est.txt.gz 2012-05-28 14:19 11K
chrVI_est.sql 2012-05-28 14:19 2.0K
chrVI_est.txt.gz 2012-05-28 14:19 30K
chrIII_est.sql 2012-05-28 14:19 2.0K
chrIII_est.txt.gz 2012-05-28 14:19 32K
chrII_est.sql 2012-05-28 14:19 2.0K
chrII_est.txt.gz 2012-05-28 14:19 71K
chrIV_est.sql 2012-05-28 14:19 2.0K
chrIV_est.txt.gz 2012-05-28 14:19 150K
chrIX_est.sql 2012-05-28 14:19 2.0K
chrIX_est.txt.gz 2012-05-28 14:19 24K
chrVI_intronEst.sql 2012-05-28 14:19 2.1K
chrVI_intronEst.txt.gz 2012-05-28 14:19 3.0K
chrXIII_est.sql 2012-05-28 14:19 2.0K
chrXIII_est.txt.gz 2012-05-28 14:19 70K
chrXII_intronEst.sql 2012-05-28 14:19 2.1K
chrXII_intronEst.txt.gz 2012-05-28 14:19 5.7K
chrXI_est.sql 2012-05-28 14:19 2.0K
chrXI_est.txt.gz 2012-05-28 14:19 49K
chrXVI_est.sql 2012-05-28 14:19 2.0K
chrXVI_est.txt.gz 2012-05-28 14:19 85K
chrXV_est.sql 2012-05-28 14:19 2.0K
chrXV_est.txt.gz 2012-05-28 14:19 100K
chrXVI_intronEst.sql 2012-05-28 14:19 2.1K
chrXVI_intronEst.txt.gz 2012-05-28 14:19 6.6K
estOrientInfo.sql 2012-05-28 14:19 1.7K
estOrientInfo.txt.gz 2012-05-28 14:19 306K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 199
growthCondition.sql 2014-10-19 15:03 1.4K
growthCondition.txt.gz 2014-10-19 15:03 685
history.sql 2014-10-19 15:03 1.6K
history.txt.gz 2014-10-19 15:03 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 109K
microsat.sql 2015-08-24 01:24 1.5K
microsat.txt.gz 2015-08-24 01:24 345
oreganno.sql 2016-05-15 11:29 1.5K
oreganno.txt.gz 2016-05-15 11:29 85K
oregannoAttr.sql 2016-05-15 11:29 1.4K
oregannoAttr.txt.gz 2016-05-15 11:29 118K
oregannoLink.sql 2016-05-15 11:29 1.4K
oregannoLink.txt.gz 2016-05-15 11:29 83K
crisprRanges.sql 2016-11-06 09:28 1.4K
crisprRanges.txt.gz 2016-11-06 09:28 22K
crisprTargets.sql 2016-11-06 09:28 1.3K
crisprTargets.txt.gz 2016-11-06 09:28 63
locusName.sql 2016-11-06 09:28 1.5K
locusName.txt.gz 2016-11-06 09:28 141K
drBlastTab.sql 2017-09-11 02:52 1.7K
drBlastTab.txt.gz 2017-09-11 02:52 61K
chromAlias.sql 2018-08-05 09:15 1.4K
chromAlias.txt.gz 2018-08-05 09:15 338
chrXII_mrna.sql 2020-05-07 04:20 2.1K
chrXII_mrna.txt.gz 2020-05-07 04:20 4.7K
chrXIV_mrna.sql 2020-05-07 04:20 2.1K
chrXIV_mrna.txt.gz 2020-05-07 04:20 2.8K
chrXVI_mrna.sql 2020-05-07 04:20 2.1K
chrXVI_mrna.txt.gz 2020-05-07 04:20 3.1K
chrXIII_mrna.sql 2020-05-07 04:20 2.1K
chrXIII_mrna.txt.gz 2020-05-07 04:20 3.3K
chrII_mrna.sql 2020-05-07 04:20 2.1K
chrII_mrna.txt.gz 2020-05-07 04:20 3.0K
chrIV_mrna.sql 2020-05-07 04:20 2.1K
chrIV_mrna.txt.gz 2020-05-07 04:20 5.5K
chrIX_mrna.sql 2020-05-07 04:20 2.1K
chrIX_mrna.txt.gz 2020-05-07 04:20 1.5K
chrVI_mrna.sql 2020-05-07 04:20 2.1K
chrVI_mrna.txt.gz 2020-05-07 04:20 1.1K
chrXI_mrna.sql 2020-05-07 04:20 2.1K
chrXI_mrna.txt.gz 2020-05-07 04:20 2.3K
chrXV_mrna.sql 2020-05-07 04:20 2.1K
chrXV_mrna.txt.gz 2020-05-07 04:20 3.2K
chrIII_mrna.sql 2020-05-07 04:20 2.1K
chrIII_mrna.txt.gz 2020-05-07 04:20 1.1K
chrVIII_mrna.sql 2020-05-07 04:20 2.1K
chrVIII_mrna.txt.gz 2020-05-07 04:20 1.8K
chrI_mrna.sql 2020-05-07 04:20 2.1K
chrI_mrna.txt.gz 2020-05-07 04:20 845
chrM_mrna.sql 2020-05-07 04:20 2.1K
chrM_mrna.txt.gz 2020-05-07 04:20 863
chrV_mrna.sql 2020-05-07 04:21 2.1K
chrV_mrna.txt.gz 2020-05-07 04:21 2.6K
chrX_mrna.sql 2020-05-07 04:25 2.1K
chrX_mrna.txt.gz 2020-05-07 04:25 3.4K
chrVII_mrna.sql 2020-05-07 04:25 2.1K
chrVII_mrna.txt.gz 2020-05-07 04:25 4.4K
all_mrna.sql 2020-05-07 04:28 2.1K
all_mrna.txt.gz 2020-05-07 04:28 43K
mrnaOrientInfo.sql 2020-05-07 04:28 1.8K
mrnaOrientInfo.txt.gz 2020-05-07 04:28 19K
xenoRefGene.sql 2020-08-20 09:46 2.0K
xenoRefGene.txt.gz 2020-08-20 09:46 1.1M
xenoRefFlat.sql 2020-08-20 09:46 1.7K
xenoRefFlat.txt.gz 2020-08-20 09:46 1.0M
xenoRefSeqAli.sql 2020-08-20 09:46 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 09:46 1.2M
gbLoaded.sql 2020-08-20 09:58 1.6K
gbLoaded.txt.gz 2020-08-20 09:58 90K
ncbiRefSeq.sql 2021-02-10 15:45 2.0K
ncbiRefSeq.txt.gz 2021-02-10 15:45 140K
ncbiRefSeqCurated.sql 2021-02-10 15:45 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:45 140K
ncbiRefSeqLink.sql 2021-02-10 15:45 2.0K
ncbiRefSeqLink.txt.gz 2021-02-10 15:45 661K
ncbiRefSeqPsl.sql 2021-02-10 15:45 2.1K
ncbiRefSeqPsl.txt.gz 2021-02-10 15:45 158K
ncbiRefSeqOther.sql 2021-02-10 16:07 1.3K
ncbiRefSeqOther.txt.gz 2021-02-10 16:07 75
ncbiRefSeqCds.sql 2021-02-10 16:08 1.4K
ncbiRefSeqCds.txt.gz 2021-02-10 16:08 30K
ncbiRefSeqPepTable.sql 2021-02-10 16:08 1.4K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:08 1.6M
extNcbiRefSeq.sql 2021-02-10 16:08 1.5K
extNcbiRefSeq.txt.gz 2021-02-10 16:08 89
seqNcbiRefSeq.sql 2021-02-10 16:08 1.6K
seqNcbiRefSeq.txt.gz 2021-02-10 16:08 88K
ensGene.sql 2021-05-25 14:46 1.9K
ensGene.txt.gz 2021-05-25 14:46 150K
ensGtp.sql 2021-05-25 14:46 1.4K
ensGtp.txt.gz 2021-05-25 14:46 59K
ensemblToGeneName.sql 2021-05-25 14:46 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:46 31K
ensemblSource.sql 2021-05-25 14:46 1.4K
ensemblSource.txt.gz 2021-05-25 14:46 22K
ensPep.sql 2021-05-25 14:46 1.3K
ensPep.txt.gz 2021-05-25 14:46 1.7M
hgBlastTab.sql 2022-07-12 17:02 1.7K
hgBlastTab.txt.gz 2022-07-12 17:02 60K
mmBlastTab.sql 2022-07-12 17:09 1.7K
mmBlastTab.txt.gz 2022-07-12 17:09 61K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 49K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 7.6K
tableList.sql 2024-11-17 03:36 1.6K
tableList.txt.gz 2024-11-17 03:36 6.9K
bigFiles.sql 2024-11-17 03:36 1.4K
bigFiles.txt.gz 2024-11-17 03:36 114