This directory contains a dump of the UCSC genome annotation database for
the June 2008 assembly of the S. cerevisiae genome (sacCer2, SGD June 2008).
The annotations were generated by UCSC and collaborators worldwide.
The data is based on sequence dated June 2008 in the Saccharomyces Genome
Database (http://www.yeastgenome.org/) and was obtained from the site
http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/
The S288C strain was used in this sequencing project.
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=sacCer2
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/sacCer2/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/sacCer2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/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 sacCer2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql sacCer2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
2micron_intronEst.sql 2009-08-06 15:37 2.3K
2micron_intronEst.txt.gz 2009-08-06 15:37 42
chrVI_gap.sql 2009-08-06 15:37 1.6K
chrVI_gap.txt.gz 2009-08-06 15:37 34
esRegGeneToModule.sql 2009-08-06 15:37 1.3K
esRegGeneToModule.txt.gz 2009-08-06 15:37 9.1K
esRegMotif.sql 2009-08-06 15:37 1.4K
esRegMotif.txt.gz 2009-08-06 15:37 17K
extFile.sql 2009-08-06 15:37 1.4K
extFile.txt.gz 2009-08-06 15:37 289
sgdDescription.sql 2009-08-06 15:37 1.3K
sgdDescription.txt.gz 2009-08-06 15:37 317K
chrIX_gold.sql 2009-08-06 15:37 1.7K
chrIX_gold.txt.gz 2009-08-06 15:37 70
chrVII_gold.sql 2009-08-06 15:37 1.7K
chrVII_gold.txt.gz 2009-08-06 15:37 72
chrXIII_gold.sql 2009-08-06 15:37 1.7K
chrXIII_gold.txt.gz 2009-08-06 15:37 75
chrXII_gap.sql 2009-08-06 15:37 1.6K
chrXII_gap.txt.gz 2009-08-06 15:37 35
chrXIV_gold.sql 2009-08-06 15:37 1.7K
chrXIV_gold.txt.gz 2009-08-06 15:37 73
multiz7wayFrames.sql 2009-08-06 15:37 1.8K
multiz7wayFrames.txt.gz 2009-08-06 15:37 79K
sgdIsoforms.sql 2009-08-06 15:37 1.4K
sgdIsoforms.txt.gz 2009-08-06 15:37 30K
sgdLocalization.sql 2009-08-06 15:37 1.3K
sgdLocalization.txt.gz 2009-08-06 15:37 19K
sgdOther.sql 2009-08-06 15:37 1.6K
sgdOther.txt.gz 2009-08-06 15:37 33K
sgdToName.sql 2009-08-06 15:37 1.3K
sgdToName.txt.gz 2009-08-06 15:37 38K
uwFootprintsMappability.sql 2009-08-06 15:37 1.4K
uwFootprintsMappability.txt.gz 2009-08-06 15:37 100K
uwFootprintsPrints.sql 2009-08-06 15:37 1.5K
uwFootprintsPrints.txt.gz 2009-08-06 15:37 52K
chrII_gold.sql 2009-08-06 15:37 1.7K
chrII_gold.txt.gz 2009-08-06 15:37 70
chrM_gold.sql 2009-08-06 15:37 1.7K
chrM_gold.txt.gz 2009-08-06 15:37 68
esRegGeneToMotif.sql 2009-08-06 15:37 1.6K
esRegGeneToMotif.txt.gz 2009-08-06 15:37 39K
chrIII_gold.sql 2009-08-09 10:20 1.7K
chrIII_gold.txt.gz 2009-08-09 10:20 72
chrXII_gold.sql 2009-08-09 10:20 1.7K
chrXII_gold.txt.gz 2009-08-09 10:20 73
yeastP2P.sql 2009-08-09 10:20 1.3K
yeastP2P.txt.gz 2009-08-09 10:20 27M
chrIV_gold.sql 2009-08-09 10:20 1.7K
chrIV_gold.txt.gz 2009-08-09 10:20 70
chrV_gap.sql 2009-08-09 10:20 1.6K
chrV_gap.txt.gz 2009-08-09 10:20 33
chrXVI_gap.sql 2009-08-09 10:20 1.6K
chrXVI_gap.txt.gz 2009-08-09 10:20 35
chromInfo.sql 2009-08-09 10:20 1.3K
chromInfo.txt.gz 2009-08-09 10:20 203
chrVII_gap.sql 2009-08-09 10:20 1.6K
chrVII_gap.txt.gz 2009-08-09 10:20 35
chrV_gold.sql 2009-08-09 10:20 1.7K
chrV_gold.txt.gz 2009-08-09 10:20 68
phastCons7way.sql 2009-08-09 10:20 1.9K
phastCons7way.txt.gz 2009-08-09 10:20 301K
transRegCodeProbe.sql 2009-08-09 10:20 1.6K
sgdToPfam.sql 2009-08-09 10:20 1.3K
sgdToPfam.txt.gz 2009-08-09 10:20 22K
sgdToSwissProt.sql 2009-08-09 10:20 1.3K
sgdToSwissProt.txt.gz 2009-08-09 10:20 32K
transRegCodeProbe.txt.gz 2009-08-09 10:20 143K
chrIV_gap.sql 2009-08-09 10:20 1.6K
chrIV_gap.txt.gz 2009-08-09 10:20 34
chrI_gap.sql 2009-08-09 10:20 1.6K
chrI_gap.txt.gz 2009-08-09 10:20 33
chrI_gold.sql 2009-08-09 10:20 1.7K
chrI_gold.txt.gz 2009-08-09 10:20 68
chrM_gap.sql 2009-08-09 10:20 1.6K
chrM_gap.txt.gz 2009-08-09 10:20 33
chrXV_gap.sql 2009-08-09 10:20 1.6K
chrXV_gap.txt.gz 2009-08-09 10:20 34
chrX_gold.sql 2009-08-09 10:20 1.7K
chrX_gold.txt.gz 2009-08-09 10:20 68
esRegUpstreamRegion.sql 2009-08-09 10:20 1.6K
esRegUpstreamRegion.txt.gz 2009-08-09 10:20 19K
multiz7way.sql 2009-08-09 10:20 1.5K
multiz7way.txt.gz 2009-08-09 10:20 537K
multiz7waySummary.sql 2009-08-09 10:20 1.6K
multiz7waySummary.txt.gz 2009-08-09 10:20 33K
sgdCanonical.sql 2009-08-09 10:20 1.6K
sgdCanonical.txt.gz 2009-08-09 10:20 102K
sgdClone.sql 2009-08-09 10:20 1.5K
sgdClone.txt.gz 2009-08-09 10:20 16K
sgdOtherDescription.sql 2009-08-09 10:20 1.3K
sgdOtherDescription.txt.gz 2009-08-09 10:20 15K
simpleRepeat.sql 2009-08-09 10:20 2.0K
simpleRepeat.txt.gz 2009-08-09 10:20 54K
2micron_gap.sql 2009-08-09 10:21 1.6K
2micron_gap.txt.gz 2009-08-09 10:21 36
2micron_mrna.sql 2009-08-09 10:21 2.3K
2micron_mrna.txt.gz 2009-08-09 10:21 37
chrIX_gap.sql 2009-08-09 10:21 1.6K
chrIX_gap.txt.gz 2009-08-09 10:21 34
chrVI_gold.sql 2009-08-09 10:21 1.7K
chrVI_gold.txt.gz 2009-08-09 10:21 70
chrXIII_gap.sql 2009-08-09 10:21 1.6K
chrXIII_gap.txt.gz 2009-08-09 10:21 36
chrXV_gold.sql 2009-08-09 10:21 1.7K
chrXV_gold.txt.gz 2009-08-09 10:21 71
gc5Base.sql 2009-08-09 10:21 1.9K
gc5Base.txt.gz 2009-08-09 10:21 43K
history.sql 2009-08-09 10:21 1.6K
history.txt.gz 2009-08-09 10:21 1.2K
sgdGene.sql 2009-08-09 10:21 1.8K
sgdGene.txt.gz 2009-08-09 10:21 131K
transRegCodeMotif.sql 2009-08-09 10:21 1.4K
transRegCodeMotif.txt.gz 2009-08-09 10:21 6.5K
2micron_gold.sql 2009-08-09 10:21 1.7K
2micron_gold.txt.gz 2009-08-09 10:21 74
chrII_gap.sql 2009-08-09 10:21 1.6K
chrII_gap.txt.gz 2009-08-09 10:21 34
chrVIII_gap.sql 2009-08-09 10:21 1.6K
chrVIII_gap.txt.gz 2009-08-09 10:21 36
chrXI_gap.sql 2009-08-09 10:21 1.6K
chrXI_gap.txt.gz 2009-08-09 10:21 34
sgdAbundance.sql 2009-08-09 10:21 1.3K
sgdAbundance.txt.gz 2009-08-09 10:21 19K
sgdPep.sql 2009-08-09 10:21 1.3K
sgdPep.txt.gz 2009-08-09 10:21 1.6M
blastHg18KG.sql 2009-08-09 10:21 2.3K
blastHg18KG.txt.gz 2009-08-09 10:21 293K
chrIII_gap.sql 2009-08-09 10:21 1.6K
chrIII_gap.txt.gz 2009-08-09 10:21 35
chrVIII_gold.sql 2009-08-09 10:21 1.7K
chrVIII_gold.txt.gz 2009-08-09 10:21 74
chrXIV_gap.sql 2009-08-09 10:21 1.6K
chrXIV_gap.txt.gz 2009-08-09 10:21 35
chrXI_gold.sql 2009-08-09 10:21 1.7K
chrXI_gold.txt.gz 2009-08-09 10:21 71
chrXVI_gold.sql 2009-08-09 10:21 1.7K
chrXVI_gold.txt.gz 2009-08-09 10:21 73
phastConsElements7way.sql 2009-08-09 10:21 1.6K
phastConsElements7way.txt.gz 2009-08-09 10:21 382K
transRegCode.sql 2009-08-09 10:21 1.6K
chrX_gap.sql 2009-08-09 10:21 1.6K
chrX_gap.txt.gz 2009-08-09 10:21 33
transRegCode.txt.gz 2009-08-09 10:21 1.4M
choExpDistance.sql 2009-08-09 10:21 1.3K
choExpDistance.txt.gz 2009-08-09 10:21 34M
uwFootprintsTagCounts.sql 2009-08-16 10:16 1.9K
uwFootprintsTagCounts.txt.gz 2009-08-16 10:16 35M
ceBlastTab.sql 2010-08-29 10:59 1.6K
ceBlastTab.txt.gz 2010-08-29 10:59 48K
dmBlastTab.sql 2010-08-29 10:59 1.6K
dmBlastTab.txt.gz 2010-08-29 10:59 49K
hgBlastTab.sql 2010-08-29 10:59 1.6K
hgBlastTab.txt.gz 2010-08-29 10:59 56K
rnBlastTab.sql 2010-08-29 10:59 1.6K
rnBlastTab.txt.gz 2010-08-29 10:59 31K
sgdBlastTab.sql 2010-08-29 10:59 1.6K
sgdBlastTab.txt.gz 2010-08-29 10:59 821K
ensGtp.sql 2011-03-15 11:37 1.4K
ensGtp.txt.gz 2011-03-15 11:37 30K
ensPep.sql 2011-03-15 11:37 1.3K
ensPep.txt.gz 2011-03-15 11:37 1.7M
ensGene.sql 2011-03-15 11:37 1.9K
ensGene.txt.gz 2011-03-15 11:37 149K
mmBlastTab.sql 2011-05-30 01:51 1.6K
mmBlastTab.txt.gz 2011-05-30 01:51 55K
growthCondition.sql 2011-09-12 00:03 1.3K
growthCondition.txt.gz 2011-09-12 00:03 685
pubsBlatPsl.sql 2012-05-09 09:26 2.1K
pubsBlat.sql 2012-05-09 09:26 1.9K
pubsBlat.txt.gz 2012-05-09 09:26 384K
pubsBlatPsl.txt.gz 2012-05-09 09:26 657K
2micron_est.sql 2012-05-28 14:19 2.3K
2micron_est.txt.gz 2012-05-28 14:19 607
drBlastTab.sql 2013-10-27 21:15 1.7K
drBlastTab.txt.gz 2013-10-27 21:15 55K
transRegCodeCondition.sql 2013-11-10 22:14 1.5K
transRegCodeCondition.txt.gz 2013-11-10 22:14 1.2K
pubsBingBlat.sql 2014-01-26 18:33 2.4K
pubsBingBlat.txt.gz 2014-01-26 18:33 1.3M
pubsBingBlatPsl.sql 2014-01-26 18:33 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 18:33 1.1M
grp.sql 2014-03-02 04:14 1.4K
grp.txt.gz 2014-03-02 04:14 199
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 01:24 341
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
mrnaOrientInfo.sql 2020-09-01 14:05 1.8K
mrnaOrientInfo.txt.gz 2020-09-01 14:05 18K
chrXII_mrna.sql 2020-09-01 14:05 2.1K
chrXII_mrna.txt.gz 2020-09-01 14:05 4.6K
chrXIV_mrna.sql 2020-09-01 14:05 2.1K
chrXIV_mrna.txt.gz 2020-09-01 14:05 2.8K
chrXVI_mrna.sql 2020-09-01 14:05 2.1K
chrXVI_mrna.txt.gz 2020-09-01 14:05 3.1K
chrXIII_mrna.sql 2020-09-01 14:05 2.1K
chrXIII_mrna.txt.gz 2020-09-01 14:05 3.4K
chrII_mrna.sql 2020-09-01 14:05 2.1K
chrII_mrna.txt.gz 2020-09-01 14:05 3.2K
chrIV_mrna.sql 2020-09-01 14:05 2.1K
chrIV_mrna.txt.gz 2020-09-01 14:05 5.6K
chrIX_mrna.sql 2020-09-01 14:05 2.1K
chrIX_mrna.txt.gz 2020-09-01 14:05 1.6K
chrVI_mrna.sql 2020-09-01 14:05 2.1K
chrVI_mrna.txt.gz 2020-09-01 14:05 1.1K
chrXI_mrna.sql 2020-09-01 14:05 2.1K
chrXI_mrna.txt.gz 2020-09-01 14:05 2.4K
chrXV_mrna.sql 2020-09-01 14:05 2.1K
chrXV_mrna.txt.gz 2020-09-01 14:05 3.2K
chrIII_mrna.sql 2020-09-01 14:05 2.1K
chrIII_mrna.txt.gz 2020-09-01 14:05 1.2K
chrVIII_mrna.sql 2020-09-01 14:05 2.1K
chrVIII_mrna.txt.gz 2020-09-01 14:05 1.9K
chrI_mrna.sql 2020-09-01 14:05 2.1K
chrI_mrna.txt.gz 2020-09-01 14:05 941
chrM_mrna.sql 2020-09-01 14:05 2.1K
chrM_mrna.txt.gz 2020-09-01 14:05 854
chrV_mrna.sql 2020-09-01 14:05 2.1K
chrV_mrna.txt.gz 2020-09-01 14:05 2.6K
chrX_mrna.sql 2020-09-01 14:05 2.1K
chrX_mrna.txt.gz 2020-09-01 14:05 3.4K
chrVII_mrna.sql 2020-09-01 14:05 2.1K
chrVII_mrna.txt.gz 2020-09-01 14:05 4.4K
all_mrna.sql 2020-09-01 14:05 2.1K
all_mrna.txt.gz 2020-09-01 14:05 44K
chrM_est.sql 2020-09-01 14:06 2.1K
chrM_est.txt.gz 2020-09-01 14:06 33
chrM_intronEst.sql 2020-09-01 14:08 2.1K
chrM_intronEst.txt.gz 2020-09-01 14:08 39
chrI_intronEst.sql 2020-09-01 14:08 2.1K
chrI_intronEst.txt.gz 2020-09-01 14:08 1.1K
xenoRefGene.sql 2020-09-01 14:19 2.0K
xenoRefGene.txt.gz 2020-09-01 14:19 689K
xenoRefFlat.sql 2020-09-01 14:19 1.7K
xenoRefFlat.txt.gz 2020-09-01 14:19 629K
xenoRefSeqAli.sql 2020-09-01 14:19 2.1K
xenoRefSeqAli.txt.gz 2020-09-01 14:19 1.0M
chrIII_intronEst.sql 2020-09-01 14:39 2.1K
chrIII_intronEst.txt.gz 2020-09-01 14:39 1.5K
chrV_intronEst.sql 2020-09-01 14:39 2.1K
chrV_intronEst.txt.gz 2020-09-01 14:39 3.5K
chrXIV_intronEst.sql 2020-09-01 14:39 2.1K
chrXIV_intronEst.txt.gz 2020-09-01 14:39 2.5K
chrXII_intronEst.sql 2020-09-01 14:39 2.1K
chrXII_intronEst.txt.gz 2020-09-01 14:39 5.7K
chrXVI_intronEst.sql 2020-09-01 14:39 2.1K
chrXVI_intronEst.txt.gz 2020-09-01 14:39 6.6K
chrXIII_intronEst.sql 2020-09-01 14:39 2.1K
chrXIII_intronEst.txt.gz 2020-09-01 14:39 5.7K
chrII_intronEst.sql 2020-09-01 14:39 2.1K
chrII_intronEst.txt.gz 2020-09-01 14:39 9.0K
chrIV_intronEst.sql 2020-09-01 14:39 2.1K
chrIV_intronEst.txt.gz 2020-09-01 14:39 12K
chrIX_intronEst.sql 2020-09-01 14:39 2.1K
chrIX_intronEst.txt.gz 2020-09-01 14:39 2.6K
chrVI_intronEst.sql 2020-09-01 14:39 2.1K
chrVI_intronEst.txt.gz 2020-09-01 14:39 2.9K
chrXI_intronEst.sql 2020-09-01 14:39 2.1K
chrXI_intronEst.txt.gz 2020-09-01 14:39 3.3K
chrXV_intronEst.sql 2020-09-01 14:39 2.1K
chrXV_intronEst.txt.gz 2020-09-01 14:39 5.3K
chrVIII_intronEst.sql 2020-09-01 14:39 2.1K
chrVIII_intronEst.txt.gz 2020-09-01 14:39 3.7K
chrX_intronEst.sql 2020-09-01 14:39 2.1K
chrX_intronEst.txt.gz 2020-09-01 14:39 3.3K
chrVII_intronEst.sql 2020-09-01 14:39 2.1K
chrVII_intronEst.txt.gz 2020-09-01 14:39 8.4K
chrI_est.sql 2020-09-01 14:39 2.1K
chrI_est.txt.gz 2020-09-01 14:39 11K
chrIII_est.sql 2020-09-01 14:39 2.1K
chrIII_est.txt.gz 2020-09-01 14:39 32K
chrIX_est.sql 2020-09-01 14:39 2.1K
chrIX_est.txt.gz 2020-09-01 14:39 24K
chrV_est.sql 2020-09-01 14:39 2.1K
chrV_est.txt.gz 2020-09-01 14:39 52K
chrXI_est.sql 2020-09-01 14:39 2.1K
chrXI_est.txt.gz 2020-09-01 14:39 49K
chrX_est.sql 2020-09-01 14:39 2.1K
chrX_est.txt.gz 2020-09-01 14:39 49K
chrXIV_est.sql 2020-09-01 14:39 2.1K
chrXIV_est.txt.gz 2020-09-01 14:39 47K
chrXV_est.sql 2020-09-01 14:39 2.1K
chrXV_est.txt.gz 2020-09-01 14:39 100K
estOrientInfo.sql 2020-09-01 14:39 1.8K
estOrientInfo.txt.gz 2020-09-01 14:39 304K
chrXII_est.sql 2020-09-01 14:39 2.1K
chrXII_est.txt.gz 2020-09-01 14:39 81K
chrXVI_est.sql 2020-09-01 14:39 2.1K
chrXVI_est.txt.gz 2020-09-01 14:39 84K
chrXIII_est.sql 2020-09-01 14:39 2.1K
chrXIII_est.txt.gz 2020-09-01 14:39 70K
chrII_est.sql 2020-09-01 14:39 2.1K
chrII_est.txt.gz 2020-09-01 14:39 71K
chrIV_est.sql 2020-09-01 14:39 2.1K
chrIV_est.txt.gz 2020-09-01 14:39 148K
chrVI_est.sql 2020-09-01 14:39 2.1K
chrVI_est.txt.gz 2020-09-01 14:39 30K
chrVIII_est.sql 2020-09-01 14:39 2.1K
chrVIII_est.txt.gz 2020-09-01 14:39 32K
chrVII_est.sql 2020-09-01 14:39 2.1K
chrVII_est.txt.gz 2020-09-01 14:39 84K
all_est.sql 2020-09-01 14:39 2.1K
all_est.txt.gz 2020-09-01 14:39 960K
gbLoaded.sql 2020-09-01 14:39 1.6K
gbLoaded.txt.gz 2020-09-01 14:39 1.4K
trackDb.sql 2023-03-28 13:53 2.1K
trackDb.txt.gz 2023-03-28 13:53 37K
hgFindSpec.sql 2023-03-28 13:53 1.8K
hgFindSpec.txt.gz 2023-03-28 13:53 944
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 8.3K
tableList.sql 2024-12-08 03:12 1.6K
tableList.txt.gz 2024-12-08 03:12 7.9K
bigFiles.sql 2024-12-08 03:12 1.4K
bigFiles.txt.gz 2024-12-08 03:12 33