This directory contains a dump of the UCSC genome annotation database for the
Jan. 2018 (Susie_PABv2/ponAbe3) assembly of the orangutan genome
(ponAbe3, University of Washington) .
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/325
https://www.ncbi.nlm.nih.gov/genome/assembly/1529631
https://www.ncbi.nlm.nih.gov/bioproject/369439
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=ponAbe3
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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/ponAbe3/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/ponAbe3/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/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 ponAbe3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ponAbe3 --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.
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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 -
chainMm10Link.txt.gz 2018-11-01 17:03 503M
chainHg38Link.txt.gz 2018-11-01 17:01 157M
windowmaskerSdust.txt.gz 2018-11-01 17:06 146M
rmsk.txt.gz 2018-11-01 17:05 141M
netMm10.txt.gz 2018-11-01 17:02 72M
chainMm10.txt.gz 2018-11-01 17:02 60M
simpleRepeat.txt.gz 2018-11-01 17:06 28M
chainHg38.txt.gz 2018-11-01 17:01 23M
xenoRefGene.txt.gz 2018-11-01 17:06 22M
xenoRefFlat.txt.gz 2018-11-01 17:06 20M
xenoRefSeqAli.txt.gz 2018-11-01 17:07 20M
nestedRepeats.txt.gz 2018-11-01 17:00 18M
netHg38.txt.gz 2018-11-01 17:01 11M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 9.3M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.3M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.1M
genscan.txt.gz 2018-11-01 17:06 2.8M
augustusGene.txt.gz 2018-11-01 17:00 2.3M
all_est.txt.gz 2018-11-01 17:00 2.1M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M
intronEst.txt.gz 2018-11-01 17:06 1.3M
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 881K
cpgIslandExtUnmasked.txt.gz 2018-11-01 17:05 862K
estOrientInfo.txt.gz 2018-11-01 17:05 648K
cpgIslandExt.txt.gz 2018-11-01 17:05 591K
all_mrna.txt.gz 2018-11-01 17:00 531K
refSeqAli.txt.gz 2018-11-01 17:05 398K
refGene.txt.gz 2018-11-01 17:05 385K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 366K
refFlat.txt.gz 2018-11-01 17:05 359K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 338K
microsat.txt.gz 2018-11-01 17:06 239K
mrnaOrientInfo.txt.gz 2018-11-01 17:06 150K
gold.txt.gz 2018-11-01 17:06 80K
trackDb.txt.gz 2025-06-11 11:58 65K
chromAlias.txt.gz 2018-11-01 17:05 54K
ucscToINSDC.txt.gz 2018-11-01 17:06 51K
ucscToRefSeq.txt.gz 2018-11-01 17:06 47K
chromInfo.txt.gz 2018-11-01 17:05 36K
cytoBandIdeo.txt.gz 2018-11-01 17:05 33K
gap.txt.gz 2018-11-01 17:05 8.7K
tableDescriptions.txt.gz 2025-11-22 09:23 6.1K
tableList.txt.gz 2025-11-23 03:13 3.0K
xenoRefSeqAli.sql 2018-11-01 17:07 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
refSeqAli.sql 2018-11-01 17:05 2.1K
intronEst.sql 2018-11-01 17:06 2.1K
all_mrna.sql 2018-11-01 17:00 2.1K
all_est.sql 2018-11-01 17:00 2.1K
netMm10.sql 2018-11-01 17:01 2.1K
netHg38.sql 2018-11-01 17:00 2.1K
trackDb.sql 2025-06-11 11:58 2.1K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
augustusGene.sql 2018-11-01 17:00 1.9K
xenoRefGene.sql 2018-11-01 17:06 1.9K
nestedRepeats.sql 2018-11-01 17:00 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
simpleRepeat.sql 2018-11-01 17:06 1.9K
refGene.sql 2018-11-01 17:05 1.9K
rmsk.sql 2018-11-01 17:05 1.9K
hgFindSpec.sql 2025-06-11 11:58 1.8K
mrnaOrientInfo.sql 2018-11-01 17:06 1.8K
estOrientInfo.sql 2018-11-01 17:05 1.8K
xenoRefFlat.sql 2018-11-01 17:06 1.7K
cpgIslandExtUnmasked.sql 2018-11-01 17:05 1.7K
refFlat.sql 2018-11-01 17:05 1.7K
chainMm10.sql 2018-11-01 17:02 1.7K
chainHg38.sql 2018-11-01 17:01 1.7K
cpgIslandExt.sql 2018-11-01 17:05 1.7K
genscan.sql 2018-11-01 17:06 1.7K
gold.sql 2018-11-01 17:06 1.7K
gap.sql 2018-11-01 17:05 1.6K
tableList.sql 2025-11-23 03:13 1.6K
history.sql 2018-11-01 17:01 1.6K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
chainMm10Link.sql 2018-11-01 17:02 1.5K
chainHg38Link.sql 2018-11-01 17:01 1.5K
cytoBandIdeo.sql 2018-11-01 17:05 1.5K
windowmaskerSdust.sql 2018-11-01 17:06 1.5K
microsat.sql 2018-11-01 17:06 1.5K
tableDescriptions.sql 2025-11-22 09:23 1.5K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ucscToRefSeq.sql 2018-11-01 17:06 1.4K
ucscToINSDC.sql 2018-11-01 17:06 1.4K
chromAlias.sql 2018-11-01 17:05 1.4K
bigFiles.sql 2025-11-23 03:13 1.4K
chromInfo.sql 2018-11-01 17:05 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
grp.sql 2018-11-01 17:05 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
gc5BaseBw.sql 2018-11-01 17:05 1.3K
hgFindSpec.txt.gz 2025-06-11 11:58 1.2K
history.txt.gz 2018-11-01 17:01 853
grp.txt.gz 2018-11-01 17:05 213
bigFiles.txt.gz 2025-11-23 03:13 95
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
gc5BaseBw.txt.gz 2018-11-01 17:05 66