Schema for UniGene - UniGene Alignments
  Database: hg19    Primary Table: uniGene_3    Row Count: 124,338   Data last updated: 2011-02-22
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1631int(10) unsigned range Number of bases that match that aren't repeats
misMatches 8int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 897int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName Hs.714157varchar(255) values Query sequence name
qSize 1673int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1639int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 11873int(10) unsigned range Alignment start position in target
tEnd 14409int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 354,109,741,296,139,longblob   Size of each block
qStarts 0,354,463,1204,1500,longblob   Start of each block in query.
tStarts 11873,12612,13220,13962,14270,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg19.seq.acc (via uniGene_3.qName)

Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

UniGene (uniGene_3) Track Description


This track shows the UniGene genes from NCBI. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.

Coding exons are represented by blocks connected by horizontal lines representing introns. In full display mode, arrowheads on the connecting intron lines indicate the direction of transcription.


The UniGene sequence file, Hs.seq.uniq.gz, is downloaded from NCBI. Sequences are aligned to base genome using BLAT to create this track.

When a single UniGene gene aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.2% of the best and at least 96.5% base identity with the genomic sequence were kept.


Thanks to UniGene for providing this annotation.