This track shows the boundaries of genes and the direction of
transcription as deduced from clustering spliced ESTs and mRNAs
against the genome. When many spliced variants of the same gene exist,
this track shows the variant that spans the greatest distance in the
ESTs and mRNAs from
GenBank were aligned against the genome using BLAT.
Alignments with less than 97.5% base identity within the aligning blocks
were filtered out. When multiple alignments occurred, only those
alignments with a percentage identity within 0.2% of the
best alignment were kept. The following alignments were also discarded:
ESTs that aligned without any introns, blocks smaller than 10 bases, and
blocks smaller than 130 bases that were not located next to an intron.
The orientations of the ESTs and mRNAs were deduced from the GT/AG splice
sites at the introns; ESTs and mRNAs with overlapping blocks
on the same strand were merged into clusters. Only the
extent and orientation of the clusters are shown in this track.
Scores for individual gene boundaries were assigned based on the number of
cDNA alignments used:
- 300 — based on a single cDNA alignment
- 600 — based on two alignments
- 900 — based on three alignments
- 1000 — based on four or more alignments
This track, which was originally developed by Jim Kent,
was generated at UCSC and uses data submitted to GenBank by
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.
GenBank: update. Nucleic Acids Res.
2004 Jan 1;32:D23-6.
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.