Gene Bounds Track Settings
Gene Boundaries as Defined by RNA and Spliced EST Clusters   (All mRNA and EST tracks)

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Show only items with score at or above:   (range: 0 to 1000)

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Data last updated at UCSC: 2010-10-20


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 genome.


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 scientists worldwide.


Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32:D23-6.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.