Description

This track shows the boundaries of genes and the direction of transcription as deduced from clustering spliced ESTs and mRNAs against the genome. When there are many spliced variants of the same gene, this track shows the variant that spans the greatest distance in the genome.

Method

ESTs and mRNAs from Genbank are aligned against the genome with the BLAT program, and filtered to keep only those alignments that have at least 97.5% base identity within the aligning blocks. When multiple alignments occur, only the alignments with a percentage identity within 0.2% of the best alignment are kept. ESTs that align without any introns are discarded. Blocks that are less than 130 bases and are not next to an intron are discarded. Blocks smaller than 10 bases are discarded. The orientations of the ESTs and mRNAs are deduced from the GT/AG splice sites at the introns, and ESTs and mRNAs with overlapping blocks on the same strand are merged into clusters. Only the extent and orientation of the clusters are shown here.

Credits

This track was generated at UCSC by Jim Kent using data submitted to Genbank by scientists worldwide.