Description

This track shows the boundaries of genes and direction of transcription as deduced from clustering spliced ESTs and mRNAs against the genome. When there are many spliced varient of the same gene, this track shows the varient which 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 only keep alignments that are 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 which align without any introns are discarded. Blocks that are less than 130 bases and not next to an intron are discarded. Blocks smaller than 10 bases are discarded. The orientation 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 in submitted to Genbank by scientists worldwide.