In-progress RT-PCR clones for Mammalian Gene Collection $organism C-list from Washington University St. Louis.
This track includes predicted amplicons that are in the process of RT-PCR. These usually consist of probabilistically inferred genomic structures. Primers are chosen so that they amplify at least one intron that is determined to be novel. Usually an intron is determined novel is there is no dbEST, genbank human mRNA, Refseq gene, or HIT from a previous experiment that supports it. Supported is defined as having a blast alignment HSP (parameters: 'W=15 V=100 B=10 M=1 N=-3 -Q=10 -R=10') with at least 98 matches on a 100bp alignment window when aligned the predicted cDNA to ESTs, mRNAs or sequences we get from previous experiments. The aligned region of this HSP need to cover at least 10bp on both sides of the splice site.
Updated 2005-05-19
Michael Brent's Computational Genomics Group at Washington University St. Louis.