Genome coordinates for 3' UTRs were obtained using Refseq annotations available from UCSC for human (hg18, March 2006) and mouse (mm8, March 2006). All distinct Refseq 3' UTRs were used by TargetRank. As a result, the same Gene Name may appear multiple times in a TargetRank output, each corresponding to a different isoform's 3' UTR (distinct Refseq IDs). For mRNA isoforms with identical 3' UTRs, only one of the Refseq IDs is reported in the TargetRank output. TargetRank excludes mRNAs mapping to multiple locations in the genome or having 3' UTRs shorter than 50 nt.
Conservation was assessed by extracting the relevant regions from alignments of 16 vertebrate genomes with human (hg18, March 2006) or mouse (mm8, March 2006) available in multiple alignment format (MAF) from UCSC. Aligned positions with identical nucleotides in human, mouse, rat, and dog genomes were considered conserved.