Cloning, sequencing and phylogenetic analysis of a human 5-hydroxytryptamine 1D receptor pseudogene

A third member of the human 5HT1D gene family has been identified using a combination of homology cloning and DNA sequence analysis. This human gene is most related to the 5HT1D alpha subtype (77% shared identity) and is a pseudogene, based on the lack of an open reading frame (ORF) caused by multiple in-frame stop codons and nucleotide (nt) deletions relative to the functional 5HT1D alpha gene (encoding the 5-hydroxytryptamine 1D alpha receptor). The 5HT1D pseudogene also contained an insertion that shares 87% identity to the Alu consensus sequence. Phylogenetic analysis of the three human genes in this family reveals that although the two functional genes, 5HT1D alpha and 5HT1D beta, are detected in all mammalian species examined, the 5HT1D pseudogene is only detected in a subset of primates (catarrhines) that evolved approximately 35-45 million years (Myr) ago. Alternatively, based on the 23% divergence between the functional 5HT1D alpha gene and the 5HT1D pseudogene, we estimate that these two genes began to diverge approximately 50 Myr ago.