Isolation and characterization of a human pseudogene (CTNNAP1) for alpha E-catenin (CTNNA1): assignment of the pseudogene to 5q22 and the alpha E-catenin gene to 5q31.

A pseudogene (CTNNAP1) for the human alpha E-catenin gene was isolated from a human genomic phage library. The pseudogene sequence shows 90% similarity to the alpha E-catenin mRNA at the nucleotide level. Thirty-eight stop codons in all three reading frames and multiple other mutations were found, indicating that the pseudogene does not encode a functional protein. No introns were found in the region corresponding to the open reading frame of the alpha E-catenin cDNA, and two direct repeats flank this same region. Hence, the pseudogene can be classified as a processed pseudogene. Polymerase chain reaction with pseudogene-specific primers on genomic DNA and cDNA from human cell lines and healthy blood donors demonstrated the general occurrence of the pseudogene and the lack of its transcription. By fluorescence in situ hybridization the pseudogene was mapped to human chromosome 5q22 and the alpha E-catenin gene to the formerly disputed locus 5q31. This is the first report of a pseudogene for a member of the cadherin-catenin cell-cell adhesion complex.