A Genomic Perspective on Protein Tyrosine Phosphatases:
Gene structure, Pseudogenes and Genetic Disease Linkage
Jannik N. Andersen, Peter G. Jansen, Søren M. Echwald, Ole H. Mortensen,
Toshiyuki Fukada, Robert Del Vecchio, Nicholas K. Tonks and Niels Peter H. Møller.
Cold Spring Harbor Laboratory, New York, USA,
Exiqon, Vedbæk, Denmark,
Scientific Computing & Signal Transduction Laboratory, Novo Nordisk, Denmark.

The results presented here support our recent analysis of the composition of the PTP gene family in the human genome (FASEB J 2004). 

Here, for the first time, we have catalogued the classical, tyrosine-specific PTPs of the human genome and conducted a comparative exon structure analysis of this gene family. The present definition of the PTP gene family is reviewed in the broader context of their amino acid sequences, three-dimensional structures, chromosomal location and disease loci. 

Using public and proprietary sequence databases, we discovered one novel human PTP gene and defined chromosomal loci and exon structure of additional 37 genes encoding known PTP transcripts. Direct orthologs were present in the mouse genome for all 38 human PTPs. In addition, we identified 12 PTP pseudogenes, which were unique to humans and which have most likely contaminated previous bioinformatic analysis of this gene family. 

On the following pages, these genes have been carefully annotated and we hope this genomic analysis may serve as a platform for future studies of this important protein family.