Genomic structure of a copy of the human TPTE gene which encompasses 87 kb on the short arm of chromosome 21

Abstract

The testis-expressed human TPTE is a putative transmembrane tyrosine phosphatase, probably involved in signal transduction pathways of the endocrine and/or the spermatogenetic function of the testis. TPTE was mapped to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y. It is unknown which of the TPTE copies are transcribed, contain intronic sequences, and/or have open reading frames. Here, in silico analysis of the genomic sequence of human chromosome 21 allowed the determination of the genomic structure of a copy of the TPTE gene. This copy consists of 24 exons and spans approximately 87 kb. The mapping position of this copy of TPTE on the short arm of chromosome 21 was confirmed by FISH using the BAC 15L0C0 clone as a probe that contains almost the entire TPTE gene. This is the first description of the genomic sequence of a non-RNR gene on the short arm of human acrocentric chromosomes.

The TPTE gene family: cellular expression, subcellular localization and alternative splicing

“…Analysis of the human genome draft sequence confirmed that TPTE maps to the short arm of chromosome 21 (GenBank Hs21 _ 29649, band 21p11.2) (Guipponi et al, 2000). Supplementary TPTE copies map to Hsa13, Hsa15, Hsa22 and the HsaY (Chen et al, 1999).…”

The structure of duplications on human acrocentric chromosome short arms derived by the analysis of 15p

“…For acrocentric chromosomes, this organization might be important for the correct expression of ribosomal genes or for genesthat are yet to be identified and that are located on the short arms. In this regard, a protein-coding gene (a putative tyrosine phosphatase) has recently been assigned to 21p for the first time (Hattori et al 2000;Guipponi et al 2000). In addition to the knowledge derived from the partial sequence characterization of chromosomes 22p and 21p (Shiels et al 1997;Hattori et al 2000), this work provides new information concerning the sequence organization of the p-arm of acrocentric chromosomes and particularly on their paralogous nature.…”

Mappability and read length

“…Secondly, genes do exist in repeat regions. The gene TPTE was found on the acrocentric arm of chromosome 21 (Chen et al, 1999; Guipponi et al, 2000; Eichler et al, 2004). Many RefGenes are located in the 1 kb-unmappable regions in the assembled reference human genome (Li and Freudenberg, 2014; Li et al, 2014).…”