Identification and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico.
LNX, functioning as E3 ubiquitin ligase for NUMB, is implicated in the cell fate determination through the inhibition of Notch signaling. LNX, PDZRN1 (LNX2), PDZRN3 (LNX3 or SEMCAP3) and PDZRN4 (LNX4 or SEMCAP3L) constitute the LNX (PDZRN) family. PDZRN4 gene encodes 2 isoforms due to alternative splicing. PDZRN4 consists of RING, 2 PDZ, PR34H1 and PR34H2 domains, and PDZRN4S consists of PDZ, PR34H1 and PR34H2 domains. Here, we identified novel PDZRN4-related genes by using bioinformatics. FLJ45072 (AK127016.1) and KIAA1444 (NM_032512.1) cDNAs were derived from human PDZRN4L (also known as PDZRN5, LNX4L, or LNX5) gene. FLJ45072 was the representative PDZRN4L cDNA, while KIAA1444 was a 5'-truncated partial PDZRN4L cDNA. MGC67228 (BC056462.1) and B230341P03 (AK046101.1) cDNAs were derived from mouse Pdzrn4l gene. MGC67228 was a 5'-truncated partial Pdzrn4l cDNA, while B230341P03 was an aberrant Pdzrn4l cDNA with exon skipping and insertions within the coding region. PDZRN4L gene, consisting of at least 8 exons, was located at human chromosome Xq28. Exons 1-8 of PDZRN4L gene corresponded to exons 1b, 4-10 of PDZRN4 gene. Because the regions corresponding to exons 1-3 of PDZRN4 gene were not identified within human genome sequences around the PDZRN4L gene, PDZRN4L isoform with RING finger domain was not identified. Human PDZRN4L (769 aa) showed 93.0% total-amino-acid identity with mouse Pdzrn4l (772 aa), and 49.9% total-amino-acid identity with human PDZRN4S. PDZ, PR34H1 and PR34H2 domains were conserved between PDZRN4L and PDZRN4S. This is the first report on human PDZRN4L and mouse Pdzrn4l genes.
Katoh
Masuko
M
M & M Medical BioInformatics, Narashino 275-0022, Japan. mkatoh@ncc.go.jp
Katoh
Masaru
M
D017398:Alternative Splicing / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002352:Carrier Proteins / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D005091:Exons / Q000235:genetics; D020224:Expressed Sequence Tags; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary / Q000235:genetics; D017386:Sequence Homology, Amino Acid
D002352:Carrier Proteins; D018076:DNA, Complementary; C485993:PDZRN4 protein, human