Comparative genomics on SFRP1 orthologs.
SFRP1, SFRP2, SFRP3, SFRP4, SFRP5, WIF1, DKK1, DKK2, DKK3, DKK4 are secreted-type WNT signaling modulators. SFRP1 tumor suppressor gene at human chromosome 8p11.21 is inactivated in colorectal cancer and other tumors by deletion and by epigenetic CpG hypermethylation. Here, we identified and characterized the rat Sfrp1 gene by using bioinformatics. Rat Sfrp1 gene, consisting of three exons, was located within AC112899.4 genome sequence. Complete coding sequence of rat Sfrp1 was determined by assembling AC112899.4 genome sequence, CK838748 EST, and BF417482 EST. Rat Sfrp1 (314 aa) consisted of a signal peptide (codon 1-31), Frizzled domain with ten conserved Cys residues (codon 49-168), and Netrin (NTR) domain with six conserved Cys residues (codon 186-314). Rat Sfrp1 showed 98.7%, 95.2%, 94.3%, 82.5% and 58.3% total-amino-acid identity with mouse Sfrp1, human SFRP1, cow Sfrp1, chicken sfrp1 and zebrafish sfrp1, respectively. SFRP1 mRNA was expressed in embryonic stem (ES) cells, neuroblastoma, liver adeno-carcinoma, and skin squamous cell carcinoma. Match program revealed that AP1, COMP1, and double ETS1-binding sites were conserved between human SFRP1 and rat Sfrp1 promoters. This is the first report on comparative integromics analyses on Sfrp1 orthologs.
Katoh
Yuriko
Y
M&M Medical BioInformatics, Hongo 113-0033, Japan.
Katoh
Masaru
M
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics; D005091:Exons; D020224:Expressed Sequence Tags; D005796:Genes / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics*; D007438:Introns; D008565:Membrane Proteins / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D021382:Protein Sorting Signals / Q000235:genetics; D051381:Rats / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D000094742:Secreted Frizzled-Related Proteins
D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D021382:Protein Sorting Signals; C500646:Sfrp1 protein, rat; D000094742:Secreted Frizzled-Related Proteins