The CCND1-EMS1 locus on human chromosome 11q13 is amplified in esophageal cancer, bladder tumors, and breast cancer. During analyses of FGF gene cluster within the CCND1-EMS1 locus, we identified a 5'-truncated partial cDNA (NM_018043.1) derived from the uncharacterized FLJ10261 gene. Here, we characterized the FLJ10261 gene by using bioinformatics. NM_018043.1 cDNA corresponded to the nucleotide position 1129-4258 of 4558-bp DKFZp686O1156 cDNA, and the nucleotide position 50-3010 of DKFZ-p686O1156 was the coding region of the FLJ10261 gene. FLJ10261 gene, consisting of 26 exons, was located between FGF3 and FADD genes within the CCND1-EMS1 locus. Two FLJ10261 isoforms with or without exon 15 were transcribed due to alternative splicing. FLJ10261 mRNA was expressed in head and neck tumors, parathyroid tumors, breast, pancreatic, and gastric cancer. Mouse Flj10261 gene (AK052589) was located between Fgf3 and Fadd genes on mouse chromosome 7. Human FLJ10261 gene was homologous to C12orf3 gene on human chromosome 12p13, C11orf25 gene on 11p14, and FLJ34272 gene on 12q23. Human FLJ10261 protein showed 89.8% total-amino-acid identity with mouse Flj10261 protein, and also 58.4%, 38.3%, and 38.6% identity with human C12orf3, C11orf25, and FLJ34272/BAC03704 proteins, respectively. FLJ10261, C12orf3, C11orf25 and FLJ34272 proteins were eight-transmembrane proteins with N- and C-terminal tails facing the cytoplasm, which might function as transporters for unidentified substrates. This is the first report on comprehensive characterization of the FLJ10261 gene located within the CCND1-ORAOV1-FGF19-FGF4-FGF3-FLJ10261-FADD-PPFIA1-EMS1 locus on human chromosome 11q13.

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