
<ArticleTitle>Mapping and characterization of the mouse and human <prot>SS18</prot> genes, two human <prot>SS18</prot>-like genes and a mouse <prot>Ss18</prot> pseudogene.</ArticleTitle>
<AbstractText>We have previously isolated and characterized a mouse cDNA orthologous to the human synovial sarcoma associated <prot>SS18</prot> (formerly named <prot>SSXT</prot> and <prot>SYT</prot>) cDNA. Here, we report the characterization of the genomic structure of the mouse <prot>Ss18</prot> gene. Through in silico methods with sequence information contained in the public databases, we did the same for the human <prot>SS18</prot> gene and two human <prot>SS18</prot> homologous genes, <prot>SS18L1</prot> and <prot>SS18L2</prot>. In addition, we identified a mouse <prot>Ss18</prot> processed pseudogene and mapped it to chromosome 1, band A2-3. The mouse <prot>Ss18</prot> gene, which is subject to extensive alternative splicing, is made up of 11 exons, spread out over approximately 45 kb of genomic sequence. The human <prot>SS18</prot> gene is also composed of 11 exons with similar intron-exon boundaries, spreading out over about 70 kb of genomic sequence. One alternatively spliced exon, which is not included in the published <prot>SS18</prot> cDNA, corresponds to a stretch of sequence which we previously identified in the mouse <prot>Ss18</prot> cDNA. The human <prot>SS18L1</prot> gene, which is also made up of 11 exons with similar intron-exon boundaries, was mapped to chromosome 20 band q13.3. The smaller <prot>SS18L2</prot> gene, which is composed of three exons with similar boundaries as the first three exons of the other three genes, was mapped to chromosome 3 band <prot>p21</prot>. Through sequence and mutation analyses this gene could be excluded as a candidate gene for <prot>3p21</prot>-associated renal cell cancer. In addition, we created a detailed BAC map around the human <prot>SS18</prot> gene, placing it unequivocally between the CA-repeat marker AFMc014wf9 and the <prot>dihydrofolate reductase</prot> pseudogene <prot>DHFRP1</prot>. The next gene in this map, located distal to <prot>SS18</prot>, was found to be the <prot><prot>TBP</prot> associated factor <prot>TAFII</prot>-105</prot> (<prot>TAF2C2</prot>). Further analogies between the mouse <prot>Ss18</prot> gene, the human <prot>SS18</prot> gene and its two homologous genes were found in the putative promoter fragments. All four promoters resemble the promoters of housekeeping genes in that they are TATA-less and embedded in canonical CpG islands, thus explaining the high and widespread expression of the <prot>SS18</prot> genes.</AbstractText>
