Atlas of Genetics and Cytogenetics in Oncology and Haematology
SS18 (synovial sarcoma translocation, chromosome 18)
| Identity |
| Other names | MGC116875 |
| SSXT | |
| SYT | |
| HGNC (Hugo) | SS18 |
| Location | 18q11.2 |
| Location_base_pair | Starts at 21850215 and ends at 21924609 bp from pter ( according to hg18-Mar_2006) [Mapping] |
| DNA/RNA |
| Note | Member of the SS18 family. SYT, one of the alternative gene names, has continued to be used in the literature for this gene. |
| Description | 11 exons, spaning approximately 75 kb of genomic DNA in the telomere-to-centromere orientation on chromosome 18q11.2 The promoter region lacks CAAT and TATA boxes but contains CpG islands, suggesting that SS18 is a housekeeping gene. |
| Transcription | Exon 8 is spliced out with different ratio in the various tissues by alternative splicing. |
| Pseudogene | SS18L2 (3p21) |
| Protein |
| Description | 418 amino acids. 2 domains; the SHN domain (the SYT N-terminal homology domain) that is found in proteins from a wide variety of species ranging from plants to human, and the QPGY domain at the C-terminal part, rich in glutamine, proline, glycine and tyrosine. Four putative src-homology binding domains and two annexin-like direct repeats were exhibited in the SS18 protein. SS18 protein binds to p300, hBRM, AF10 and SIN3A proteins. The QPGY domain activates transcription when coupled to a DNA-binding domain. |
| Expression | Ubiquitous |
| Localisation | Nuclear |
| Function | Transcriptional coactivator |
| Homology | SS18L1, SS18L2 |
| Implicated in |
| Entity | Synovial sarcoma |
| Prognosis | A high grade sarcoma that leads to death in at least 25% of patients within five years of diagnosis. Prognosis may be different between the synovial sarcoma patients with SYT-SSX1 and SYT-SSX2. |
| Cytogenetics | t(X;18)(p11.2;q11.2) |
| Hybrid/Mutated Gene | SYT-SSX1, SYT-SSX2, SYT-SSX4; the exon 10 of the SS18 (SYT) gene is fused to exon 6 of the SSX genes. |
| Abnormal Protein | The last 8 amino acid residues of the SS18 (SYT) protein are replaced by 78 amino acids from the C-terminal part of SSX proteins. |
| Breakpoints |
 | |
| External links |
| Nomenclature | |
|---|---|
| HGNC (Hugo) | SS18 11340 |
| Entrez_Gene (NCBI) | SS18 6760 synovial sarcoma translocation, chromosome 18 |
| Cards | |
| Atlas | SS18ID84ch18q11 |
| GeneCards (Weizmann) | SS18 |
| Ensembl (Hinxton) | ENSG00000141380 [Gene_View] SS18 [Vega] |
| AceView (NCBI) | SS18 |
| Genatlas (Paris) | SS18 |
| euGene (Indiana) | 6760 |
| SOURCE (Stanford) | NM_001007559 NM_005637 |
| Genomic and cartography | |
| GoldenPath (UCSC) | SS18 - 18q11.2 chr18:21850215-21924609 - 18q11.2 [Description] (hg18-Mar_2006) |
| Ensembl | SS18 - 18q11.2 [CytoView] |
| Mapping of homologs : NCBI | SS18 [Mapview] |
| OMIM | 600192 |
| Gene and transcription | |
| Gene : Genbank (Entrez) | AB300354 AB300355 AB300356 AB300357 AF244972 |
| Reference sequence (RefSeq transcript) :SRS | NM_001007559 NM_005637 |
| Reference transcript : Entrez | NM_001007559 NM_005637 |
| RefSeq genomic : SRS | AC_000061 AC_000150 NC_000018 NT_010966 NW_001838467 NW_927095 |
| RefSeq genomic : Entrez | AC_000061 AC_000150 NC_000018 NT_010966 NW_001838467 NW_927095 |
| Consensus coding sequences : CCDS NCBI | SS18 |
| Cluster EST : Unigene | Hs.404263 [ SRS ] Hs.404263 [ NCBI ] |
| Alternative Splicing : Fast-db (Paris) | 2799 |
| Protein : pattern, domain, 3D structure | |
| Protein : UniProt/SwissProt | Q15532 (SRS) Q15532 (Expasy) Q15532 (Uniprot) |
| With graphics : InterPro | Q15532 |
| Splice isoforms : VarSplice FASTA | Q15532(VarSplice FASTA) |
| Domains : Interpro (SRS) | SSXT |
| Domains : Interpro (EBI) | SSXT |
| Related proteins : CluSTr | Q15532 |
| Domain families : Pfam SRS | SSXT (PF05030) |
| Domain families : Pfam Sanger | SSXT (PF05030) |
| Domain families : Pfam NCBI | pfam05030 |
| Blocks (Seattle) | Q15532 |
| Crystal structure of protein : PDB SRS | |
| Crystal structure of protein : PDBSum | |
| Crystal structure of protein : IMB | |
| Crystal structure of protein : PDB RSDB | |
| HPRD | 02559 |
| Protein Interaction databases | |
| DIP (DOE-UCLA) | Q15532 |
| IntAct (EBI) | Q15532 |
| Polymorphism : SNP, mutations, diseases | |
| Single Nucleotide Polymorphism (SNP) : dbSNP NCBI | SS18 |
| SNP : GeneSNP Utah | SS18 |
| SNP : HGBase | SS18 |
| Genetic variants : HAPMAP | SS18 |
| Somatic Mutations in Cancer : COSMIC | SS18 |
| Translocation Breakpoints in Cancer : TICdb | SS18 |
| Mutations and Diseases : HGMD | SS18 |
| Hereditary diseases : OMIM | 600192 |
| Hereditary diseases : GENETests | 600192 |
| Diseases : Genetic Association | SS18 |
| General knowledge | |
| Homologs : HomoloGene | SS18 |
| Homology/Alignments : Family Browser UCSC | SS18 |
| Phylogenetic Trees/Animal Genes : TreeFam | SS18 |
| Chemical/Protein Interactions : CTD | 6760 |
| Keywords Ontology : AmiGO | nucleus |
| Keywords Ontology : EGO-EBI | nucleus |
| Pathways : BIOCARTA | |
| Pathways : KEGG | |
| Other databases | |
| Probes | |
| Probes : Imagenes | SS18 Related clones (RZPD - Berlin) |
| Literature | |
| PubMed | 29 Pubmed reference(s) in Entrez |
| PubGene | SS18 |
| Bibliography |
| Identification of novel genes, SYT and SSX, involved in the t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma. |
| Clark J, Rocques PJ, Crew AJ, Gill S, Shipley J, Chan AM, Gusterson BA, Cooper CS |
| Nature genetics. 1994 ; 7 (4) : 502-508. |
| PMID 7951320 |
| Isolation and characterization of the mouse homolog of SYT, a gene implicated in the development of human synovial sarcomas. |
| de Bruijn DR, Baats E, Zechner U, de Leeuw B, Balemans M, Olde Weghuis D, Hirning-Folz U, Geurts van Kessel AG |
| Oncogene. 1996 ; 13 (3) : 643-648. |
| PMID 8760306 |
| SYT-SSX gene fusion as a determinant of morphology and prognosis in synovial sarcoma. |
| Kawai A, Woodruff J, Healey JH, Brennan MF, Antonescu CR, Ladanyi M |
| The New England journal of medicine. 1998 ; 338 (3) : 153-160. |
| PMID 9428816 |
| A novel fusion gene, SYT-SSX4, in synovial sarcoma. |
| Skytting B, Nilsson G, Brodin B, Xie Y, Lundeberg J, Uhlˆ©n M, Larsson O |
| Journal of the National Cancer Institute. 1999 ; 91 (11) : 974-975. |
| PMID 10359553 |
| Functional domains of the SYT and SYT-SSX synovial sarcoma translocation proteins and co-localization with the SNF protein BRM in the nucleus. |
| Thaete C, Brett D, Monaghan P, Whitehouse S, Rennie G, Rayner E, Cooper CS, Goodwin G |
| Human molecular genetics. 1999 ; 8 (4) : 585-591. |
| PMID 10072425 |
| p300 interacts with the nuclear proto-oncoprotein SYT as part of the active control of cell adhesion. |
| Eid JE, Kung AL, Scully R, Livingston DM |
| Cell. 2000 ; 102 (6) : 839-848. |
| PMID 11030627 |
| A reverse transcriptase-polymerase chain reaction assay in the diagnosis of soft tissue sarcomas. |
| Naito N, Kawai A, Ouchida M, Dan'ura T, Morimoto Y, Ozaki T, Shimizu K, Inoue H |
| Cancer. 2000 ; 89 (9) : 1992-1998. |
| PMID 11064357 |
| The synovial sarcoma associated protein SYT interacts with the acute leukemia associated protein AF10. |
| de Bruijn DR, dos Santos NR, Thijssen J, Balemans M, Debernardi S, Linder B, Young BD, Geurts van Kessel A |
| Oncogene. 2001 ; 20 (25) : 3281-3289. |
| PMID 11423977 |
| Mapping and characterization of the mouse and human SS18 genes, two human SS18-like genes and a mouse Ss18 pseudogene. |
| de Bruijn DR, Kater-Baats E, Eleveld M, Merkx G, Geurts Van Kessel A |
| Cytogenetics and cell genetics. 2001 ; 92 (3-4) : 310-319. |
| PMID 11435705 |
| Splicing isoform of SYT-SSX fusion protein accelerates transcriptional activity and cell proliferation. |
| Morimoto Y, Ouchida M, Ozaki T, Kawai A, Ito T, Yoshida A, Inoue H, Shimizu K |
| Cancer letters. 2003 ; 199 (1) : 35-43. |
| PMID 12963121 |
| SYT, a partner of SYT-SSX oncoprotein in synovial sarcomas, interacts with mSin3A, a component of histone deacetylase complex. |
| Ito T, Ouchida M, Ito S, Jitsumori Y, Morimoto Y, Ozaki T, Kawai A, Inoue H, Shimizu K |
| Laboratory investigation; a journal of technical methods and pathology. 2004 ; 84 (11) : 1484-1490. |
| PMID 15467731 |
| REVIEW articles | automatic search in PubMed |
| Last year publications | automatic search in PubMed |
| Contributor(s) |
| Written | 05-2006 | Mamoru Ouchida |
| Department of Molecular Genetics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University. Shikata-cho 2-5-1, Okayama 700-8558, Japan |
| Citation |
| This paper should be referenced as such : |
| Ouchida M . SS18 (synovial sarcoma translocation, chromosome 18). Atlas Genet Cytogenet Oncol Haematol. May 2006 . URL : http://AtlasGeneticsOncology.org/Genes/SS18ID84ch18q11.html |
| © Atlas of Genetics and Cytogenetics in Oncology and Haematology | indexed on : Sat Jun 27 16:37:35 CEST 2009 |
For comments and suggestions or contributions, please contact us