LOCUS       NM_005635               1223 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens SSX family member 1 (SSX1), transcript variant 2,
            mRNA.
ACCESSION   NM_005635 XM_937476
VERSION     NM_005635.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1223)
  AUTHORS   Liu,C., Si,W., Tu,C., Tian,S., He,X., Wang,S., Yang,X., Yao,C.,
            Li,C., Kherraf,Z.E., Ye,M., Zhou,Z., Ma,Y., Gao,Y., Li,Y., Liu,Q.,
            Tang,S., Wang,J., Saiyin,H., Zhao,L., Yang,L., Meng,L., Chen,B.,
            Tang,D., Zhou,Y., Wu,H., Lv,M., Tan,C., Lin,G., Kong,Q., Shi,H.,
            Su,Z., Li,Z., Yao,Y.G., Jin,L., Zheng,P., Ray,P.F., Tan,Y.Q.,
            Cao,Y. and Zhang,F.
  TITLE     Deficiency of primate-specific SSX1 induced asthenoteratozoospermia
            in infertile men and cynomolgus monkey and tree shrew models
  JOURNAL   Am J Hum Genet 110 (3), 516-530 (2023)
   PUBMED   36796361
REFERENCE   2  (bases 1 to 1223)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 1223)
  AUTHORS   Panigrahi,M.K., Pradhan,G., Sahoo,N., Mishra,P., Patra,S. and
            Mohapatra,P.R.
  TITLE     Primary pulmonary synovial sarcoma: A reappraisal
  JOURNAL   J Cancer Res Ther 14 (3), 481-489 (2018)
   PUBMED   29893303
  REMARK    GeneRIF: Synovial sarcoma (SS) is considered as high-grade tumors
            with a poor prognosis. Novel therapies targeted at fusion oncogene,
            SS18-SSX-derived peptide vaccine, epidermal growth factor receptor,
            and vascular endothelial growth factor are the future hope in SS.
REFERENCE   4  (bases 1 to 1223)
  AUTHORS   Banito,A., Li,X., Laporte,A.N., Roe,J.S., Sanchez-Vega,F.,
            Huang,C.H., Dancsok,A.R., Hatzi,K., Chen,C.C., Tschaharganeh,D.F.,
            Chandwani,R., Tasdemir,N., Jones,K.B., Capecchi,M.R., Vakoc,C.R.,
            Schultz,N., Ladanyi,M., Nielsen,T.O. and Lowe,S.W.
  TITLE     The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial
            Sarcoma
  JOURNAL   Cancer Cell 33 (3), 527-541 (2018)
   PUBMED   29502955
  REMARK    GeneRIF: SS18-SSX1 deregulates developmental programs to drive
            transformation by hijacking a transcriptional repressive complex to
            aberrantly activate gene expression
            Erratum:[Cancer Cell. 2018 Aug 13;34(2):346-348. doi:
            10.1016/j.ccell.2018.07.006.. PMID: 30107180]
REFERENCE   5  (bases 1 to 1223)
  AUTHORS   Gure,A.O., Wei,I.J., Old,L.J. and Chen,Y.T.
  TITLE     The SSX gene family: characterization of 9 complete genes
  JOURNAL   Int J Cancer 101 (5), 448-453 (2002)
   PUBMED   12216073
REFERENCE   6  (bases 1 to 1223)
  AUTHORS   Thaete,C., Brett,D., Monaghan,P., Whitehouse,S., Rennie,G.,
            Rayner,E., Cooper,C.S. and Goodwin,G.
  TITLE     Functional domains of the SYT and SYT-SSX synovial sarcoma
            translocation proteins and co-localization with the SNF protein BRM
            in the nucleus
  JOURNAL   Hum Mol Genet 8 (4), 585-591 (1999)
   PUBMED   10072425
REFERENCE   7  (bases 1 to 1223)
  AUTHORS   Chand,A., Clark,J., Cooper,C.S. and Craig,I.W.
  TITLE     Long-range organization of reiterated sequences, including the SSX1
            cDNA at the OATL1 cluster in Xp11.23
  JOURNAL   Genomics 30 (3), 545-552 (1995)
   PUBMED   8825641
REFERENCE   8  (bases 1 to 1223)
  AUTHORS   de Leeuw,B., Balemans,M., Olde Weghuis,D. and Geurts van Kessel,A.
  TITLE     Identification of two alternative fusion genes, SYT-SSX1 and
            SYT-SSX2, in t(X;18)(p11.2;q11.2)-positive synovial sarcomas
  JOURNAL   Hum Mol Genet 4 (6), 1097-1099 (1995)
   PUBMED   7655467
REFERENCE   9  (bases 1 to 1223)
  AUTHORS   Crew,A.J., Clark,J., Fisher,C., Gill,S., Grimer,R., Chand,A.,
            Shipley,J., Gusterson,B.A. and Cooper,C.S.
  TITLE     Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with
            homology to the Kruppel-associated box in human synovial sarcoma
  JOURNAL   EMBO J 14 (10), 2333-2340 (1995)
   PUBMED   7539744
REFERENCE   10 (bases 1 to 1223)
  AUTHORS   Sinke,R.J., de Leeuw,B., Janssen,H.A., Weghuis,D.O.,
            Suijkerbuijk,R.F., Meloni,A.M., Gilgenkrantz,S., Berger,W.,
            Ropers,H.H., Sandberg,A.A. et al.
  TITLE     Localization of X chromosome short arm markers relative to synovial
            sarcoma- and renal adenocarcinoma-associated translocation
            breakpoints
  JOURNAL   Hum Genet 92 (3), 305-308 (1993)
   PUBMED   8406438
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC150487.2 and BQ774004.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_005635.3.
            
            Summary: The product of this gene belongs to the family of highly
            homologous synovial sarcoma X (SSX) breakpoint proteins. These
            proteins may function as transcriptional repressors. They are also
            capable of eliciting spontaneous humoral and cellular immune
            responses in cancer patients, and are potentially useful targets in
            cancer vaccine-based immunotherapy. This gene, and also the SSX2
            and SSX4 family members, have been involved in t(X;18)(p11.2;q11.2)
            translocations that are characteristically found in all synovial
            sarcomas. This translocation results in the fusion of the synovial
            sarcoma translocation gene on chromosome 18 to one of the SSX genes
            on chromosome X. The encoded hybrid proteins are likely responsible
            for transforming activity. Alternative splicing of this gene
            results in multiple transcript variants. A related pseudogene has
            been identified on chromosome X. [provided by RefSeq, Jul 2013].
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Both variants 1 and 2 encode the same protein.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC001003.2, BU170242.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000376919.4/ ENSP00000366118.3
            RefSeq Select criteria :: based on expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1114              BC150487.2         23-1136
            1115-1223           BQ774004.1         19-127              c
FEATURES             Location/Qualifiers
     source          1..1223
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp11.23"
     gene            1..1223
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /note="SSX family member 1"
                     /db_xref="GeneID:6756"
                     /db_xref="HGNC:HGNC:11335"
                     /db_xref="MIM:312820"
     exon            1..41
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     exon            42..130
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     CDS             62..628
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /note="cancer/testis antigen family 5, member 1; sarcoma,
                     synovial, X-chromosome-related 1; cancer/testis antigen
                     5.1; synovial sarcoma, X breakpoint 1"
                     /codon_start=1
                     /product="protein SSX1"
                     /protein_id="NP_005626.1"
                     /db_xref="CCDS:CCDS14290.1"
                     /db_xref="GeneID:6756"
                     /db_xref="HGNC:HGNC:11335"
                     /db_xref="MIM:312820"
                     /translation="MNGDDTFAKRPRDDAKASEKRSKAFDDIATYFSKKEWKKMKYSE
                     KISYVYMKRNYKAMTKLGFKVTLPPFMCNKQATDFQGNDFDNDHNRRIQVEHPQMTFG
                     RLHRIIPKIMPKKPAEDENDSKGVSEASGPQNDGKQLHPPGKANISEKINKRSGPKRG
                     KHAWTHRLRERKQLVIYEEISDPEEDDE"
     exon            131..245
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     exon            246..341
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     exon            342..391
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     exon            392..527
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     exon            528..632
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     exon            633..1223
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1203..1208
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /note="hexamer: AATAAA"
     polyA_site      1223
                     /gene="SSX1"
                     /gene_synonym="CT5.1; SPGFX5; SSRC"
                     /note="major polyA site"
ORIGIN      
        1 accactgctg ccgacctcgc aaccactgct ttgtctctga agtgagactg ctcctggtgc
       61 catgaacgga gacgacacct ttgcaaagag acccagggat gatgctaaag catcagagaa
      121 gagaagcaag gcctttgatg atattgccac atacttctct aagaaagagt ggaaaaagat
      181 gaaatactcg gagaaaatca gctatgtgta tatgaagaga aactataagg ccatgactaa
      241 actaggtttc aaagtcaccc tcccaccttt catgtgtaat aaacaggcca cagacttcca
      301 ggggaatgat tttgataatg accataaccg caggattcag gttgaacatc ctcagatgac
      361 tttcggcagg ctccacagaa tcatcccgaa gatcatgccc aagaagccag cagaggacga
      421 aaatgattcg aagggagtgt cagaagcatc tggcccacaa aacgatggga aacaactgca
      481 ccccccagga aaagcaaata tttctgagaa gattaataag agatctggac ccaaaagggg
      541 gaaacatgcc tggacccaca gactgcgtga gagaaagcag ctggtgattt atgaagagat
      601 cagtgaccct gaggaagatg acgagtaact cccctggggg atacgacaca tgcccttgat
      661 gagaagcaga acgtggtgac ctttcacgaa catgggcatg gctgcggctc cctcgtcatc
      721 aggtgcatag caagtgaaag caagtgttca caacggtgaa acttgagcgt catttttctt
      781 agtgtgccaa gagttcgatg ttagtgtttc cattgtattt tcttacagtg tgccattctg
      841 ttagatacta tccttataat tgatgagcaa gacatactga atgcatattt cggtttgtgt
      901 atccatgcac ctacgtcaga aaacaagtat tgtcaggtat tctctccata gaacagcact
      961 atcctcatct ctccccagat gtgactactg agggcagttc tgagtgttta atttcagact
     1021 ttttcctctg catttacaca cacacacaca cacacacgca cacacacaca ccaagtacca
     1081 gtataagcat ctcccatctg cttttcccat tgccatgcgt cctggtcaag cccccctcac
     1141 tctgtttcct gttcagcatg tactcccctc atccgattcc cctgtatcag tcactgacag
     1201 ttaataaacc tttgcaaacg ttc
//
