LOCUS       NM_175723               1293 bp    mRNA    linear   PRI 21-SEP-2024
DEFINITION  Homo sapiens SSX family member 5 (SSX5), transcript variant 2,
            mRNA.
ACCESSION   NM_175723
VERSION     NM_175723.2
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 1293)
  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   2  (bases 1 to 1293)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1293)
  AUTHORS   Chen,S., Fragoza,R., Klei,L., Liu,Y., Wang,J., Roeder,K., Devlin,B.
            and Yu,H.
  TITLE     An interactome perturbation framework prioritizes damaging missense
            mutations for developmental disorders
  JOURNAL   Nat Genet 50 (7), 1032-1040 (2018)
   PUBMED   29892012
REFERENCE   4  (bases 1 to 1293)
  AUTHORS   Smith,H.A., Cronk,R.J., Lang,J.M. and McNeel,D.G.
  TITLE     Expression and immunotherapeutic targeting of the SSX family of
            cancer-testis antigens in prostate cancer
  JOURNAL   Cancer Res 71 (21), 6785-6795 (2011)
   PUBMED   21880588
REFERENCE   5  (bases 1 to 1293)
  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 1293)
  AUTHORS   Chen,C.H., Chen,G.J., Lee,H.S., Huang,G.T., Yang,P.M., Tsai,L.J.,
            Chen,D.S. and Sheu,J.C.
  TITLE     Expressions of cancer-testis antigens in human hepatocellular
            carcinomas
  JOURNAL   Cancer Lett 164 (2), 189-195 (2001)
   PUBMED   11179834
REFERENCE   7  (bases 1 to 1293)
  AUTHORS   dos Santos,N.R., de Bruijn,D.R. and van Kessel,A.G.
  TITLE     Molecular mechanisms underlying human synovial sarcoma development
  JOURNAL   Genes Chromosomes Cancer 30 (1), 1-14 (2001)
   PUBMED   11107170
  REMARK    Review article
REFERENCE   8  (bases 1 to 1293)
  AUTHORS   dos Santos,N.R., Torensma,R., de Vries,T.J., Schreurs,M.W., de
            Bruijn,D.R., Kater-Baats,E., Ruiter,D.J., Adema,G.J., van
            Muijen,G.N. and van Kessel,A.G.
  TITLE     Heterogeneous expression of the SSX cancer/testis antigens in human
            melanoma lesions and cell lines
  JOURNAL   Cancer Res 60 (6), 1654-1662 (2000)
   PUBMED   10749136
REFERENCE   9  (bases 1 to 1293)
  AUTHORS   Lasota,J., Jasinski,M., Debiec-Rychter,M., Szadowska,A., Limon,J.
            and Miettinen,M.
  TITLE     Detection of the SYT-SSX fusion transcripts in formaldehyde-fixed,
            paraffin-embedded tissue: a reverse transcription polymerase chain
            reaction amplification assay useful in the diagnosis of synovial
            sarcoma
  JOURNAL   Mod Pathol 11 (7), 626-633 (1998)
   PUBMED   9688183
REFERENCE   10 (bases 1 to 1293)
  AUTHORS   Gure,A.O., Tureci,O., Sahin,U., Tsang,S., Scanlan,M.J., Jager,E.,
            Knuth,A., Pfreundschuh,M., Old,L.J. and Chen,Y.T.
  TITLE     SSX: a multigene family with several members transcribed in normal
            testis and human cancer
  JOURNAL   Int J Cancer 72 (6), 965-971 (1997)
   PUBMED   9378559
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC245047.1, BE896093.1,
            U90842.1 and BC016640.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Aug 13, 2020 this sequence version replaced NM_175723.1.
            
            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. While some of the related SSX
            genes are involved in t(X;18)(p11.2;q11.2) translocations that are
            characteristically found in all synovial sarcomas, this gene does
            not appear to be involved in such translocations. Two transcript
            variants encoding distinct isoforms have been identified for this
            gene. [provided by RefSeq, Jul 2013].
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon in the 5' coding region, compared to variant 1, resulting in
            an isoform (b) that is shorter than isoform a.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR11853558.25124.1,
                                           SRR5189667.81274.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2149178, SAMEA2151119
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000347757.6/ ENSP00000290558.1
            RefSeq Select criteria :: based on manual assertion, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-52                AC245047.1         90497-90548
            53-139              BE896093.1         1-87
            140-140             AC245047.1         91988-91988
            141-453             U90842.1           56-368
            454-454             AC245047.1         97062-97062
            455-916             BC016640.2         512-973
            917-1147            AC245047.1         100696-100926
            1148-1293           BC016640.2         1203-1348
FEATURES             Location/Qualifiers
     source          1..1293
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp11.23"
     gene            1..1293
                     /gene="SSX5"
                     /note="SSX family member 5"
                     /db_xref="GeneID:6758"
                     /db_xref="HGNC:HGNC:11339"
                     /db_xref="MIM:300327"
     exon            1..65
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     exon            66..154
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     CDS             86..652
                     /gene="SSX5"
                     /note="isoform b is encoded by transcript variant 2;
                     protein SSX5; synovial sarcoma, X breakpoint 5"
                     /codon_start=1
                     /product="protein SSX5 isoform b"
                     /protein_id="NP_783729.1"
                     /db_xref="CCDS:CCDS14289.1"
                     /db_xref="GeneID:6758"
                     /db_xref="HGNC:HGNC:11339"
                     /db_xref="MIM:300327"
                     /translation="MNGDDAFVRRPRVGSQIPEKMQKAFDDIAKYFSEKEWEKMKASE
                     KIIYVYMKRKYEAMTKLGFKATLPPFMRNKRVADFQGNDFDNDPNRGNQVEHPQMTFG
                     RLQGIFPKITPEKPAEEGNDSKGVPEASGPQNNGKQLRPSGKLNTSEKVNKTSGPKRG
                     KHAWTHRVRERKQLVIYEEISDPQEDDE"
     exon            155..269
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     exon            270..365
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     exon            366..415
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     exon            416..551
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     exon            552..656
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
     exon            657..1293
                     /gene="SSX5"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 ctctctctct cgatttttcc acagagtacg cacgctctga ttgtttcgat tcttccaaaa
       61 tcagagacag agtgctcccg gtgccatgaa cggagacgat gcctttgtac ggagacctag
      121 ggttggttct caaataccag agaagatgca aaaggccttc gatgatattg ccaaatactt
      181 ctctgagaaa gagtgggaaa agatgaaagc ctcggagaaa atcatctatg tgtatatgaa
      241 gagaaagtat gaggccatga ctaaactagg tttcaaggcc accctcccac ctttcatgcg
      301 taataaacgg gtcgcagact tccaggggaa tgattttgat aatgacccta accgtgggaa
      361 tcaggttgaa catcctcaga tgactttcgg caggctccag ggaatcttcc cgaagatcac
      421 gcccgagaag ccagcagagg aaggaaatga ttcgaaggga gtgccagaag catctggccc
      481 acagaacaat gggaaacagc tgcgcccctc aggaaaacta aatacctctg agaaggttaa
      541 caagacatct ggacccaaaa gggggaaaca tgcctggacc cacagagtgc gtgagagaaa
      601 gcaactggtg atttatgaag agatcagcga ccctcaggaa gatgacgagt aactcccctc
      661 ggggatatga cacatgccca tgatgagaag cagaacgtgg tgacctttca cgaacatggg
      721 catggctgcg gatccctcgt catcaggtgt atagcaagtg aaagcaagtg ttcacaacag
      781 tgaaaagttg agcgtcattt ttcttagtgt gccaagagtt cgatgttagt gtttctgttg
      841 tattttgtta cagtgtgcca ttctgttaga tattagcgtt ttcactgatg agcaagacat
      901 acttaatgca tatttcagtt tgtgtatcca tgcacctacc tcagaaaaca agtatcgtca
      961 ggtattctct gcatagaaca acactaccct cctctcttcc cagatgtgac cactgagggc
     1021 agttctgagt gtttaatttc agattttttc ctctgcattt acacaaacac acacacatgc
     1081 cacacagaca cacatgcgcg cgcgcgcgca cacacacaca cacacacaca cacacacaca
     1141 cacacaccaa gtaccagtat aggcatctcc caactgcttt tccccatgtg tcctggtcaa
     1201 gcccccctca ctctgtttcc tgttcagcat gtactcccct catccgattc ccctctatca
     1261 gtcactgcca gttaataaac ctttgcaaac gtt
//
