LOCUS       NM_001007559            3402 bp    mRNA    linear   PRI 03-OCT-2024
DEFINITION  Homo sapiens SS18 subunit of BAF chromatin remodeling complex
            (SS18), transcript variant 1, mRNA.
ACCESSION   NM_001007559
VERSION     NM_001007559.3
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 3402)
  AUTHORS   Warmke,L.M., Strike,S.A., Fayad,L.M., Ahlawat,S., Liu,Y.J.,
            Mata,D.A., Rooper,L., Baraban,E., Zou,Y.S. and Gross,J.M.
  TITLE     Undifferentiated Round Cell Sarcoma With CRTC1::SS18 Fusion:
            Expanding Clinicopathologic Features of a Rare Translocation
            Sarcoma With Prominent Desmoplastic Stroma
  JOURNAL   Mod Pathol 37 (9), 100555 (2024)
   PUBMED   38972355
  REMARK    GeneRIF: Undifferentiated Round Cell Sarcoma With CRTC1::SS18
            Fusion: Expanding Clinicopathologic Features of a Rare
            Translocation Sarcoma With Prominent Desmoplastic Stroma.
REFERENCE   2  (bases 1 to 3402)
  AUTHORS   Challa,B., Mohanty,S.K., Jha,S., Sampat,N.Y., Sardana,R., Lobo,A.,
            Sharma,S., Arora,S., Rath,D., Munjal,G., Pattnaik,N., Jain,D.,
            Jain,E., Dewan,A., Dixit,M., Malik,V., Shinde,S., Balzer,B.L. and
            Parwani,A.
  TITLE     SS18-SSX Expression in a Contemporary Cohort of Primary Renal
            Synovial Sarcoma: A Multi-Institutional Experience of Fourteen
            Patients
  JOURNAL   Int J Surg Pathol 31 (7), 1232-1243 (2023)
   PUBMED   36591871
  REMARK    GeneRIF: SS18-SSX Expression in a Contemporary Cohort of Primary
            Renal Synovial Sarcoma: A Multi-Institutional Experience of
            Fourteen Patients.
REFERENCE   3  (bases 1 to 3402)
  AUTHORS   Weinreb,I., Hahn,E., Dickson,B.C., Rooper,L.M., Rupp,N.J.,
            Freiberger,S.N., Lubin,D., Gagan,J. and Bishop,J.A.
  TITLE     Microcribriform Adenocarcinoma of Salivary Glands: A Unique Tumor
            Entity Characterized by an SS18::ZBTB7A Fusion
  JOURNAL   Am J Surg Pathol 47 (2), 194-201 (2023)
   PUBMED   36221318
  REMARK    GeneRIF: Microcribriform Adenocarcinoma of Salivary Glands: A
            Unique Tumor Entity Characterized by an SS18::ZBTB7A Fusion.
REFERENCE   4  (bases 1 to 3402)
  AUTHORS   Tay,T.K.Y., Sukma,N.B., Lim,T.H., Kuick,C.H., Goh,J.Y. and
            Chang,K.T.E.
  TITLE     Correlating SS18-SSX immunohistochemistry (IHC) with SS18
            fluorescent in situ hybridization (FISH) in synovial sarcomas: a
            study of 36 cases
  JOURNAL   Virchows Arch 479 (4), 785-793 (2021)
   PUBMED   34091760
  REMARK    GeneRIF: Correlating SS18-SSX immunohistochemistry (IHC) with SS18
            fluorescent in situ hybridization (FISH) in synovial sarcomas: a
            study of 36 cases.
REFERENCE   5  (bases 1 to 3402)
  AUTHORS   Kuang,J., Zhai,Z., Li,P., Shi,R., Guo,W., Yao,Y., Guo,J., Zhao,G.,
            He,J., Xu,S., Wu,C., Yu,S., Zhou,C., Wu,L., Qin,Y., Cai,B., Li,W.,
            Wu,Z., Li,X., Chu,S., Yang,T., Wang,B., Cao,S., Li,D., Zhang,X.,
            Chen,J., Liu,J. and Pei,D.
  TITLE     SS18 regulates pluripotent-somatic transition through phase
            separation
  JOURNAL   Nat Commun 12 (1), 4090 (2021)
   PUBMED   34215745
  REMARK    GeneRIF: SS18 regulates pluripotent-somatic transition through
            phase separation.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3402)
  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 3402)
  AUTHORS   Brett,D., Whitehouse,S., Antonson,P., Shipley,J., Cooper,C. and
            Goodwin,G.
  TITLE     The SYT protein involved in the t(X;18) synovial sarcoma
            translocation is a transcriptional activator localised in nuclear
            bodies
  JOURNAL   Hum Mol Genet 6 (9), 1559-1564 (1997)
   PUBMED   9285794
REFERENCE   8  (bases 1 to 3402)
  AUTHORS   Fligman,I., Lonardo,F., Jhanwar,S.C., Gerald,W.L., Woodruff,J. and
            Ladanyi,M.
  TITLE     Molecular diagnosis of synovial sarcoma and characterization of a
            variant SYT-SSX2 fusion transcript
  JOURNAL   Am J Pathol 147 (6), 1592-1599 (1995)
   PUBMED   7495284
REFERENCE   9  (bases 1 to 3402)
  AUTHORS   Clark,J., Rocques,P.J., Crew,A.J., Gill,S., Shipley,J., Chan,A.M.,
            Gusterson,B.A. and Cooper,C.S.
  TITLE     Identification of novel genes, SYT and SSX, involved in the
            t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma
  JOURNAL   Nat Genet 7 (4), 502-508 (1994)
   PUBMED   7951320
REFERENCE   10 (bases 1 to 3402)
  AUTHORS   Shipley,J.M., Clark,J., Crew,A.J., Birdsall,S., Rocques,P.J.,
            Gill,S., Chelly,J., Monaco,A.P., Abe,S., Gusterson,B.A. et al.
  TITLE     The t(X;18)(p11.2;q11.2) translocation found in human synovial
            sarcomas involves two distinct loci on the X chromosome
  JOURNAL   Oncogene 9 (5), 1447-1453 (1994)
   PUBMED   8152806
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AU279615.1, AF343880.1, X79201.1, AC091021.8 and AW081610.1.
            
            On Nov 22, 2018 this sequence version replaced NM_001007559.2.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            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 :: SRR1660805.159235.1,
                                           SRR1660805.208549.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN03267770 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000415083.7/ ENSP00000414516.2
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-35                AU279615.1         40-74
            36-1535             AF343880.1         4-1503
            1536-1807           X79201.1           1414-1685
            1808-1808           AC091021.8         132101-132101
            1809-3041           X79201.1           1687-2919
            3042-3402           AW081610.1         5-365               c
FEATURES             Location/Qualifiers
     source          1..3402
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="18"
                     /map="18q11.2"
     gene            1..3402
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /note="SS18 subunit of BAF chromatin remodeling complex"
                     /db_xref="GeneID:6760"
                     /db_xref="HGNC:HGNC:11340"
                     /db_xref="MIM:600192"
     exon            1..113
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     CDS             45..1301
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /note="isoform 1 is encoded by transcript variant 1;
                     protein SSXT; synovial sarcoma, translocated to X
                     chromosome; SS18, nBAF chromatin remodeling complex
                     subunit; synovial sarcoma translocation, chromosome 18;
                     synovial sarcoma translocated to X chromosome protein"
                     /codon_start=1
                     /product="protein SSXT isoform 1"
                     /protein_id="NP_001007560.1"
                     /db_xref="CCDS:CCDS32807.1"
                     /db_xref="GeneID:6760"
                     /db_xref="HGNC:HGNC:11340"
                     /db_xref="MIM:600192"
                     /translation="MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKT
                     SECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSH
                     NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSM
                     GGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMP
                     QGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYS
                     HGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQD
                     AYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRP
                     TQPGPPQPPQQRPYGYDQGQYGNYQQ"
     exon            114..190
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            191..275
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            276..429
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            430..651
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            652..819
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            820..924
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            925..1017
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            1018..1140
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            1141..1274
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     exon            1275..3402
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3381..3386
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /note="hexamer: AATAAA"
     polyA_site      3402
                     /gene="SS18"
                     /gene_synonym="SMARCL1; SSXT; SYT"
                     /note="major polyA site"
ORIGIN      
        1 acccggagcg ctcgggactt gccgatagtg gtgacggcgg caacatgtct gtggctttcg
       61 cggccccgag gcagcgaggc aagggggaga tcactcccgc tgcgattcag aagatgttgg
      121 atgacaataa ccatcttatt cagtgtataa tggactctca gaataaagga aagacctcag
      181 agtgttctca gtatcagcag atgttgcaca caaacttggt ataccttgct acaatagcag
      241 attctaatca aaatatgcag tctcttttac cagcaccacc cacacagaat atgcctatgg
      301 gtcctggagg gatgaatcag agcggccctc ccccacctcc acgctctcac aacatgcctt
      361 cagatggaat ggtaggtggg ggtcctcctg caccgcacat gcagaaccag atgaacggcc
      421 agatgcctgg gcctaaccat atgcctatgc agggacctgg acccaatcaa ctcaatatga
      481 caaacagttc catgaatatg ccttcaagta gccatggatc catgggaggt tacaaccatt
      541 ctgtgccatc atcacagagc atgccagtac agaatcagat gacaatgagt cagggacaac
      601 caatgggaaa ctatggtccc agaccaaata tgagtatgca gccaaaccaa ggtccaatga
      661 tgcatcagca gcctccttct cagcaataca atatgccaca gggaggcgga cagcattacc
      721 aaggacagca gccacctatg ggaatgatgg gtcaagttaa ccaaggcaat catatgatgg
      781 gtcagagaca gattcctccc tatagacctc ctcaacaggg cccaccacag cagtactcag
      841 gccaggaaga ctattacggg gaccaataca gtcatggtgg acaaggtcct ccagaaggca
      901 tgaaccagca atattaccct gatggtcata atgattacgg ttatcagcaa ccgtcgtatc
      961 ctgaacaagg ctacgatagg ccttatgagg attcctcaca acattactac gaaggaggaa
     1021 attcacagta tggccaacag caagatgcat accagggacc acctccacaa cagggatatc
     1081 caccccagca gcagcagtac ccagggcagc aaggttaccc aggacagcag cagggctacg
     1141 gtccttcaca gggtggtcca ggtcctcagt atcctaacta cccacaggga caaggtcagc
     1201 agtatggagg atatagacca acacagcctg gaccaccaca gccaccccag cagaggcctt
     1261 atggatatga ccagggacag tatggaaatt accagcagtg aaaaagtact tacattccag
     1321 tagccagtat ctattagcag ccatattgtc acctcagcac tgtggacacc tccctgtgaa
     1381 gagatccttc cattccatct agtttttgga aaaaccttgt ggataagtgg ctgtttcatc
     1441 agtaagcagc ctttgtggtt tagttataaa aggctttagt agctcaaaaa tactcttgat
     1501 ttcacatttc tactctagat ggcaacattg gacagaaaat gcaatgacat aaccaatttg
     1561 taatgatttt ggaactgtgt ttcaaatgga ctgttacaga ctgaaaggtg tgaacagctt
     1621 tgtatgttta tgaagggtaa gggaatttaa tacttttcca cagatttttt tgtaagggga
     1681 agagggaaat gtacactttt tacagcagca atattttgta tattatgttt atttcatgtg
     1741 gtgaatatgc aaggcggtac actacgcact ggacagcatc agaaatcctc tgttaatgtg
     1801 gactggaaca tggtagatgc ttgattgttt tggtctcaaa atggtgtgct ataaagataa
     1861 aggtgagggg aagacaaagc acaccatatg tccactgttc tgttctcata gaggaaattc
     1921 aaatcccttt tatctattag ataatcaagg gcactgtgat acagttttga gtaaaaagac
     1981 attttttaaa agccttccag ttttgtggat taaacctttt tataaagatc atttataata
     2041 ctgttttaaa atgtgaggca ataagaatta ctttgtgttg gatctgagga ggctttggta
     2101 aaacagtttc atctaaatga aagtggtaat cctcttctaa aatagcaata actgaaaatg
     2161 aaagtgttaa ttttaccttg tttgagttat cagggaactt agtaagtaat atcaaagcat
     2221 tttataaatg atatcaaaga agagtcaaca ttgatccagt cattttattt tgtaatattg
     2281 agggataatt ggttattaaa ctgaatagtt caggagactt tacaaacctt tgtttcaact
     2341 ttcttatctg gaaataatat catttataaa gggacacttt tatgtttttc ccttttttat
     2401 gttggttgat ataacacaaa gagatattta ggaaaatgct tattgatgag gtttattcta
     2461 tctgttttta aagcaccgag gttgcattct agataacctt gtttattagc atggcatatt
     2521 ttaatcatta tttgagactg tcctgtgcct gattatttta gctaaattca gggagattgc
     2581 gtggggcagg aaagcatgca ttgaaaaatt tctaaccacg gttatttaag cataatctga
     2641 aaacatctag cccaaaggta agttgctatt ttcatcacag ttgcctatgc ccagggaata
     2701 agatgtattc tttataattg aattggtttt tcccacgtct aactggaaac aaaacagaag
     2761 gggcgtcata aatttgaata agcagaacat actgttctca acatactgta atcaaaagga
     2821 ggaatttcag tgggtctctg tgtgtgtatg agagagagag tgtgtgtttg tgtgtttcaa
     2881 ggtcagaaca ggtttttttg tttttgtttt ttgttctttg tttttttttt tgagatggag
     2941 tcttgctctt gtcgcccagg ctggagtgca gtggcgcaat ctcagctcac tgcaacctcc
     3001 gcctcccagg ttcaagcagt tctcctgcct cagcctcctg agtagctggg atgacaggca
     3061 cccgccacca cacccagcta atttttgtac ttttagtaga gacgaggttt cgccatgttg
     3121 gccaggctgg tctcgaactc ctgacctcag gtgatccacc cgcctcggcc ttccaaagtg
     3181 ctgggattac aggcgtgagc caccgtgcct ggccagaata ggttttttct ttcaacttga
     3241 tcagtagaaa atggacatca agtttgaaca gataaatcat ggacagcctt attgtgattg
     3301 aaatgcttgt aggttctgtg ccaattttcc accactgtgt actttgttgc tatttaaaac
     3361 tgtatcaact ctaacggaag aataaattat ttgtgatttt aa
//
