LOCUS       NM_001161369            3017 bp    mRNA    linear   ROD 12-JUN-2024
DEFINITION  Mus musculus SS18, subunit of BAF chromatin remodeling complex
            (Ss18), transcript variant 2, mRNA.
ACCESSION   NM_001161369
VERSION     NM_001161369.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3017)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 3017)
  AUTHORS   Fulton,S.L., Wenderski,W., Lepack,A.E., Eagle,A.L., Fanutza,T.,
            Bastle,R.M., Ramakrishnan,A., Hays,E.C., Neal,A., Bendl,J.,
            Farrelly,L.A., Al-Kachak,A., Lyu,Y., Cetin,B., Chan,J.C.,
            Tran,T.N., Neve,R.L., Roper,R.J., Brennand,K.J., Roussos,P.,
            Schimenti,J.C., Friedman,A.K., Shen,L., Blitzer,R.D., Robison,A.J.,
            Crabtree,G.R. and Maze,I.
  TITLE     Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn
            mouse model of Down syndrome
  JOURNAL   Nat Commun 13 (1), 6384 (2022)
   PUBMED   36289231
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3017)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3017)
  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   5  (bases 1 to 3017)
  AUTHORS   Gatchalian,J., Malik,S., Ho,J., Lee,D.S., Kelso,T.W.R.,
            Shokhirev,M.N., Dixon,J.R. and Hargreaves,D.C.
  TITLE     A non-canonical BRD9-containing BAF chromatin remodeling complex
            regulates naive pluripotency in mouse embryonic stem cells
  JOURNAL   Nat Commun 9 (1), 5139 (2018)
   PUBMED   30510198
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3017)
  AUTHORS   McClive,P.J., Hurley,T.M., Sarraj,M.A., van den Bergen,J.A. and
            Sinclair,A.H.
  TITLE     Subtractive hybridisation screen identifies sexually dimorphic gene
            expression in the embryonic mouse gonad
  JOURNAL   Genesis 37 (2), 84-90 (2003)
   PUBMED   14595844
REFERENCE   7  (bases 1 to 3017)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   8  (bases 1 to 3017)
  AUTHORS   de Bruijn,D.R., Kater-Baats,E., Eleveld,M., Merkx,G. and Geurts Van
            Kessel,A.
  TITLE     Mapping and characterization of the mouse and human SS18 genes, two
            human SS18-like genes and a mouse Ss18 pseudogene
  JOURNAL   Cytogenet Cell Genet 92 (3-4), 310-319 (2001)
   PUBMED   11435705
REFERENCE   9  (bases 1 to 3017)
  AUTHORS   de Bruijn,D.R., Baats,E., Zechner,U., de Leeuw,B., Balemans,M.,
            Olde Weghuis,D., Hirning-Folz,U. and Geurts van Kessel,A.G.
  TITLE     Isolation and characterization of the mouse homolog of SYT, a gene
            implicated in the development of human synovial sarcomas
  JOURNAL   Oncogene 13 (3), 643-648 (1996)
   PUBMED   8760306
REFERENCE   10 (bases 1 to 3017)
  AUTHORS   Phelan,J.P.
  TITLE     Genetic variability and rodent models of human aging
  JOURNAL   Exp Gerontol 27 (2), 147-159 (1992)
   PUBMED   1521591
  REMARK    Review article
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BY021731.1, CF104258.1 and BC065062.1.
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon compared to variant 1. The resulting isoform (2) has the same
            N- and C-termini but is shorter compared to 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 :: BC065062.1, AK083622.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN02146467 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-22                BY021731.1         94-115
            23-163              CF104258.1         21-161
            164-3017            BC065062.1         1-2854
FEATURES             Location/Qualifiers
     source          1..3017
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="18"
                     /map="18 8.14 cM"
     gene            1..3017
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /note="SS18, subunit of BAF chromatin remodeling complex"
                     /db_xref="GeneID:268996"
                     /db_xref="MGI:MGI:107708"
     exon            1..248
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     CDS             180..1343
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /note="isoform 2 is encoded by transcript variant 2;
                     synovial sarcoma, translocated to X chromosome; protein
                     SSXT; synovial sarcoma associated SS18-gamma; SS18, nBAF
                     chromatin remodeling complex subunit; synovial sarcoma
                     associated SS18-beta; synovial sarcoma associated
                     SS18-delta; synovial sarcoma-associated Ss18-alpha;
                     synovial sarcoma translocation, Chromosome 18"
                     /codon_start=1
                     /product="protein SSXT isoform 2"
                     /protein_id="NP_001154841.1"
                     /db_xref="CCDS:CCDS57116.1"
                     /db_xref="GeneID:268996"
                     /db_xref="MGI:MGI:107708"
                     /translation="MSVAFAAPRQRGKGEITPAAIQKMLDENNHLIQCIMDYQNKGKA
                     SECSQYQQILHTNLVYLATIADSNQNMQSLLPAPPTQTMPMGPGGMSQSGPPPPPRSH
                     NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPSQLSMTNSSMNMPSSSHGSM
                     GGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMP
                     PGGAQHYQGQQAPMGLMGQVNQGSHMMGQRQMPPYRPPQQGPPQQYSGQEDYYGDQYS
                     HGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQSY
                     GPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNYQQ"
     exon            249..325
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            326..410
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            411..564
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            565..786
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            787..954
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            955..1059
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            1060..1182
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            1183..1316
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     exon            1317..2999
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2978..2983
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /note="hexamer: AATAAA"
     polyA_site      2999
                     /gene="Ss18"
                     /gene_synonym="D130059H17; Ssxt; Syt"
                     /note="major polyA site"
ORIGIN      
        1 ccttgctggg agctgcggct cagcgttaag gccaagccgg ccagcgaggg acgcggcccg
       61 ggagcatcct ccccccaccg cgcgccctaa ggtggaactg cccggaggcg ggcgtcgggc
      121 ccccagctcc gcgggccctg gagcgctcgg gactcgctga tcgcgggctc ggcggcaaca
      181 tgtctgtggc gttcgcagcc ccgaggcagc ggggcaaggg cgaaatcacg cccgccgcca
      241 tccagaagat gctggatgaa aacaaccatc ttattcagtg tataatggac tatcagaaca
      301 aagggaaggc ctcggagtgc tcgcagtatc agcagatatt gcatacaaac ctggtatacc
      361 ttgctacaat agcagactct aatcaaaata tgcagtctct cttaccagca ccgcccacac
      421 agactatgcc aatgggtcct ggagggatga gtcagagtgg ccctccaccc cctccccgct
      481 ctcacaacat gccttcagat ggaatggtgg gtgggggccc tcctgcacca cacatgcaga
      541 accagatgaa cggccagatg cctgggccta accatatgcc aatgcaggga cctggaccca
      601 gtcagctcag catgacaaac agctccatga atatgccttc aagtagccat ggctccatgg
      661 gaggttacaa ccattctgtg ccgtcatccc agagcatgcc cgtgcagaac cagatgacaa
      721 tgagtcaggg gcagccaatg ggaaactatg gtcccagacc aaacatgaat atgcaaccaa
      781 atcaagggcc gatgatgcac cagcagcctc cttctcagca gtacaatatg ccacctggag
      841 gggcacagca ttaccaagga cagcaggcgc ccatggggct gatgggccaa gttaaccaag
      901 gcagtcacat gatgggccag cgacagatgc ctccctacag acctccgcaa cagggcccac
      961 cacagcagta ctcaggccag gaagactatt atggggacca atacagtcat ggtggacaag
     1021 gtcctccaga aggcatgaac cagcaatatt accctgatgg aaactcccag tatggccaac
     1081 agcaagacgc ttaccaggga ccacctccac agcaaggata cccaccccag cagcagcagt
     1141 acccgggaca gcagggatac ccagggcagc agcagagcta tggtccttcg cagggcggtc
     1201 caggtcctca gtatcctaat tatcctcagg gtcaaggtca gcagtatggg ggctatagac
     1261 caacacagcc aggaccaccc cagccacccc agcagaggcc ttatgggtac gaccagggac
     1321 agtatggaaa ttaccagcag tgaaaatgtc cttacattcc aatagccagt acctattagc
     1381 aggcacgttg tcacagcact gcaccatgga cacccccctg ggaagactcc ttccattcca
     1441 gctaggtttt tgggaaaacc tttggctaag tggctgcttc gtcagcaagt agctgttatg
     1501 gtttagtttg taaaggcttc gtagctaccg atgcacctga tttcacgttt ctactctaga
     1561 tggcaacatt ggacagaaaa tgcattgacg tgaggagttt gcagcggttt cagaactgtg
     1621 ctgcaaatgg actgtcacag cctgaaaggt gtgagcagct gggtgtgtgt tcgcggagct
     1681 tcagggggtt tcatactttt ccaccgatta ttttgtaagg ggaaggggga aatgtacact
     1741 ttttacagca gcaatatttt gtctattatg tttatttcat gtgataaata tgcaaagcgg
     1801 tacactacac actgggcaga atcagaaccc ctgttaatgt ggagtgtggt agatgctcgg
     1861 tgctgtggtg ctctgaagac aggcgagggg aggcagaagc ccaccacagg cccgctgtta
     1921 gttcttagag gaaactcctc tctctcttat ctaccagatt agcaagggcg ctgtgataca
     1981 gttttttgag tacaaagaca ttttttaaaa agccttccag ttttgtgcat taaaaccttt
     2041 ttgtaaatat ggtttataat actgttttca aacgcaaggc aataattatg ttgcatctgt
     2101 gaactttggc aggtttgtgt aaaaggaggg aagcctctct taaaacagca ataacagaaa
     2161 aggaggaagc gggatgtttt taccttgtct tgtaatcagg gagctctcac cacgtcagag
     2221 aggaggcagc attggtctca ccttactgtt ttttacatta ccatgattgg ttcatggagc
     2281 agggaggagt ccacgagact tcacacgctt gtgctttaac tttcttaact gggcacaagc
     2341 aaagggcgcc ttcgtgttcc tctcttcatc ttagttaatg cgcgaggaaa atgctttgat
     2401 ggccatttct cattcgcact gaaagccgag aggtgacatt ttacggtttc ttgtttttaa
     2461 gcacgacata cttaatcatt atttgagact gattatttta gctaaatttg gggatatgcc
     2521 atggggcaag aaaacatgta ctgagagatt tctaaacaca tctatttaag catactttaa
     2581 aaatatctag cccaaaggta agttgctgta tcctcacagt tgtctgcatc cagggaatat
     2641 gactgaatat aacatatctt tgtaattgaa ttagtttttg ccacttctaa ctgaaaacag
     2701 aacagaagga gtgccataaa tgcaaagaag caaagtgtac tgttgtcaac atactgtaat
     2761 cagaggaggg gtttcaatgt gtctggatga gagtgtgtgt gtttaaggtc agagtatagg
     2821 gtgttcttca acttggacag tagaaaatag gcatcaagtg tgaaccggtg aggcgtggac
     2881 agccttcttg tgactgagat gcttgtaagt tctgtgccag gttctccacc actgtgtact
     2941 ttattgctat ttaaaactgt atcaactcta acgaaagaat aaattatttg tgattttaaa
     3001 aaaaaaaaaa aaaaaaa
//
