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    Ss18 SS18 subunit of BAF chromatin remodeling complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361295, updated on 17-Aug-2024

    Summary

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    Official Symbol
    Ss18provided by RGD
    Official Full Name
    SS18 subunit of BAF chromatin remodeling complexprovided by RGD
    Primary source
    RGD:1311919
    See related
    EnsemblRapid:ENSRNOG00000016800 AllianceGenome:RGD:1311919
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable nuclear receptor coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including ephrin receptor signaling pathway; intracellular signal transduction; and neuronal stem cell population maintenance. Predicted to be located in microtubule cytoskeleton. Predicted to be part of SWI/SNF complex and npBAF complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in synovial sarcoma. Orthologous to human SS18 (SS18 subunit of BAF chromatin remodeling complex). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 261.2), Lung (RPKM 253.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ss18 in Genome Data Viewer
    Location:
    18p13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (6047619..6169151, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (5773042..5835696, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (6020267..6083055, complement)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120098243 Neighboring gene uncharacterized LOC120098206 Neighboring gene mitochondrial ribosomal protein S18B, pseudogene 1 Neighboring gene proteasome 20S subunit alpha 8 Neighboring gene TATA-box binding protein associated factor 4b Neighboring gene small nucleolar RNA SNORA17

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Genetic variability and rodent models of human aging. Phelan JP. Exp Gerontol, 1992. PMID 1521591
    2. 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, et al. Nat Genet, 1994 Aug. PMID 7951320
    3. Synovial sarcoma translocation (SYT) encodes a nuclear receptor coactivator. Iwasaki T, et al. Endocrinology, 2005 Sep. PMID 15919756
    4. SYT-SSX1 (synovial sarcoma translocated) regulates PIASy ligase activity to cause overexpression of NCOA3 protein. Sun Y, et al. J Biol Chem, 2011 May 27. PMID 21454665, Free PMC Article
    5. The synovial sarcoma SYT-SSX2 oncogene remodels the cytoskeleton through activation of the ephrin pathway. Barco R, et al. Mol Biol Cell, 2007 Oct. PMID 17686994, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables nuclear receptor coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within cell morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within ephrin receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within intracellular signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within microtubule cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuronal stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of npBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein SSXT
    Names
    SS18, nBAF chromatin remodeling complex subunit
    synovial sarcoma translocation, Chromosome 18

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001100900.1 → NP_001094370.1  protein SSXT

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/TrEMBL
      D4ABC5, Q5XI66
      Related
      ENSRNOP00000038436.3, ENSRNOT00000032454.5
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086036.1 Reference GRCr8

      Range
      6047619..6169151 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063277462.1 → XP_063133532.1  protein SSXT isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZJA9, A6KLT7

    2. XM_006254438.5 → XP_006254500.1  protein SSXT isoform X2

      UniProtKB/TrEMBL
      Q5XI66
      Related
      ENSRNOP00000076846.2, ENSRNOT00000113631.2
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    3. XM_006254437.5 → XP_006254499.1  protein SSXT isoform X3

      UniProtKB/TrEMBL
      A0A8I6B652
      Related
      ENSRNOP00000097716.1, ENSRNOT00000100800.2
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)
    Nucleotide Protein Strain
    Heading Accession and Version

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