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    Ss18 SS18, subunit of BAF chromatin remodeling complex [ Mus musculus (house mouse) ]

    Gene ID: 268996, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Ss18provided by MGI
    Official Full Name
    SS18, subunit of BAF chromatin remodeling complexprovided by MGI
    Primary source
    MGI:MGI:107708
    See related
    Ensembl:ENSMUSG00000037013 AllianceGenome:MGI:107708
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Syt; Ssxt; D130059H17
    Summary
    Predicted to enable nuclear receptor coactivator activity. Acts upstream of or within several processes, including ephrin receptor signaling pathway; microtubule cytoskeleton organization; and neuronal stem cell population maintenance. Located in microtubule cytoskeleton. Part of SWI/SNF complex and npBAF complex. Is expressed in cerebral cortex subventricular zone; cerebral cortex ventricular layer; ovary; and primary sex cord. 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, Oct 2024]
    Expression
    Ubiquitous expression in ovary adult (RPKM 47.3), limb E14.5 (RPKM 38.6) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ss18 in Genome Data Viewer
    Location:
    18 A1; 18 8.14 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (14758686..14817476, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (14625629..14684419, complement)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 52378 Neighboring gene STARR-seq mESC enhancer starr_43874 Neighboring gene predicted pseudogene 6457 Neighboring gene STARR-seq mESC enhancer starr_43875 Neighboring gene predicted gene, 24924 Neighboring gene STARR-seq mESC enhancer starr_43877 Neighboring gene proteasome subunit alpha 8 Neighboring gene STARR-positive B cell enhancer ABC_E1951 Neighboring gene TATA-box binding protein associated factor 4b Neighboring gene non-POU-domain-containing, octamer binding protein pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Isolation and characterization of the mouse homolog of SYT, a gene implicated in the development of human synovial sarcomas. de Bruijn DR, et al. Oncogene, 1996 Aug 1. PMID 8760306
    2. Human synovial sarcoma proto-oncogene Syt is essential for early embryonic development through the regulation of cell migration. Kimura T, et al. Lab Invest, 2009 Jun. PMID 19333234
    3. SS18 regulates pluripotent-somatic transition through phase separation. Kuang J, et al. Nat Commun, 2021 Jul 2. PMID 34215745, Free PMC Article
    4. Targeted disruption of the synovial sarcoma-associated SS18 gene causes early embryonic lethality and affects PPARBP expression. de Bruijn DR, et al. Hum Mol Genet, 2006 Oct 1. PMID 16926188
    5. Genetic variability and rodent models of human aging. Phelan JP. Exp Gerontol, 1992. PMID 1521591

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SS18 regulates pluripotent-somatic transition through phase separation.
      Title: SS18 regulates pluripotent-somatic transition through phase separation.
    2. Syt may contribute to the signaling pathway important for various cellular functions in vivo and in vitro, and we propose that Syt-deficient MEFs would be a powerful means to understand the biological roles of SYT in vitro.
      Title: Human synovial sarcoma proto-oncogene Syt is essential for early embryonic development through the regulation of cell migration.
    3. disruption of the Ss18 gene results in a recessive embryonic lethal phenotype, due to placental failure caused by impairment of placental vascularization and/or chorio-allantoic fusion
      Title: Targeted disruption of the synovial sarcoma-associated SS18 gene causes early embryonic lethality and affects PPARBP expression.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (1)  1 citation

    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 MGI

    Function Evidence Code Pubs
    enables nuclear receptor coactivator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    acts_upstream_of_or_within cell morphogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within cell morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within cytoskeleton organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within ephrin receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within intracellular signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within microtubule cytoskeleton organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within neuronal stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cell population proliferation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within response to xenobiotic stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of GBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of npBAF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    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 associated SS18-beta
    synovial sarcoma associated SS18-delta
    synovial sarcoma associated SS18-gamma
    synovial sarcoma translocation, Chromosome 18
    synovial sarcoma, translocated to X chromosome
    synovial sarcoma-associated Ss18-alpha

    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_001161369.1 → NP_001154841.1  protein SSXT isoform 2

      See identical proteins and their annotated locations for NP_001154841.1

      Status: VALIDATED

      Description
      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.
      Source sequence(s)
      BC065062, BY021731, CF104258
      Consensus CDS
      CCDS57116.1
      UniProtKB/TrEMBL
      Q6P1I1, Q8BJJ6
      Related
      ENSMUSP00000089673.4, ENSMUST00000092041.11
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    2. NM_001161370.1 → NP_001154842.1  protein SSXT isoform 3

      See identical proteins and their annotated locations for NP_001154842.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK051601, BC065062, BY021731, CF104258
      Consensus CDS
      CCDS50225.1
      UniProtKB/TrEMBL
      Q8BJH8, Q8BKL1
      Related
      ENSMUSP00000047867.7, ENSMUST00000040964.13
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    3. NM_001161371.1 → NP_001154843.1  protein SSXT isoform 4

      See identical proteins and their annotated locations for NP_001154843.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK052476, BC065062, BY021731, CF104258
      Consensus CDS
      CCDS89193.1
      UniProtKB/TrEMBL
      Q8VHA8, Q8VHA9
      Related
      ENSMUSP00000157096.2, ENSMUST00000234524.2
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    4. NM_009280.2 → NP_033306.2  protein SSXT isoform 1

      See identical proteins and their annotated locations for NP_033306.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK166053, BC065062, BY021731, CF104258
      Consensus CDS
      CCDS29070.1
      UniProtKB/Swiss-Prot
      Q3TM96, Q62280
      UniProtKB/TrEMBL
      Q8BJH8
      Related
      ENSMUSP00000046320.8, ENSMUST00000040924.9
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000084.7 Reference GRCm39 C57BL/6J

      Range
      14758686..14817476 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030250469.2 → XP_030106329.1  protein SSXT isoform X2

      Conserved Domains (2) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)
      pfam09770
      Location:76 → 193
      PAT1; Topoisomerase II-associated protein PAT1

    2. XM_006525948.4 → XP_006526011.1  protein SSXT isoform X1

      UniProtKB/TrEMBL
      Q8VHB0
      Conserved Domains (3) summary
      TIGR01628
      Location:163 → 268
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)
      pfam11593
      Location:68 → 217
      Med3; Mediator complex subunit 3 fungal
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q62280.2 GenPept UniProtKB/Swiss-Prot:Q62280

    Gene LinkOut

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