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

Gene ID: 268996, updated on 11-Apr-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; intracellular signal transduction; and neuronal stem cell population maintenance. Located in microtubule cytoskeleton. Part of SWI/SNF complex and npBAF complex. Is expressed in 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, Apr 2022]
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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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
  • 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. 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
  2. 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
  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. Mapping and characterization of the mouse and human SS18 genes, two human SS18-like genes and a mouse Ss18 pseudogene. de Bruijn DR, et al. Cytogenet Cell Genet, 2001. PMID 11435705

See all (35) 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)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (1) 

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 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 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
  
part_of 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 
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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