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

Summary

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, Nov 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

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_000084.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SS18 regulates pluripotent-somatic transition through phase separation.
Title: SS18 regulates pluripotent-somatic transition through phase separation.
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.
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.

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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

X93357 (e-PCR)
- UniSTS:163595

MT1122 (e-PCR)
- UniSTS:128305

D18Mit92.3 (e-PCR), detects polymorphism
- UniSTS:128306

NoName (e-PCR)
- UniSTS:488550

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)

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)
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)
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)
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

NC_000084.7 Reference GRCm39 C57BL/6J

Range

14758686..14817476 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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