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SSX4B SSX family member 4B [ Homo sapiens (human) ]

Gene ID: 548313, updated on 5-Mar-2024

Summary

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Official Symbol
SSX4Bprovided by HGNC
Official Full Name
SSX family member 4Bprovided by HGNC
Primary source
HGNC:HGNC:16880
See related
Ensembl:ENSG00000269791 AllianceGenome:HGNC:16880
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CT5.4
Summary
The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneously humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. SSX1, SSX2 and SSX4 genes have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas. This translocation results in the fusion of the synovial sarcoma translocation gene on chromosome 18 to one of the SSX genes on chromosome X. Chromosome Xp11 contains a segmental duplication resulting in two identical copies of synovial sarcoma, X breakpoint 4, SSX4 and SSX4B, in tail-to-tail orientation. This gene, SSX4B, represents the more centromeric copy. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression
Restricted expression toward testis (RPKM 3.3) See more
Orthologs
all
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Genomic context

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See SSX4B in Genome Data Viewer
Location:
Xp11.23
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (48402082..48411960, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (47811054..47820934, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48261524..48271405, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ornithine aminotransferase, mitochondrial-like Neighboring gene SSX family member 4 Neighboring gene ornithine aminotransferase pseudogene Neighboring gene SSX family member 16, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. CD4+ T cell responses to SSX-4 in melanoma patients. Ayyoub M, et al. J Immunol, 2005 Apr 15. PMID 15814740
  2. A novel fusion gene, SYT-SSX4, in synovial sarcoma. Skytting B, et al. J Natl Cancer Inst, 1999 Jun 2. PMID 10359553
  3. Cloning and characterization of spliced fusion transcript variants of synovial sarcoma: SYT/SSX4, SYT/SSX4v, and SYT/SSX2v. Possible regulatory role of the fusion gene product in wild type SYT expression. Brodin B, et al. Gene, 2001 May 2. PMID 11368913
  4. Expressions of cancer-testis antigens in human hepatocellular carcinomas. Chen CH, et al. Cancer Lett, 2001 Mar 26. PMID 11179834
  5. Molecular mechanisms underlying human synovial sarcoma development. dos Santos NR, et al. Genes Chromosomes Cancer, 2001 Jan. PMID 11107170

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC169015, MGC169016

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein SSX4
Names
cancer/testis antigen 5.4
synovial sarcoma, X breakpoint 4B

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_001034832.5 → NP_001030004.1  protein SSX4 isoform a

    See identical proteins and their annotated locations for NP_001030004.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AA312651, AL606490, BC137395, BE866727, CD671168
    Consensus CDS
    CCDS35241.1
    UniProtKB/Swiss-Prot
    A8MYD4, B2RPE3, O60224, Q3SYD4, Q5JQZ0, Q9UJU9
    Related
    ENSP00000469394.1, ENST00000595235.6
    Conserved Domains (2) summary
    smart00349
    Location:23 → 82
    KRAB; krueppel associated box
    pfam09514
    Location:156 → 187
    SSXRD; SSXRD motif

  2. NM_001040612.4 → NP_001035702.1  protein SSX4 isoform b

    See identical proteins and their annotated locations for NP_001035702.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' coding region compared to variant 1. This results in a frame-shift, and a shorter isoform (b) with a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AA312651, AL606490, BC137395, BE866727, CD671168
    Consensus CDS
    CCDS43935.1
    UniProtKB/Swiss-Prot
    O60224
    Related
    ENSP00000481765.1, ENST00000619890.1
    Conserved Domains (2) summary
    cd07765
    Location:24 → 61
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00349
    Location:23 → 82
    KRAB; krueppel associated box

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    48402082..48411960 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029613.2 → XP_016885102.1  protein SSX4 isoform X1

    UniProtKB/Swiss-Prot
    A8MYD4, B2RPE3, O60224, Q3SYD4, Q5JQZ0, Q9UJU9
    Conserved Domains (2) summary
    smart00349
    Location:23 → 82
    KRAB; krueppel associated box
    pfam09514
    Location:156 → 187
    SSXRD; SSXRD motif

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    47811054..47820934 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327291.1 → XP_054183266.1  protein SSX4 isoform X1

    UniProtKB/Swiss-Prot
    A8MYD4, B2RPE3, O60224, Q3SYD4, Q5JQZ0, Q9UJU9
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60224.1 GenPept UniProtKB/Swiss-Prot:O60224

Gene LinkOut

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