SSX4 SSX family member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SSX4provided by HGNC
Official Full Name: SSX family member 4provided by HGNC
Primary source: HGNC:HGNC:11338
See related: Ensembl:ENSG00000268009 MIM:300326; AllianceGenome:HGNC:11338
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, SSX4, represents the more telomeric 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

Location:: Xp11.23

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (48383539..48393347)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (47792507..47802319)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (48242980..48252789)

Chromosome X - NC_000023.11 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

loss of miR-4731 expression in stage IV patient tumors supports melanoma growth by, in part, reducing its regulatory control of SSX expression levels
Title: The "melanoma-enriched" microRNA miR-4731-5p acts as a tumour suppressor.
SSX2, SSX3, and SSX4 are expressed only in 3.5% early-stage non-small cell lung cancer patients.
Title: SSX2-4 expression in early-stage non-small cell lung cancer.
The mRNA levels of SSX1 and SSX4 are associated with multiple myeloma clinical stage
Title: Expression of cancer-testis antigen in multiple myeloma.
Our results suggest that GAGE, XAGE1 and SSX4 might each have a role in melanoma progression
Title: Effects of CT-Xp gene knock down in melanoma cell lines.
we found that the SSX4 and MAGE-A3 genes are frequently expressed in brain tumor cell lines
Title: Identification and functional characterization of glioma-specific promoters and their application in suicide gene therapy.
existence of CD4+ T cells specific for multiple SSX-4 derived sequences in circulating lymphocytes from melanoma patients
Title: CD4+ T cell responses to SSX-4 in melanoma patients.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-H99655 (e-PCR)
- UniSTS:50770

RH102836 (e-PCR)
- UniSTS:97170

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 4

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_005636.4 → NP_005627.1 protein SSX4 isoform a

See identical proteins and their annotated locations for NP_005627.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AL606490

Consensus CDS

CCDS35240.1

UniProtKB/Swiss-Prot

A8MYD4, B2RPE3, O60224, Q3SYD4, Q5JQZ0, Q9UJU9

Related

ENSP00000469011.1, ENST00000595689.3

Conserved Domains (2) summary

smart00349
Location:23 → 82

KRAB; krueppel associated box

pfam09514
Location:156 → 187

SSXRD; SSXRD motif
NM_175729.2 → NP_783856.1 protein SSX4 isoform b

See identical proteins and their annotated locations for NP_783856.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a segment in the coding region which leads to a frameshift, compared to variant 1. The resulting isoform (b) contains a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AL606490

Consensus CDS

CCDS43934.1

UniProtKB/Swiss-Prot

O60224

Related

ENSP00000483262.1, ENST00000620320.4

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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

48383539..48393347

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017029759.2 → XP_016885248.1 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