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Aliases for SSX3 Gene

Aliases for SSX3 Gene

  • Synovial Sarcoma, X Breakpoint 3 2 3
  • Cancer/Testis Antigen 5.3 3 4
  • CT5.3 3 4
  • Kruppel-Associated Box Containing Gene Product SSX3 3

External Ids for SSX3 Gene

Previous GeneCards Identifiers for SSX3 Gene

  • GC0XM047008
  • GC0XM046466
  • GC0XM047200
  • GC0XM047251
  • GC0XM047962
  • GC0XM048090
  • GC0XM048205
  • GC0XM045914

Summaries for SSX3 Gene

Entrez Gene Summary for SSX3 Gene

  • 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 spontaneous humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. While some of the related SSX genes are involved in t(X;18)(p11.2;q11.2) translocations that are characteristically found in all synovial sarcomas, this gene does not appear to be involved in such translocations. [provided by RefSeq, Jul 2013]

GeneCards Summary for SSX3 Gene

SSX3 (Synovial Sarcoma, X Breakpoint 3) is a Protein Coding gene. Diseases associated with SSX3 include sarcoma, synovial and sarcoma. GO annotations related to this gene include nucleic acid binding. An important paralog of this gene is SSX2.

UniProtKB/Swiss-Prot for SSX3 Gene

  • Could act as a modulator of transcription

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SSX3 Gene

Genomics for SSX3 Gene

Regulatory Elements for SSX3 Gene

Genomic Location for SSX3 Gene

48,346,428 bp from pter
48,356,753 bp from pter
10,326 bases
Minus strand

Genomic View for SSX3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SSX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SSX3 Gene

Proteins for SSX3 Gene

  • Protein details for SSX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein SSX3
    Protein Accession:
    Secondary Accessions:
    • O60223
    • Q5JQZ3
    • Q9BRW7

    Protein attributes for SSX3 Gene

    188 amino acids
    Molecular mass:
    21697 Da
    Quaternary structure:
    • Interacts with SSX2IP.

    Alternative splice isoforms for SSX3 Gene


neXtProt entry for SSX3 Gene

Proteomics data for SSX3 Gene at MOPED

Post-translational modifications for SSX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SSX3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SSX3 Gene

Domains & Families for SSX3 Gene

Protein Domains for SSX3 Gene

Suggested Antigen Peptide Sequences for SSX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 KRAB-related domain.
  • Belongs to the SSX family.
  • Contains 1 KRAB-related domain.
  • Belongs to the SSX family.
genes like me logo Genes that share domains with SSX3: view

No data available for Gene Families for SSX3 Gene

Function for SSX3 Gene

Molecular function for SSX3 Gene

GENATLAS Biochemistry:
protein SSX3 with homology to Kruppel associated box,KRAB,not implicated in t(X;18) synovial sarcoma
UniProtKB/Swiss-Prot Function:
Could act as a modulator of transcription

Gene Ontology (GO) - Molecular Function for SSX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003714 transcription corepressor activity IBA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SSX3: view

Phenotypes for SSX3 Gene

genes like me logo Genes that share phenotypes with SSX3: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SSX3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SSX3 Gene

Localization for SSX3 Gene

Subcellular locations from

Jensen Localization Image for SSX3 Gene COMPARTMENTS Subcellular localization image for SSX3 gene
Compartment Confidence
nucleus 2

Gene Ontology (GO) - Cellular Components for SSX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with SSX3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SSX3 Gene

Pathways & Interactions for SSX3 Gene

SuperPathways for SSX3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SSX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:1903507 negative regulation of nucleic acid-templated transcription IBA --
genes like me logo Genes that share ontologies with SSX3: view

No data available for Pathways by source and SIGNOR curated interactions for SSX3 Gene

Drugs & Compounds for SSX3 Gene

No Compound Related Data Available

Transcripts for SSX3 Gene

mRNA/cDNA for SSX3 Gene

(3) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(10) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SSX3 Gene

Synovial sarcoma, X breakpoint 3:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SSX3

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SSX3 Gene

No ASD Table

Relevant External Links for SSX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SSX3 Gene

mRNA expression in normal human tissues for SSX3 Gene

mRNA differential expression in normal tissues according to GTEx for SSX3 Gene

This gene is overexpressed in Testis (x51.9).

Protein differential expression in normal tissues from HIPED for SSX3 Gene

This gene is overexpressed in Ovary (35.5) and Testis (33.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SSX3 Gene

SOURCE GeneReport for Unigene cluster for SSX3 Gene Hs.558445

genes like me logo Genes that share expression patterns with SSX3: view

Protein tissue co-expression partners for SSX3 Gene

- Elite partner

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for SSX3 Gene

Orthologs for SSX3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SSX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC737502 35
  • 94.33 (n)
  • 87.77 (a)
SSX3 36
  • 96 (a)
(Bos Taurus)
Mammalia SSX5 36
  • 28 (a)
(Canis familiaris)
Mammalia -- 36
  • 47 (a)
(Mus musculus)
Mammalia Gm14459 36
  • 32 (a)
Gm21876 36
  • 41 (a)
Gm5751 36
  • 35 (a)
Gm6592 36
  • 32 (a)
Ssx9 36
  • 32 (a)
Ssxa1 36
  • 47 (a)
Ssxb1 36
  • 34 (a)
Ssxb10 36
  • 34 (a)
Ssxb2 36
  • 31 (a)
Ssxb3 36
  • 33 (a)
Ssxb5 36
  • 35 (a)
Ssxb6 36
  • 28 (a)
Ssxb8 36
  • 34 (a)
Ssxb9 36
  • 32 (a)
Species with no ortholog for SSX3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SSX3 Gene

Gene Tree for SSX3 (if available)
Gene Tree for SSX3 (if available)

Paralogs for SSX3 Gene

Paralogs for SSX3 Gene

(16) SIMAP similar genes for SSX3 Gene using alignment to 2 proteins: Pseudogenes for SSX3 Gene

genes like me logo Genes that share paralogs with SSX3: view

Variants for SSX3 Gene

Sequence variations from dbSNP and Humsavar for SSX3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs3125215 -- 48,346,587(+) TGTGT(C/G)TGTGT utr-variant-3-prime
rs3889065 -- 48,354,476(-) TATAT(C/G)CTGTC intron-variant
rs4606187 -- 48,352,359(+) GTTTA(C/T)CACAT intron-variant
rs4824707 -- 48,350,670(+) CTACC(A/G)AGGCA intron-variant
rs5905681 -- 48,347,874(+) TACCT(A/C)ATTTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SSX3 Gene

Variant ID Type Subtype PubMed ID
esv25781 CNV Gain 19812545
esv32909 CNV Gain+Loss 17666407
esv2671998 CNV Deletion 23128226
nsv523595 CNV Gain 19592680
nsv508769 CNV Insertion 20534489
nsv7441 OTHER Inversion 18451855

Variation tolerance for SSX3 Gene

Residual Variation Intolerance Score: 66.86% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.41; 9.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SSX3 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SSX3 Gene

Disorders for SSX3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SSX3 Gene - From: DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
sarcoma, synovial
  • synovial sarcoma
  • tumor of soft tissue and skeleton
- elite association
Search SSX3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SSX3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SSX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SSX3 Gene

Publications for SSX3 Gene

  1. SSX: a multigene family with several members transcribed in normal testis and human cancer. (PMID: 9378559) Gure A.O. … Chen Y.-T. (Int. J. Cancer 1997) 2 23 67
  2. A novel Kruppel-associated box containing the SSX gene (SSX3) on the human X chromosome is not implicated in t(X;18)-positive synovial sarcomas. (PMID: 8697803) de Leeuw B. … Geurts van Kessel A. (Cytogenet. Cell Genet. 1996) 2 23 67
  3. The cancer-related protein SSX2 interacts with the human homologue of a Ras-like GTPase interactor, RAB3IP, and a novel nuclear protein, SSX2IP. (PMID: 12007189) de Bruijn D.R.H. … van Kessel A.G. (Genes Chromosomes Cancer 2002) 23 67
  4. Heterogeneous expression of the SSX cancer/testis antigens in human melanoma lesions and cell lines. (PMID: 10749136) dos Santos N.R. … Geurts van Kessel A. (Cancer Res. 2000) 23 67
  5. Detection of the SYT-SSX fusion transcripts in formaldehyde-fixed, paraffin-embedded tissue: a reverse transcription polymerase chain reaction amplification assay useful in the diagnosis of synovial sarcoma. (PMID: 9688183) Lasota J. … Miettinen M. (Mod. Pathol. 1998) 23 67

Products for SSX3 Gene

Sources for SSX3 Gene

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