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Aliases for SSX3 Gene

Aliases for SSX3 Gene

  • SSX Family Member 3 2 3 5
  • Synovial Sarcoma, X Breakpoint 3 2 3
  • Cancer/Testis Antigen 5.3 3 4
  • Protein SSX3 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 (SSX Family Member 3) is a Protein Coding gene. Diseases associated with SSX3 include Sarcoma, Synovial and Sarcoma. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is SSX5.

UniProtKB/Swiss-Prot for SSX3 Gene

Additional gene information for SSX3 Gene

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

Genomics for SSX3 Gene

GeneHancer (GH) Regulatory Elements for SSX3 Gene

Promoters and enhancers for SSX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ048356 Promoter 0.8 EPDnew 600.7 +0.0 32 0.1 PKNOX1 GABPA NRF1 ZBTB40 L3MBTL2 E2F1 ENSG00000225055 LOC791093 SSX3 FTSJ1 ENSG00000270747
GH0XJ048785 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 1.6 -431.1 -431148 5 MLLT1 CDC5L MCM2 PRDM1 ZNF639 SMARCA4 MTA1 DPF2 IKZF1 ZNF512 GATA1 ENSG00000204620 ENSG00000270012 ZNF81 FTSJ1 PQBP1 CCDC22 ZNF182 RBM3 SLC38A5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SSX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SSX3 gene promoter:
  • C/EBPalpha
  • C/EBPbeta
  • HNF-1
  • HNF-1A
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • Sox9

Genomic Locations for SSX3 Gene

Genomic Locations for SSX3 Gene
10,326 bases
Minus strand
10,280 bases
Minus strand

Genomic View for SSX3 Gene

Genes around SSX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SSX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for SSX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SSX3 Gene

No data available for DME Specific Peptides for SSX3 Gene

Domains & Families for SSX3 Gene

Gene Families for SSX3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SSX3 Gene

Suggested Antigen Peptide Sequences for SSX3 Gene

GenScript: Design optimal peptide antigens:
  • Cancer/testis antigen 5.3 (SSX3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SSX family.
  • Belongs to the SSX family.
genes like me logo Genes that share domains with SSX3: view

Function for SSX3 Gene

Molecular function for SSX3 Gene

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

Gene Ontology (GO) - Molecular Function for SSX3 Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SSX3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SSX3 Gene

Localization for SSX3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SSX3 gene
Compartment Confidence
nucleus 4
cytosol 2
extracellular 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SSX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IBA 21873635
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

PathCards logo

SuperPathways for SSX3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SSX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
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

(2) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(10) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Unigene Clusters for SSX3 Gene

Synovial sarcoma, X breakpoint 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SSX3

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Protein tissue co-expression partners for SSX3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SSX3 Gene:


SOURCE GeneReport for Unigene cluster for SSX3 Gene:


Evidence on tissue expression from TISSUES for SSX3 Gene

  • Bone marrow(4)
genes like me logo Genes that share expression patterns with SSX3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 SSX3 35
  • 96 (a)
LOC737502 34
  • 94.33 (n)
(Mus musculus)
Mammalia Ssxa1 35
  • 47 (a)
Gm21876 35
  • 41 (a)
Gm5751 35
  • 35 (a)
Ssxb5 35
  • 35 (a)
Ssxb1 35
  • 34 (a)
Ssxb10 35
  • 34 (a)
Ssxb8 35
  • 34 (a)
Ssxb3 35
  • 33 (a)
Ssxb9 35
  • 32 (a)
Gm6592 35
  • 32 (a)
Ssx9 35
  • 32 (a)
Gm14459 35
  • 32 (a)
Ssxb2 35
  • 31 (a)
Ssxb6 35
  • 28 (a)
(Canis familiaris)
Mammalia -- 35
  • 47 (a)
(Bos Taurus)
Mammalia SSX5 35
  • 28 (a)
Species where no ortholog for SSX3 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for SSX3: view image

Paralogs for SSX3 Gene

Variants for SSX3 Gene

Sequence variations from dbSNP and Humsavar for SSX3 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs112625608 -- 48,357,307(-) G/A upstream_transcript_variant
rs112850154 -- 48,357,379(-) C/T upstream_transcript_variant
rs11323384 -- 48,355,580(-) A/ intron_variant
rs113398904 -- 48,353,846(-) A/G intron_variant
rs113403735 -- 48,354,694(-) T/C coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv25781 CNV gain 19812545
esv2671998 CNV deletion 23128226
esv32909 CNV gain+loss 17666407
nsv508769 CNV insertion 20534489
nsv523595 CNV gain 19592680
nsv7441 OTHER inversion 18451855

Variation tolerance for SSX3 Gene

Residual Variation Intolerance Score: 66.9% 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)

Additional Variant Information for SSX3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Human Gene Mutation Database (HGMD)

SNP Genotyping and Copy Number Assay Products

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

Disorders for SSX3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SSX3 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
sarcoma, synovial
  • synovial sarcoma
  • connective and soft tissue neoplasm
synovium cancer
  • malignant tumor of synovium
- elite association - COSMIC cancer census association via MalaCards
Search SSX3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SSX3

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 AO … Chen YT (International journal of cancer 1997) 2 3 4 23 58
  2. A novel Krüppel-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 (Cytogenetics and cell genetics 1996) 2 3 4 23 58
  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 DR … van Kessel AG (Genes, chromosomes & cancer 2002) 3 4 23 58
  4. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SSX3 Gene

Sources for SSX3 Gene

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