Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SSX1 Gene

Aliases for SSX1 Gene

  • Synovial Sarcoma, X Breakpoint 1 2 3 4
  • Cancer/Testis Antigen 5.1 3 4
  • CT5.1 3 4
  • SSRC 3 6
  • Sarcoma, Synovial, X-Chromosome-Related 1 3
  • Cancer/Testis Antigen Family 5, Member 1 3
  • Cancer/Testis Antigen Family 5 2
  • Protein SSX1 3
  • Member 1 2

External Ids for SSX1 Gene

Previous GeneCards Identifiers for SSX1 Gene

  • GC0XP046917
  • GC0XP046332
  • GC0XP046794
  • GC0XP047160
  • GC0XP047871
  • GC0XP047999
  • GC0XP047958
  • GC0XP048114
  • GC0XP045828

Summaries for SSX1 Gene

Entrez Gene Summary for SSX1 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. This gene, and also the SSX2 and SSX4 family members, have been involved in t(X;18)(p11.2;q11.2) translocations that are 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. The encoded hybrid proteins are likely responsible for transforming activity. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Jul 2013]

GeneCards Summary for SSX1 Gene

SSX1 (Synovial Sarcoma, X Breakpoint 1) is a Protein Coding gene. Diseases associated with SSX1 include sarcoma, synovial and extraskeletal mesenchymal chondrosarcoma. Among its related pathways are Transcriptional misregulation in cancer. GO annotations related to this gene include nucleic acid binding and transcription corepressor activity. An important paralog of this gene is SSX3.

UniProtKB/Swiss-Prot for SSX1 Gene

  • Could act as a modulator of transcription

Gene Wiki entry for SSX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SSX1 Gene

Genomics for SSX1 Gene

Regulatory Elements for SSX1 Gene

Genomic Location for SSX1 Gene

48,255,317 bp from pter
48,267,444 bp from pter
12,128 bases
Plus strand

Genomic View for SSX1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SSX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SSX1 Gene

Proteins for SSX1 Gene

  • Protein details for SSX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein SSX1
    Protein Accession:
    Secondary Accessions:
    • A3KN76
    • Q08AJ2
    • Q5JQ64

    Protein attributes for SSX1 Gene

    188 amino acids
    Molecular mass:
    21931 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SSX1 Gene

Proteomics data for SSX1 Gene at MOPED

Post-translational modifications for SSX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SSX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SSX1 Gene

Domains for SSX1 Gene

Protein Domains for SSX1 Gene

Suggested Antigen Peptide Sequences for SSX1 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 SSX1: view

No data available for Gene Families for SSX1 Gene

Function for SSX1 Gene

Molecular function for SSX1 Gene

GENATLAS Biochemistry:
protein SSX1 with homology to Kruppel associated box,KRAB,transcriptional corepressor,complexing with polycomb group (PcG) proteins RING1 or BMI1 and associating with chromatin,fused with SYT (SSXT) in synovial sarcoma with translocation t(X;18)(p11.2;q11.2) (see BSSX)
UniProtKB/Swiss-Prot Function:
Could act as a modulator of transcription

Gene Ontology (GO) - Molecular Function for SSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003714 transcription corepressor activity TAS 10072425
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SSX1: view

Animal Model Products

CRISPR Products

miRNA for SSX1 Gene

miRTarBase miRNAs that target SSX1

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SSX1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targets and HOMER Transcription for SSX1 Gene

Localization for SSX1 Gene

Subcellular locations from

Jensen Localization Image for SSX1 Gene COMPARTMENTS Subcellular localization image for SSX1 gene
Compartment Confidence
nucleus 4
cytosol 3
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for SSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SSX1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SSX1 Gene

Pathways for SSX1 Gene

genes like me logo Genes that share pathways with SSX1: view

Pathways by source for SSX1 Gene

1 KEGG pathway for SSX1 Gene

Interacting Proteins for SSX1 Gene

Selected Interacting proteins: Q16384-SSX1_HUMAN for SSX1 Gene via UniProtKB I2D

Gene Ontology (GO) - Biological Process for SSX1 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 TAS 10072425
genes like me logo Genes that share ontologies with SSX1: view

Transcripts for SSX1 Gene

mRNA/cDNA for SSX1 Gene

Unigene Clusters for SSX1 Gene

Synovial sarcoma, X breakpoint 1:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SSX1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SSX1 Gene

No ASD Table

Relevant External Links for SSX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SSX1 Gene

mRNA expression in normal human tissues for SSX1 Gene

mRNA differential expression in normal tissues according to GTEx for SSX1 Gene

This gene is overexpressed in Testis (46.4).

SOURCE GeneReport for Unigene cluster for SSX1 Gene Hs.434142

mRNA Expression by UniProt/SwissProt for SSX1 Gene

Tissue specificity: Expressed at high level in the testis. Expressed at low level in thyroid. Not detected in tonsil, colon, lung, spleen, prostate, kidney, striated and smooth muscles. Detected in rhabdomyosarcoma and fibrosarcoma cell lines. Not detected in mesenchymal and epithelial cell lines
genes like me logo Genes that share expressions with SSX1: view

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 , Protein differential expression in normal tissues , Protein expression and Expression partners for SSX1 Gene

Orthologs for SSX1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SSX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC465644 35
  • 95.92 (n)
  • 91.49 (a)
SSX1 36
  • 96 (a)
(Mus musculus)
Mammalia Ssxb2 16
Gm14459 36
  • 33 (a)
Gm21876 36
  • 43 (a)
Gm5751 36
  • 37 (a)
Gm6592 36
  • 33 (a)
Ssx9 36
  • 32 (a)
Ssxa1 36
  • 44 (a)
Ssxb1 36
  • 34 (a)
Ssxb10 36
  • 34 (a)
Ssxb2 36
  • 32 (a)
Ssxb3 36
  • 34 (a)
Ssxb5 36
  • 36 (a)
Ssxb6 36
  • 30 (a)
Ssxb8 36
  • 35 (a)
Ssxb9 36
  • 34 (a)
(Bos Taurus)
Mammalia SSX5 36
  • 32 (a)
(Canis familiaris)
Mammalia -- 36
  • 50 (a)
Species with no ortholog for SSX1:
  • 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 SSX1 Gene

Gene Tree for SSX1 (if available)
Gene Tree for SSX1 (if available)

Paralogs for SSX1 Gene

Paralogs for SSX1 Gene

(14) SIMAP similar genes for SSX1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SSX1: view

Variants for SSX1 Gene

Sequence variations from dbSNP and Humsavar for SSX1 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs4313283 -- 48,253,647(+) AACAA(A/G)TAGTC upstream-variant-2KB
rs4500195 -- 48,253,787(+) tcagc(A/G)gggac upstream-variant-2KB
rs5002540 -- 48,262,864(+) GGCGC(A/G)GGGGC intron-variant
rs5013456 -- 48,266,983(+) TGAAA(C/G)TTGAG utr-variant-3-prime
rs5902415 -- 48,258,810(+) GCAAA(-/AC)AGTAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SSX1 Gene

Variant ID Type Subtype PubMed ID
dgv2442e1 CNV Complex 17122850
esv2752324 CNV Gain 17911159
esv25781 CNV Gain 19812545
esv32909 CNV Gain+Loss 17666407
nsv519165 CNV Loss 19592680
esv2740145 CNV Deletion 23290073
esv2671998 CNV Deletion 23128226
nsv523595 CNV Gain 19592680
esv2740147 CNV Deletion 23290073
nsv519305 CNV Gain 19592680

Relevant External Links for SSX1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SSX1 Gene

Disorders for SSX1 Gene

(1) OMIM Diseases for SSX1 Gene (312820)


  • Note=A chromosomal aberration involving SSX1 may be a cause of synovial sarcoma. Translocation t(X;18)(p11.2;q11.2). The translocation is specifically found in more than 80% of synovial sarcoma. The fusion products SSXT-SSX1 or SSXT-SSX2 are probably responsible for transforming activity. Heterogeneity in the position of the breakpoint can occur (low frequency).

(3) University of Copenhagen DISEASES for SSX1 Gene

(4) Novoseek inferred disease relationships for SSX1 Gene

Disease -log(P) Hits PubMed IDs
sarcoma synovial 93.8 19
sarcoma 62.2 2
melanoma 25.6 2
cancer 0 2

Relevant External Links for SSX1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SSX1: view

No data available for Genatlas for SSX1 Gene

Publications for SSX1 Gene

  1. Identification of two alternative fusion genes, SYT-SSX1 and SYT- SSX2, in t(X;18)(p11.2;q11.2)-positive synovial sarcomas. (PMID: 7655467) de Leeuw B. … Geurts van Kessel A. (Hum. Mol. Genet. 1995) 2 3 4
  2. Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial sarcoma. (PMID: 7539744) Crew A.J. … Cooper C.S. (EMBO J. 1995) 3 4 23
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 3 4
  4. Functional domains of the SYT and SYT-SSX synovial sarcoma translocation proteins and co-localization with the SNF protein BRM in the nucleus. (PMID: 10072425) Thaete C. … Goodwin G. (Hum. Mol. Genet. 1999) 3 23
  5. 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) 3 23

Products for SSX1 Gene

Sources for SSX1 Gene

Back to Top