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SSX4 Gene

protein-coding   GIFtS: 45
GCID: GC0XP048242

Synovial Sarcoma, X Breakpoint 4

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Synovial Sarcoma, X Breakpoint 41 2
Cancer/Testis Antigen 5.42 3
CT5.42 3
Protein SSX42
SSX4A3

External Ids:    HGNC: 113381   Entrez Gene: 67592   Ensembl: ENSG000002046457   OMIM: 3003265   UniProtKB: O602243   

Export aliases for SSX4 gene to outside databases

Previous GC identifers: GC0XM047064 GC0XM046522 GC0XP047069 GC0XP047288 GC0XM048017 GC0XP048127


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SSX4 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 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)

GeneCards Summary for SSX4 Gene:
SSX4 (synovial sarcoma, X breakpoint 4) is a protein-coding gene. Diseases associated with SSX4 include synovial sarcoma, and sarcoma. An important paralog of this gene is SSX5.

UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224
Function: Could act as a modulator of transcription

Gene Wiki entry for SSX4 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the SSX4 gene promoter:
         NCX/Ncx   HNF-1A   C/EBPalpha   POU2F1   HNF-1   POU2F1a   Sox9   POU2F1c   RSRFC4   En-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SSX4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xp11.23   Ensembl cytogenetic band:  Xp11.23   HGNC cytogenetic band: Xp11.23

SSX4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SSX4 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP048242:  view genomic region     (about GC identifiers)

Start:
48,242,863 bp from pter      End:
48,252,785 bp from pter
Size:
9,923 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224 (See protein sequence)
Recommended Name: Protein SSX4  
Size: 188 amino acids; 21858 Da
Secondary accessions: B2RPE3 Q5JQZ0 Q9UJU9

Explore the universe of human proteins at neXtProt for SSX4: NX_O60224

Explore proteomics data for SSX4 at MOPED


See SSX4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_005627.1  NP_783856.1  

ENSEMBL proteins: 
 ENSP00000366083   ENSP00000364667  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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4 InterPro protein domains:
 IPR003655 Krueppel-associated_box-rel
 IPR019041 SSXRD_motif
 IPR028804 SSX
 IPR001909 Krueppel-associated_box

Graphical View of Domain Structure for InterPro Entry O60224

ProtoNet protein and cluster: O60224

1 Blocks protein domain: IPB001909 KRAB box

UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224
Similarity: Belongs to the SSX family
Similarity: Contains 1 KRAB-related domain


SSX4 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: SSX4_HUMAN, O60224
Function: Could act as a modulator of transcription

     Genatlas biochemistry entry for SSX4:
protein SSX4 with homology to Kruppel associated box,KRAB,not implicated in t(X;18) synovial sarcoma

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003676nucleic acid binding ----
     
SSX4 for ontologies           About GeneDecksing


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol2
extracellular1

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005622intracellular ----
GO:0005634nucleus ----

SSX4 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SSX4
Interactions:

    Search GeneGlobe Interaction Network for SSX4

STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

5 Interacting proteins for SSX4 (O602242, 3 ENSP000003660834) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
HIF1AQ166652, 3, ENSP000003380184MINT-66671 I2D: score=5 STRING: ENSP00000338018
PAX9P557713, ENSP000003552454I2D: score=1 STRING: ENSP00000355245
XBP1P178613, ENSP000002160374I2D: score=1 STRING: ENSP00000216037
LZTR1Q8N6533, ENSP000002157394I2D: score=1 STRING: ENSP00000215739
ALDH18A1ENSP000003602684STRING: ENSP00000360268
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Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated ----
GO:0006355regulation of transcription, DNA-templated ----

SSX4 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for SSX4



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SSX4 gene (2 alternative transcripts): 
NM_005636.3  NM_175729.1  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000376886(uc004djf.1 uc004djg.1) ENST00000375517
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hsa-miR-222* hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p
Browse SwitchGear 3'UTR luciferase reporter plasmids
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  QuantiFast Probe-based Assays in human, mouse, rat SSX4

16 AceView cDNA sequences:

CD671169 NM_005636 AA312651 BU632654 U90841 NM_175729 CD671168 BX102714 
BX279816 BC005325 AI699644 BE866727 H99655 N24445 N72228 W00507 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SSX4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SSX4 Expression
About this image

SSX4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SSX4 Protein Expression
    Custom PCR Arrays for SSX4
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SSX4

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for SSX4 gene from Selected species (see all 4)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ssxb21 synovial sarcoma, X member B, breakpoint 2 66.29(n)
56.18(a)
  387132  NM_001134226.1  NP_001127698.1 


ENSEMBL Gene Tree for SSX4 (if available)
TreeFam Gene Tree for SSX4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SSX4 gene
SSX4B1 2  SSX52  SSX2B2  SSX22  SSX72  SSX12  SSX32  
13 SIMAP similar genes for SSX4 using alignment to 2 protein entries:     SSX4_HUMAN (see all proteins):
SSX4B    SSX3    SSX9    SSX1    SSX7    SSX5
SSX2B    SSX6    SSX2    SSX8    SYT-SSX2    SSX10
SYT-SSX1

SSX4 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for SSX4
PGOHUM00000241751


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SSX4 (see all 30)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1808322651,2
C--48241285(+) GAGGCC/TGAGGC 2 -- us2k10--------
rs2008716731,2
--48241361(+) CTAAT-/AAGAAGAA 2 -- us2k10--------
rs2002671241,2
C--48243015(+) GCATGC/TGCTGA 2 -- int10--------
rs2013327121,2
C--48244036(+) CTAAGA/GAAGAG 4 K E mis10--------
rs1407484171,2
C,F--48244866(+) TGGTAA/GCGATC 4 N S mis11Minor allele frequency- G:0.00NA 2280
rs1860666291,2
--48244994(+) ACATCA/GGGGCT 2 -- int10--------
rs2005956761,2
----48244072(+) AAATCG/TTCTAT 4 V F mis10--------
rs3742628311,2
----48248392(+) GTTTTC/TCATTT 2 -- int10--------
rs3727281211,2
----48244261(+) GTTCTC/GTCTTC 2 -- int10--------
rs2008611701,2
----48244000(+) TTTTCC/TAGGCC 2 -- int10--------

HapMap Linkage Disequilibrium report for SSX4 (48242863 - 48252785 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for SSX4:    About this table    
Variant IDTypeSubtypePubMed ID
esv2671998CNV Deletion23128226
esv25781CNV Gain19812545
esv32909CNV Gain+Loss17666407
nsv7441OTHER Inversion18451855

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300326    OMIM disorders: --

5 diseases for SSX4:    About MalaCards
synovial sarcoma    sarcoma    lung cancer    melanoma
hepatocellular carcinoma

1 disease from the University of Copenhagen DISEASES database for SSX4:
Synovial sarcoma

SSX4 for disorders           About GeneDecksing

4 Novoseek inferred disease relationships for SSX4 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
sarcoma synovial 88.4 3 18519690 (1), 12007189 (1), 11308259 (1)
melanoma 31.7 3 12007189 (1), 10749136 (1), 9378559 (1)
tumors 18.8 1 16299236 (1)
cancer 6.93 5 15603546 (2), 10749136 (1)


Export disorders for SSX4 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SSX4 gene, integrated from 10 sources (see all 24):
(articles sorted by number of sources associating them with SSX4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. SSX: a multigene family with several members transcribed in normal testis and human cancer. (PubMed id 9378559)1, 2, 9 Gure A.O.... Chen Y.-T. (Int. J. Cancer 1997)
  2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. The cancer-related protein SSX2 interacts with the human homologue of a Ras-like GTPase interactor, RAB3IP, and a novel nuclear protein, SSX2IP. (PubMed id 12007189)1, 9 de Bruijn D.R.H....van Kessel A.G. (Genes Chromosomes Cancer 2002)
  5. 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. (PubMed id 11368913)1, 9 Brodin B.... Larsson O. (Gene 2001)
  6. Clinical impact of molecular and cytogenetic findings in synovial sarcoma. (PubMed id 11433527)1, 9 Panagopoulos I....Mandahl N. (amp 2001)
  7. Effects of CT-Xp gene knock down in melanoma cell lines. (PubMed id 23625514)1 Caballero O.L....Simpson A.J. (Oncotarget 2013)
  8. Identification and functional characterization of glioma-specific promoters and their application in suicide gene therapy. (PubMed id 21347689)1 Yawata T....Shimizu K. (J. Neurooncol. 2011)
  9. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (Cell 2010)
  10. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 6759 HGNC: 11338 AceView: SSX4.1 Ensembl:ENSG00000204645 euGenes: HUgn6759
ECgene: SSX4 H-InvDB: SSX4

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SSX4 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for SSX4 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SSX4 gene:
Search GeneIP for patents involving SSX4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Browse OriGene Antibodies   OriGene RNAi products in human, mouse, rat for SSX4  
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 OriGene qSTAR qPCR primer pairs in human, mouse for SSX4   OriGene Purified Protein for SSX4  
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 Block miRNA regulation of human, mouse, rat SSX4 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing SSX4
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 QuantiFast Probe-based Assays in human, mouse, rat SSX4 QuantiTect SYBR Green Assays in human, mouse, rat SSX4
 Custom PCR Arrays for SSX4 Search Chromatin IP Primers for SSX4
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 Browse ESI BIO Cell Lines and PureStem Progenitors for SSX4
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SSX4
 Browse SwitchGear 3'UTR luciferase reporter plasmids for SSX4
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 Search ThermoFisher Antibodies for SSX4
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSX4
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SSX4
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SSX4
 LSBio Antibodies in human, mouse, rat for SSX4
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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