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SSX4B Gene

protein-coding   GIFtS: 37

GC0XM048261
synovial sarcoma, X breakpoint 4B
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Products    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases & Descriptions
synovial sarcoma, X breakpoint 4B1 2     SSX42
OTTHUMT000000565101 2     protein SSX42
Cancer/testis antigen 5.42 3     MGC1690162
CT5.42 3     SSX4A3
MGC1690152     

External Ids:    HGNC: 168801   Entrez Gene: 5483132   Ensembl: ENSG000001989467   UniProtKB: O602243   

Export aliases for SSX4B gene to outside databases

Previous GC identifers: GC00U921552 GC0XU900601 GC0XM048146


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SSX4B:
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,
SSX4B, represents the more centromeric copy. Two transcript variants encoding distinct isoforms have been identified
for this gene. (provided by RefSeq)

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


(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SSX4B gene promoter:
         GATA-1   NF-1   CUTL1   POU2F1   ER-alpha   C/EBPbeta   HOXA9B   Meis-1   HNF-1A   RSRFC4   
         Other transcription factors

   Search SABiosciences Chromatin IP Primers for SSX4B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 


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

SSX4B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SSX4B gene location

GeneLoc gene densities for chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM048261:  view genomic region     (about GC identifiers)

Start:
48,261,524 bp from pter
End:
48,271,344 bp from pter
Size:
9,821 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000023.10  NT_079573.4  

(According to 1UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

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 SSX4B: NX_O60224 

REFSEQ proteins (2 alternative transcripts): 
NP_001030004.1  NP_001035702.1  


ENSEMBL proteins: 
ENSP00000366081 ENSP00000380134 


Human Recombinant Proteins 
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2 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005622 intracellular IEA--
GO:0005634 nucleus IEA--
About this table

SSX4B for ontologies           About GeneDecksing



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Browse ELISAs and CLIAs at Uscn 


(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

SSX4B for domains           About GeneDecksing

3 InterPro domains/families:
 IPR003655 Krueppel-associated_box-rel
 IPR019041 SSXRD_motif
 IPR001909 Krueppel-associated_box

Graphical View of Domain Structure for InterPro Entry O60224

ProtoNet protein and cluster: O60224

1 Blocks protein family: IPB001909 KRAB box

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


(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section

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

Inhib.
RNA:
    
Browse for Gene Knock-down Tools from Millipore
Browse Nano Scale siRNA at Sigma-Aldrich
Sigma-Aldrich siRNA for SSX4B
Sigma-Aldrich shRNA for SSX4B
OriGene 29mer shRNA kits in GFP-retroviral vector (see all 2): SSX4B
OriGene shRNA RFP (see all 2): SSX4B
OriGene basic RS shRNA (see all 2): SSX4B
OriGene siRNA (see all 2): SSX4B
QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of SSX4B 
miRNA:Sigma-Aldrich microRNA Mimics for SSX4B
Browse microRNA target validation systems at Sigma-Aldrich 
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of SSX4B 
Search SABiosciences for Assays for microRNAs that regulate SSX4B

Gene
Editing:
Browse CompoZr Knockout ZFN at Sigma-Aldrich 

Clones:Browse Clones for the Expression of Recombinant Proteins Available from Millipore
Browse iPSC Reprogramming Factors at Sigma-Aldrich
OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): SSX4B
OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): SSX4B
OriGene untagged cDNA clones in CMV expression vector (see all 2): SSX4B
Browse 3'-UTR reporter clones for miRNA target validation 
Browse MicroRNA Expression Plasmids 
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Browse Sino Biological Human cDNA Clones

Cell
Lines:
  
GenScript Custom overexpressing Cell Line Services for SSX4B 

1 Gene Ontology (GO) molecular function term (GO ID links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003676 nucleic acid binding IEA--
About this table

SSX4B for ontologies           About GeneDecksing


(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section

    SABiosciences Custom Pathway-Focused PCR Arrays for SSX4B 

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SSX4B

1 Interacting protein for SSX4B (O602242) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
HIF1AQ166652MINT-66671
About this table

1 Gene Ontology (GO) biological process term (GO ID links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006355 regulation of transcription, DNA-dependent IEA--
About this table

SSX4B for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section
Browse Small Molecules at Sigma-Aldrich
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SSX4B


(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section

Inhib.
RNA:
     
Browse for Gene Knock-down Tools from Millipore
Browse Nano Scale siRNA at Sigma-Aldrich
Sigma-Aldrich siRNA for SSX4B
Sigma-Aldrich shRNA for SSX4B
OriGene 29mer shRNA kits in GFP-retroviral vector (see all 2): SSX4B
OriGene shRNA RFP (see all 2): SSX4B
OriGene basic RS shRNA (see all 2): SSX4B
OriGene siRNA (see all 2): SSX4B
QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of SSX4B 
miRNA: Sigma-Aldrich microRNA Mimics for SSX4B
Browse microRNA target validation systems at Sigma-Aldrich 
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of SSX4B 
Search SABiosciences for Assays for microRNAs that regulate SSX4B
Clones: Browse FLAG tag genes at Sigma-Aldrich
OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): SSX4B
OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): SSX4B
OriGene untagged cDNA clones in CMV expression vector (see all 2): SSX4B
Browse 3'-UTR reporter clones for miRNA target validation 
Browse OriGene MicroRNA Expression Plasmids 
GenScript Custom cDNA clone Services for SSX4B 
Primers: OriGene genome-wide validated SYBR primer pairs: SSX4B
Browse OriGene validated miRNA SYBR primer pairs 
SABiosciences RT2 qPCR Primer Assay for SSX4B: PPH63498A

REFSEQ mRNAs for SSX4B gene (2 alternative transcripts): 

NM_001034832.2  NM_001040612.1  

2 DOTS entries:

DT.40305548  DT.40127997 

highest scoring ESTs for SSX4B:

NM_001034832 NM_001040612 

Unigene Clusters for SSX4B:

Synovial sarcoma, X breakpoint 4B
Hs.558402  [show with all ESTs], Hs.648298
Unigene Representative Sequences: NM_005636, NM_001034832


GeneLoc Exon Structure

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000376884(uc004djh.1) ENST00000396928(uc004dji.1)

(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

SSX4B expression in normal and diseased human tissues

1  / 2  / 3

1 probe-set matching SSX4B gene

Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
35950_at2, 3 U95-A 11 0.81 0.14 1.00 1.00 U90841 0.20 0.04 0.14 2
About this table

SSX4B for expression           About GeneDecksing

Data from Genenote  (Publications) and GNF BioGPS
    About these images
SSX4B gene expression
SSX4B gene electronic northern expression
SSX4B gene sage expression
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene clusters: Hs.558402 Hs.648298
Primers: OriGene genome-wide validated SYBR primer pairs: SSX4B
Browse OriGene validated miRNA SYBR primer pairs 
SABiosciences RT2 qPCR Primer Assay for SSX4B: PPH63498A
    SABiosciences Custom PCR Arrays for SSX4B 


(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section
ENSEMBL Gene Tree for SSX4B (if available)

(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
Paralogs for SSX4B gene
SSX41 2  SSX22  SSX2B2  SSX62  SSX72  SSX12  SSX52  SSX92  
SSX32  

SSX4B for paralogs           About GeneDecksing



(SNPs according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 7 variations for SSX4B
     5 CNVs: 96641 83494 67975 67974 7789
     2 Inversions: 37376 37375
Search QIAGEN SeqTarget long-range PCR primers for resequencing for SSX4B 

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section
  --

(Possibly Related Articles in Doctor's Guide)
About This Section
  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6UniProtKB/TrEMBL, and/or 7Novoseek)
About This Section

10/11 PubMed articles for SSX4B gene, integrated from 7 sources (see all 11):
(articles sorted by number of sources associating them with SSX4B)
  1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)
  2. 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. (2004)
  3. SSX: a multigene family with several members transcribed in normal testis and human cancer. (PubMed id 9378559)1, 2 Gure A.O....Chen Y.T. (1997)
  4. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
  5. CD4+ T cell responses to SSX-4 in melanoma patients. (PubMed id 15814740)1 Ayyoub M....Valmori D. (2005)
  6. The SSX gene family: characterization of 9 complete genes. (PubMed id 12216073)1 Gure A.O.... Chen Y.-T. (2002)
  7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
  8. Molecular mechanisms underlying human synovial sarcoma development. (PubMed id 11107170)1 dos Santos N.R....van Kessel A.G. (2001)
  9. 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 Brodin B.... Larsson O. (2001)
  10. Expressions of cancer-testis antigens in human hepatocellular carcinomas. (PubMed id 11179834)1 Chen C.H....Sheu J.C. (2001)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
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)
About This Section
Entrez Gene: 548313 HGNC: 16880 Ensembl:ENSG00000198946 euGenes: HUgn548313 ECgene: SSX4B
H-InvDB: SSX4B

(According to HUGE)
About This Section
  --

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
ATLAS Chromosomes in Cancer entry for SSX4B Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from XenneX, Inc.)
About This Section
Patent Information for SSX4B gene:
Search GeneIP for patents involving SSX4B

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



(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
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About This Section

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 QIAGEN Custom miScript Target Protector blocks miRNA-binding site of SSX4B
 Search QIAGEN SeqTarget long-range PCR primers for resequencing for SSX4B
 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays
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