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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SSX4B Gene

protein-coding   GIFtS: 44
GCID: GC0XM048261

Synovial Sarcoma, X Breakpoint 4B

  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)
About This Section

Aliases
Synovial Sarcoma, X Breakpoint 4B1 2
Cancer/Testis Antigen 5.42 3
CT5.42 3
OTTHUMT000000565102
Protein SSX42
SSX4A3

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, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SSX4B 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, SSX4B, represents the more centromeric copy. Two transcript variants
encoding distinct isoforms have been identified for this gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for SSX4B Gene: 
SSX4B (synovial sarcoma, X breakpoint 4B) is a protein-coding gene. Diseases associated with SSX4B include synovial sarcoma, and sarcoma. GO annotations related to this gene include nucleic acid binding. An important paralog of this gene is SSX2B.

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_079573.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SSX4B gene promoter:
         HOXA9B   HOXA9   NCX/Ncx   Meis-1b   HNF-1A   C/EBPalpha   HNF-1   Meis-1   RSRFC4   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSSX4B promoter sequence
   Search SABiosciences Chromatin IP Primers for SSX4B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SSX4B


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 information about 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

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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

Explore proteomics data for SSX4B at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O60224

  • SSX4B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SSX4B Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001030004.1  NP_001035702.1  

    ENSEMBL proteins: 
     ENSP00000366081   ENSP00000380134  

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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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

    SSX4B for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    3 InterPro protein domains:
     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 domain: IPB001909 KRAB box

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


    SSX4B 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
         
    SSX4B for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SSX4B:
     Increased 8N DNA content 

    Animal Models:
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    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

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

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    4 Interacting proteins for SSX4B (O602242, 3 ENSP000003660814) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIF1AQ166652, 3, ENSP000003380184MINT-66671 I2D: score=5 STRING: ENSP00000338018
    LZTR1Q8N6533I2D: score=1 
    PAX9P557713I2D: score=1 
    XBP1P178613I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

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

    SSX4B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SSX4B (SSX4)

    Search CenterWatch for drugs/clinical trials and news about SSX4B / 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SSX4B gene (2 alternative transcripts): 
    NM_001034832.3  NM_001040612.2  

    Unigene Clusters for SSX4B:

    Synovial sarcoma, X breakpoint 4B
    Hs.558402  [show with all ESTs], Hs.648298  [show with all ESTs]
    Unigene Representative Sequences: NM_005636, NM_001034832
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376884(uc004djh.1) ENST00000396928(uc004dji.1)
    miRNA
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    4 QIAGEN miScript miRNA Assays for microRNAs that regulate SSX4B:
    hsa-miR-222* hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p
    SwitchGear 3'UTR luciferase reporter plasmidSSX4B 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSX4B

    2 DOTS entries:

    DT.40305548  DT.40127997 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SSX4B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SSX4B Expression
    About this image


    See SSX4B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SSX4B

    SOURCE GeneReport for Unigene clusters: Hs.558402 Hs.648298
        SABiosciences Custom PCR Arrays for SSX4B
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SSX4B
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSX4B
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SSX4B

    (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)
    About This Section
      --

    ENSEMBL Gene Tree for SSX4B (if available)
    TreeFam Gene Tree for SSX4B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SSX4B gene
    SSX41 2  SSX2B2  SSX22  SSX62  SSX72  SSX12  SSX52  SSX92  
    SSX32  
    14 SIMAP similar genes for SSX4B using alignment to 2 protein entries:     SSX4_HUMAN (see all proteins):
    SSX4    SSX9    SSX11    SSX3    SSX6    SSX1
    SSX7    SSX5    SSX2B    SSX2    SSX8    SSX10
    SYT-SSX2    SYT-SSX1

    SSX4B for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/21 SNPs in SSX4B are shown (see all 21)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1999247661,2
    C--48269486(+) TACTAC/TGCATG 4 H R mis10--------
    rs1430228141,2
    F--48270302(+) TCATCG/AAAGGC 4 /F syn11Minor allele frequency- A:0.00NA 4124
    rs1395274381,2
    C--48272639(+) CTCCCA/GCCTCC 2 -- us2k10--------
    rs2003143581,2
    --48272944(+) GGTTG-/TTCTTCTT 2 -- us2k10--------
    rs3710378261,2
    ----48270279(+) TCTTAG/TAGAAG 4 Y S mis10--------
    rs3745121391,2
    ----48270248(+) TTCTCC/TGAGGA 4 S syn10--------
    rs2005195081,2
    ----48272251(+) CATCAA/TTTTTT 2 -- us2k10--------
    rs3700826891,2
    ----48270158(+) TGTGTA/CCCCAG 2 -- int10--------
    rs3722794281,2
    ----48269443(+) CGATCA/GTTACC 4 N syn10--------
    rs1998890951,2
    ----48270148(+) GGGATA/GCTCAT 2 -- int10--------

    HapMap Linkage Disequilibrium report for SSX4B (48261524 - 48271344 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for SSX4B:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2671998CNV Deletion23128226
    esv25781CNV Gain19812545
    esv32909CNV Gain+Loss17666407
    nsv7441OTHER Inversion18451855

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    5 diseases for SSX4B:    About MalaCards
    synovial sarcoma    sarcoma    retinitis    hepatocellular carcinoma
    melanoma

    1 disease from the University of Copenhagen DISEASES database for SSX4B:
    Synovial sarcoma

    SSX4B for disorders           About GeneDecksing


    Export disorders for SSX4B 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)
    About This Section

    PubMed articles for SSX4B gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with SSX4B)
        Utopia: connect your pdf to the dynamic
    world of online information

    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. Expressed sequence tag analysis of adult human iris for the NEIBank project: steroid-response factors and similarities with retinal pigment epithelium. (PubMed id 12107412)1 Wistow G.... Peterson K. (2002)
    7. The SSX gene family: characterization of 9 complete genes. (PubMed id 12216073)1 Gure A.O.... Chen Y.-T. (2002)
    8. 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)
    9. Molecular mechanisms underlying human synovial sarcoma development. (PubMed id 11107170)1 dos Santos N.R....van Kessel A.G. (2001)
    10. 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)

    (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 PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SSX4B Pharmacogenomics, SNPs, Pathways
    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 LifeMap Sciences, 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 from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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