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SSX9 Gene

pseudogene   GIFtS: 34
GCID: GC0XM048154

Synovial Sarcoma, X Breakpoint 9

  See SSX9-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 91 2

External Ids:    HGNC: 196551   Entrez Gene: 2806602   Ensembl: ENSG000002046487   OMIM: 3005445   UniProtKB: Q7RTT33   

Export aliases for SSX9 gene to outside databases

Previous GC identifers: GC0XU900003 GC0XM046981 GC0XM047201 GC0XM047202 GC0XM047911 GC0XM048039


(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 SSX9 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 gene appears not to be involved in this type of
chromosome translocation. (provided by RefSeq, Jul 2008)

GeneCards Summary for SSX9 Gene:
SSX9 (synovial sarcoma, X breakpoint 9) is a pseudogene. Diseases associated with SSX9 include synovial sarcoma, and sarcoma. GO annotations related to this gene include nucleic acid binding.

UniProtKB/Swiss-Prot: SSX9_HUMAN, Q7RTT3
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 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 SSX9 gene promoter:
         HOXA9B   ATF-2   CUTL1   HNF-1A   C/EBPalpha   HNF-4alpha1   COMP1   HNF-1   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSSX9 promoter sequence
   Search Chromatin IP Primers for SSX9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SSX9


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

SSX9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SSX9 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM048154:  view genomic region     (about GC identifiers)

Start:
48,154,885 bp from pter      End:
48,165,732 bp from pter
Size:
10,848 bases      Orientation:
minus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SSX9_HUMAN, Q7RTT3 (See protein sequence)
Recommended Name: Protein SSX9  
Size: 188 amino acids; 21553 Da

Explore the universe of human proteins at neXtProt for SSX9: NX_Q7RTT3

Explore proteomics data for SSX9 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SSX9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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 Q7RTT3

    ProtoNet protein and cluster: Q7RTT3

    1 Blocks protein domain: IPB001909 KRAB box

    UniProtKB/Swiss-Prot: SSX9_HUMAN, Q7RTT3
    Similarity: Belongs to the SSX family
    Similarity: Contains 1 KRAB-related domain


    Find genes that share domains with SSX9           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SSX9_HUMAN, Q7RTT3
    Function: Could act as a modulator of transcription

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
         
    Find genes that share ontologies with SSX9           About GenesLikeMe


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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
    golgi apparatus1
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with SSX9           About GenesLikeMe


    (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 SSX9
    Interactions:

        Search GeneGlobe Interaction Network for SSX9

    Gene Ontology (GO): 2 biological process terms:    About this table

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

    Find genes that share ontologies with SSX9           About GenesLikeMe



    (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 SSX9



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SSX9 gene: 
    NM_174962.3  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376909 ENST00000608568 ENST00000407081(uc022bvu.1)
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    2 AceView cDNA sequences:

    NM_174962 BK000689 

    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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    SSX9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SSX9 Expression
    About this image

    SSX9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SSX9 Protein Expression

    UniProtKB/Swiss-Prot: SSX9_HUMAN, Q7RTT3
    Tissue specificity: Not detected in any normal or tumor tissues

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    In Situ
    Assay Products:
     

     
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    (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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      --

    ENSEMBL Gene Tree for SSX9 (if available)
    TreeFam Gene Tree for SSX9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SSX9 gene
    17 SIMAP similar genes for SSX9 using alignment to 1 protein entry:     SSX9_HUMAN:
    SSX10    SSX7    SYT-SSX2    SSX2B    SSX3    SSX5
    SS18/SSX2 fusion    SSX2    SSX4B    SSX-HSTT    SSX1    SSX4
    SSX8    SYT-SSX1    SSX6    SS18/SSX1 fusion    PRDM7_V2

    Find genes that share paralogs with SSX9           About GenesLikeMe



    (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 SSX9 (see all 139)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1410183191,2
    --48160510(+) TGTTGC/TGAGAG 1 -- ds50010--------
    rs1903497671,2
    --48160516(+) GAGAGC/TGGGTG 1 -- ds50010--------
    rs48246921,2
    C,F,A,H--48160540(+) ACCAGG/CAGGCC 1 -- ds50011Minor allele frequency- C:0.50NA 4
    rs1825258261,2
    --48160635(+) GGATTA/CGACTA 1 -- ds50010--------
    rs1849924151,2
    --48160753(+) CTTTAC/TTTCCA 1 -- ds50010--------
    rs1882368081,2
    --48160895(+) GAGGTA/CTTCTT 1 -- ds50010--------
    rs128457511,2
    C--48160923(+) ATCCAC/TGTGAA 1 -- ds50014Minor allele frequency- T:0.00NA CSA 5
    rs1485134761,2
    --48160970(+) AAAGAA/TGTATT 1 -- ds50010--------
    rs66097001,2
    C,F,H--48160974(+) ATGTAT/CTGAGG 1 -- ds50015Minor allele frequency- C:0.02NS NA 790
    rs66097011,2
    C--48161114(+) CAAAGA/GTTCTC 1 -- nc-transcript-variant4Minor allele frequency- G:0.00NA CSA 5

    HapMap Linkage Disequilibrium report for SSX9 (48154885 - 48165732 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SSX9: --
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    SeqTarget long-range PCR primers for resequencing SSX9
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300544    OMIM disorders: --

    2 diseases for SSX9:    
    About MalaCards
    synovial sarcoma    sarcoma


    Find genes that share disorders with SSX9           About GenesLikeMe


    Export disorders for SSX9 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 SSX9 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SSX9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The SSX gene family: characterization of 9 complete genes. (PubMed id 12216073)1, 2, 3 Gure A.O.... Chen Y.-T. (Int. J. Cancer 2002)
    2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    4. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 280660 HGNC: 19655 AceView: SSX9 Ensembl:ENSG00000204648 euGenes: HUgn280660
    ECgene: SSX9 H-InvDB: SSX9

    (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 SSX9 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SSX9 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 SSX9 gene:
    Search GeneIP for patents involving SSX9

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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     Search ThermoFisher Antibodies for SSX9
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSX9
     inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SSX9
     inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SSX9
     Search LSBio for Antibodies for SSX9
    Customized transgenic rodents for:
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     Browse compounds at ApexBio
     Search Addgene for plasmids for SSX9
      Search eBioscience for proteins for SSX9
      Search eBioscience for elisas for SSX9
      eBioscience FlowRNA Probe Sets
           
    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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