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SSX6 Gene

pseudogene   GIFtS: 40
GCID: GC0XP047967

Synovial Sarcoma, X Breakpoint 6 (Pseudogene)

(Previous names: SSX family pseudogene 2, synovial sarcoma, X breakpoint...)
(Previous symbol: SSXP2)
  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 6 (Pseudogene)1 2
SSXP21 2
SSX Family Pseudogene 21
Synovial Sarcoma, X Breakpoint 61
dJ54B20.12
psiSSX22

External Ids:    HGNC: 196521   Entrez Gene: 2806572   Ensembl: ENSG000001714837   OMIM: 3005415   UniProtKB: Q7RTT63   

Export aliases for SSX6 gene to outside databases

Previous GC identifers: GC0XU900001 GC0XP046793 GC0XP047013 GC0XP047723 GC0XP047852


(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 SSX6 Gene:
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 is classified as a pseudogene because a splice donor in the 3' UTR has changed
compared to other family members, rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
(provided by RefSeq, Aug 2009)

GeneCards Summary for SSX6 Gene:
SSX6 (synovial sarcoma, X breakpoint 6 (pseudogene)) is a pseudogene. Diseases associated with SSX6 include synovial sarcoma, and sarcoma. GO annotations related to this gene include nucleic acid binding.

UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6
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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RefSeq DNA sequence:
NC_000023.11  NC_018934.2  NT_079573.5  
Regulatory elements:
   Regulatory transcription factor binding sites in the SSX6 gene promoter:
         CRE-BP1   SREBP-1a   SREBP-1c   ATF-2   FOXD3   SREBP-1b   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSSX6 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SSX6


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

Entrez Gene cytogenetic band: Xp11.2   Ensembl cytogenetic band:  Xp11.23   HGNC cytogenetic band: Xp11.23

SSX6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SSX6 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP047967:  view genomic region     (about GC identifiers)

Start:
47,967,367 bp from pter      End:
47,980,068 bp from pter
Size:
12,702 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6 (See protein sequence)
Recommended Name: Putative protein SSX6  
Size: 188 amino acids; 21688 Da
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for SSX6: NX_Q7RTT6

Explore proteomics data for SSX6 at MOPED


See SSX6 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 Q7RTT6

ProtoNet protein and cluster: Q7RTT6

1 Blocks protein domain: IPB001909 KRAB box

UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6
Similarity: Belongs to the SSX family
Similarity: Contains 1 KRAB-related domain


SSX6 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: SSX6_HUMAN, Q7RTT6
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--
     
SSX6 for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for SSX6:
 Decreased Wnt reporter activit 

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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

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

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

SSX6 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 SSX6
Interactions:

    Search GeneGlobe Interaction Network for SSX6

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--

SSX6 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 SSX6



(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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SSX6 gene: 
NM_173357.2  

Unigene Cluster for SSX6:

Synovial sarcoma, X breakpoint 6 (pseudogene)
Hs.511998  [show with all ESTs]
Unigene Representative Sequence: AK302765
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000412590(uc011mlv.2) ENST00000376932 ENST00000509958 ENST00000319275(uc022bvt.1)

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Additional mRNA sequence: 

AK302765.1 NR_028366.1 

4 AceView cDNA sequences:

NM_173357 BM835112 BK000686 BF173737 

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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SSX6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SSX6 Expression
About this image

SSX6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SSX6 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.511998

UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6
Tissue specificity: Not detected in any normal tissues. Expressed in a melanoma cell line

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In Situ
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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 SSX6 (if available)
TreeFam Gene Tree for SSX6 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SSX6 gene
16 SIMAP similar genes for SSX6 using alignment to 1 protein entry:     SSX6_HUMAN:
SYT-SSX2    SS18/SSX2 fusion    SSX-HSTT    SYT-SSX1    SS18/SSX1 fusion    SSX1
SSX8    SSX5    SSX3    SSX2    SSX7    SSX2B
SSX4B    SSX9    SSX4    SSX10

SSX6 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for SSX6
PGOHUM00000250069


(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 SSX6 (see all 321)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1113556401,2
C,F--47965452(+) AGCCTG/CTGGAG 1 -- us2k11Minor allele frequency- C:0.50WA 2
rs1928858561,2
--47965453(+) GCCTCC/TGGAGG 1 -- us2k10--------
rs1503327951,2
--47965472(+) CCTGCC/TGACAA 1 -- us2k10--------
rs1850722411,2
--47965473(+) CTGCCA/GACAAC 1 -- us2k10--------
rs1879981311,2
--47965598(+) GGAATA/TTGGGG 1 -- us2k10--------
rs1382604251,2
--47965736(+) GGGATC/GGTTCA 1 -- us2k10--------
rs5650281,2
C,F,A,H--47966001(-) cagtgC/Tgcaga 1 -- us2k13Minor allele frequency- T:0.33NA 6
rs1928349681,2
--47966165(+) TGTAGA/GTGGAA 1 -- us2k10--------
rs1838496371,2
--47966201(+) TGGAGA/GTACTA 1 -- us2k10--------
rs5235471,2
C,F,O,A,H--47966274(-) AATTCA/GGGCCC 1 -- us2k117Minor allele frequency- G:0.56NS EA NA WA 1804

HapMap Linkage Disequilibrium report for SSX6 (47967367 - 47980068 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for SSX6 (see all 25):    About this table    
Variant IDTypeSubtypePubMed ID
nsv6892CNV Insertion18451855
nsv438131CNV Loss16468122
nsv470351CNV Loss18288195
nsv519165CNV Loss19592680
nsv6890CNV Loss18451855
dgv268e55CNV Loss17911159
nsv521227CNV Gain19592680
dgv37n14CNV Gain18776910
nsv9941CNV Gain18304495
nsv9940CNV Gain18304495

Locus Specific Mutation Databases (LSDB): SSX6

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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: 300541    OMIM disorders: --

3 diseases for SSX6:    
About MalaCards
synovial sarcoma    sarcoma    melanoma


SSX6 for disorders           About GeneDecksing


Export disorders for SSX6 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 SSX6 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SSX6)
    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. The (epi)genetics of human synovial sarcoma. (PubMed id 17117414)1 de Bruijn D.R....van Kessel A.G. (amp 2007)
  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)
  5. Molecular mechanisms underlying human synovial sarcoma development. (PubMed id 11107170)1 dos Santos N.R....van Kessel A.G. (amp 2001)

(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: 280657 HGNC: 19652 AceView: SSX6 Ensembl:ENSG00000171483 euGenes: HUgn280657
ECgene: SSX6 H-InvDB: SSX6

(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 SSX6 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for SSX6 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 SSX6 gene:
Search GeneIP for patents involving SSX6

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
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 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SSX6
 LSBio Antibodies in human, mouse, rat for SSX6
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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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