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synovial sarcoma, X breakpoint 6 (pseudogene)(Previous names: SSX family pseudogene 2, synovial sarcoma, X breakpoint...)
(Previous symbol: SSXP2)
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Aliases
for SSX6 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA
Quality score for the ORGUL clustered with this gene is 3
| Aliases |
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| Synovial Sarcoma, X Breakpoint 6 (Pseudogene)1 2 | | SSXP21 2 | | PsiSSX21 | | SSX Family Pseudogene 21 | | Synovial Sarcoma, X Breakpoint 61 | | DJ54B20.11 |
| External Ids: | HGNC: 196521 | Entrez Gene: 2806572 | Ensembl: ENSG000001714837 | OMIM: 3005415 | UniProtKB: Q7RTT63 |
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| | ORGUL members: | |
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| NONCODE:n408214 | |
Export aliases for SSX6 gene to outside databasesPrevious GC identifers: GC0XU900001 GC0XP046793 GC0XP047013 GC0XP047723 GC0XP047852
Summaries
for SSX6 gene(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 SSX6:
This gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins mayfunction as transcriptional repressors. They are also capable of eliciting spontaneously humoral and cellular immuneresponses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. SSX1, SSX2 andSSX4 genes have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas. Thisgene 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)
UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6Function: Could act as a modulator of transcription
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Genomic Views
for SSX6 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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000023.10 NC_018934.1 NT_079573.4
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the SSX6 gene promoter:
CRE-BP1 SREBP-1a SREBP-1c ATF-2 FOXD3 SREBP-1b
Other transcription factors
Search SABiosciences Chromatin IP Primers for SSX6
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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: Xp11.23SSX6 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome X GeneLoc Exon Structure GeneLoc location for GC0XP047967: view genomic region
(about GC identifiers)
Start:
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47,967,365 bp from pter |
End:
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47,980,073 bp from pter |
Size:
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12,709 bases |
Orientation:
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plus strand |
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Proteins
for SSX6 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
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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 pseudogeneExplore the universe of human proteins at neXtProt for SSX6: NX_Q7RTT6
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q7RTT6
SSX6 Protein expression data from MOPED and PaxDb: About this image 
ENSEMBL proteins: ENSP00000366131 ENSP00000423277 ENSP00000325176
Human Recombinant Protein Products:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- |
SSX6 for ontologies About GeneDecksing
SSX6 Antibody Products:
Assay Products for SSX6: |
Protein
Domains /
Families
for SSX6 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
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SSX6 for domains About GeneDecksing
3 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q7RTT6ProtoNet protein and cluster: Q7RTT6 1 Blocks protein family: IPB001909 KRAB box
UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6Similarity: Belongs to the SSX familySimilarity: Contains 1 KRAB-related domain |
Function
for SSX6 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
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,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
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Function Summary:
UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6Function: Could act as a modulator of transcription
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
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| GO:0003676 | nucleic acid binding |
IEA | -- |
SSX6 for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for SSX6:
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Pathways & Interactions
for SSX6 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SSX6
Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
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| GO:0006351 | transcription, DNA-dependent |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
IEA | -- |
SSX6 for ontologies About GeneDecksing
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Drugs & Compounds
for SSX6 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for SSX6
Search CenterWatch for drugs/clinical trials and news about SSX6 
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Transcripts
for SSX6 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
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,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
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: AK3027654 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000376932 ENST00000412590(uc011mlv.2) ENST00000509958 ENST00000319275(uc022bvt.1)
Additional cDNA sequence: AK302765.1 NR_028366.1 4 AceView cDNA sequences: BM835112 NM_173357 BK000686 BF173737
GeneLoc Exon Structure
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Expression
for SSX6 gene
(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
| SSX6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See SSX6 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SSX6
SOURCE GeneReport for Unigene cluster: Hs.511998
UniProtKB/Swiss-Prot: SSX6_HUMAN, Q7RTT6Tissue specificity: Not detected in any normal tissues. Expressed in a melanoma cell line
SABiosciences Custom PCR Arrays for SSX6
Primer
Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SSX6
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat SSX6 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SSX6 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSX6 |
Orthologs
for SSX6 gene
(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 SSX6 (if available)
TreeFam Gene Tree for SSX6 (if available) |
Paralogs
for SSX6 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for SSX6 gene
- SSX52 SSX2B2 SSX22 SSX92 SSX42 SSX4B2 SSX72 SSX12
- SSX32
18 SIMAP similar genes for SSX6 using alignment to 3 protein entries: SSX6_HUMAN (see all proteins):SYT-SSX2 SS18/SSX2 fusion SSX-HSTT SSX1 SYT-SSX1 SSX2B
SSX7 SSX8 SS18/SSX1 fusion SSX3 SSX5 SSX2
SSX9 SSX11 SSX4B SSX4 SSX10 PRDM9
SSX6 for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for SSX6
PGOHUM00000250069
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Genomic Variants
for SSX6 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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
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| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr X pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for SSX6 (47967365 - 47980073 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 33 variations for SSX6
15/32 CNVs (see all 32): 83493 34416 4149 67975 0822 8912 53004 7789 2277 8304 37578 8306 8305 1847 67974
1 Indel: 33485
Locus Specific Mutation Databases (LSDB): SSX6
| SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for SSX6 gene
(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.)
About This Section
|
SSX6 for disorders About GeneDecksing
OMIM gene information: 300541
OMIM disorders: --
3  diseases for SSX6: About MalaCardssynovial sarcoma sarcoma melanoma
Export disorders for SSX6 gene to outside databases
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Publications
for SSX6 gene (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 SSX6 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SSX6) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- The SSX gene family: characterization of 9 complete genes. (PubMed id 12216073)1, 2, 3 Gure A.O.... Chen Y.-T. (2002)
- The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)
- The (epi)genetics of human synovial sarcoma. (PubMed id 17117414)1 de Bruijn D.R....van Kessel A.G. (2007)
- 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)
- Molecular mechanisms underlying human synovial sarcoma development. (PubMed id 11107170)1 dos Santos N.R....van Kessel A.G. (2001)
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External Searches for SSX6 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
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Genome Databases showing SSX6 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
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Other Databases showing SSX6 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing SSX6 gene(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
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About This Section
| 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
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Products
for SSX6 gene(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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
About This Section
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|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SSX6 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SSX6 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SSX6 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SSX6 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSX6 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SSX6 |
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| | | | Search Tocris compounds for SSX6 |
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 | | | SSX6 Proteins, Antibodies, CLIAs, and ELISAs |
| | | |  |  |  | | | | Search ThermoFisher Antibodies for SSX6 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSX6 |
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GeneCards Homepage -
Last full update: 18 Mar 2013 -
Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013
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