SSX4B Gene
protein-coding GIFtS: 43
GCID: GC0XM048261
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synovial sarcoma, X breakpoint 4B
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Aliases
for SSX4B gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Synovial Sarcoma, X Breakpoint 4B1 2 | | OTTHUMT000000565101 2 | | Cancer/Testis Antigen 5.42 3 | | CT5.42 3 | | Protein SSX42 | | SSX4A3 |
Export aliases for SSX4B gene to outside databasesPrevious GC identifers: GC00U921552 GC0XU900601 GC0XM048146 |
Summaries
for SSX4B 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 SSX4B:
The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. Theseproteins may function as transcriptional repressors. They are also capable of eliciting spontaneously humoral andcellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-basedimmunotherapy. SSX1, SSX2 and SSX4 genes have been involved in the t(X;18) translocation characteristically found inall synovial sarcomas. This translocation results in the fusion of the synovial sarcoma translocation gene onchromosome 18 to one of the SSX genes on chromosome X. Chromosome Xp11 contains a segmental duplication resulting intwo 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 identifiedfor this gene. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224Function: Could act as a modulator of transcription
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Genomic Views
for SSX4B 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 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
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: Xp11.23SSX4B 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 GC0XM048261: view genomic region
(about GC identifiers)
Start:
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48,261,524 bp from pter |
End:
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48,271,344 bp from pter |
Size:
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9,821 bases |
Orientation:
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minus strand |
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Proteins
for SSX4B 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
|
UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224 (See
protein sequence)Recommended Name: Protein SSX4 Size: 188 amino acids; 21858 Da
Secondary accessions: B2RPE3 Q5JQZ0 Q9UJU9Explore the universe of human proteins at neXtProt for SSX4B: NX_O60224
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_O60224
SSX4B Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_001030004.1 NP_001035702.1
ENSEMBL proteins: ENSP00000366081 ENSP00000380134
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
SSX4B for ontologies About GeneDecksing
SSX4B Antibody Products:
Assay Products for SSX4B: |
Protein
Domains /
Families
for SSX4B gene(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:Graphical View of Domain Structure for InterPro Entry O60224ProtoNet protein and cluster: O60224 1 Blocks protein family: IPB001909 KRAB box
UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224Similarity: Belongs to the SSX familySimilarity: Contains 1 KRAB-related domain |
Function
for SSX4B 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
|
Function Summary:
UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224Function: Could act as a modulator of transcription
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SSX4B (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SSX4B (see all 2)
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Synthesis Service for SSX4B | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSX4B |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0003676 | nucleic acid binding |
IEA | -- |
SSX4B for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for SSX4B:
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Pathways & Interactions
for SSX4B 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 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 I2DAbout this table
Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006351 | transcription, DNA-dependent |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
IEA | -- |
SSX4B for ontologies About GeneDecksing
|
Drugs & Compounds
for SSX4B 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 SSX4B
Search CenterWatch for drugs/clinical trials and news about SSX4B / SSX4
|
Transcripts
for SSX4B 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 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, BC0053252 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000376884(uc004djh.1) ENST00000396928(uc004dji.1)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SSX4B (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SSX4B (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): SSX4B (NM_001034832) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for SSX4B | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSX4B |
Additional cDNA sequence: BC005325.1 BC103864.1 2 DOTS entries: DT.40305548 DT.40127997
GeneLoc Exon Structure
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Expression
for SSX4B 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
| SSX4B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
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
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SSX4B
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat SSX4B | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SSX4B | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSX4B |
Orthologs
for SSX4B 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 SSX4B (if available)
TreeFam Gene Tree for SSX4B (if available) |
Paralogs
for SSX4B gene(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
15 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 PRDM9
SSX4B for paralogs About GeneDecksing
|
Genomic Variants
for SSX4B 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
|
| 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 SSX4B (48261524 - 48271344 bp)
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 | SABiosciences Cancer Mutation PCR Assays |
|
Disorders
/ Diseases
for SSX4B 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
|
SSX4B for disorders About GeneDecksing
6  diseases for SSX4B: About MalaCardssynovial sarcoma sarcoma hepatocellular carcinoma melanoma
carcinoma retinitis
1 disease from the University of Copenhagen DISEASES database for SSX4B:Synovial sarcoma Export disorders for SSX4B gene to outside databases
|
Publications
for SSX4B 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 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 |
- The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)
- 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)
- 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)
- Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
- CD4+ T cell responses to SSX-4 in melanoma patients. (PubMed id 15814740)1 Ayyoub M....Valmori D. (2005)
- 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)
- The SSX gene family: characterization of 9 complete genes. (PubMed id 12216073)1 Gure A.O.... Chen Y.-T. (2002)
- 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)
- 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)
|
External Searches for SSX4B gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
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Genome Databases showing SSX4B gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing SSX4B gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing SSX4B 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
|
|
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
|
Products
for SSX4B 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 SSX4B | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SSX4B | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SSX4B | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SSX4B | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSX4B | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SSX4B |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSX4B |
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