Human Gene SSX4B (uc004djh.2)
  Description: Homo sapiens synovial sarcoma, X breakpoint 4B (SSX4B), transcript variant 1, mRNA.
RefSeq Summary (NM_001034832): 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].
Transcript (Including UTRs)
   Position: hg19 chrX:48,261,524-48,271,355 Size: 9,832 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chrX:48,262,898-48,270,814 Size: 7,917 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:48,261,524-48,271,355)mRNA (may differ from genome)Protein (188 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SSX4_HUMAN
DESCRIPTION: RecName: Full=Protein SSX4; AltName: Full=Cancer/testis antigen 5.4; Short=CT5.4;
FUNCTION: Could act as a modulator of transcription.
SIMILARITY: Belongs to the SSX family.
SIMILARITY: Contains 1 KRAB-related domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SSX4B
Diseases sorted by gene-association score: sarcoma (8), synovium cancer (3), sarcoma, synovial (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.1069-0.219 Picture PostScript Text
3' UTR -155.97592-0.263 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001909 - Krueppel-associated_box
IPR003655 - Krueppel-associated_box-rel
IPR019041 - SSXRD_motif

Pfam Domains:
PF01352 - KRAB box
PF09514 - SSXRD motif

SCOP Domains:
109640 - KRAB domain (Kruppel-associated box, Pfam 01352)

ModBase Predicted Comparative 3D Structure on O60224
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003714 transcription corepressor activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC005325 - Homo sapiens synovial sarcoma, X breakpoint 4, mRNA (cDNA clone MGC:12411 IMAGE:3961688), complete cds.
JD285863 - Sequence 266887 from Patent EP1572962.
JD411575 - Sequence 392599 from Patent EP1572962.
JD067830 - Sequence 48854 from Patent EP1572962.
JD213968 - Sequence 194992 from Patent EP1572962.
JD297767 - Sequence 278791 from Patent EP1572962.
JD417283 - Sequence 398307 from Patent EP1572962.
AF114234 - Homo sapiens SYT-SSX4 fusion mRNA, partial sequence.
JD267802 - Sequence 248826 from Patent EP1572962.
JD090320 - Sequence 71344 from Patent EP1572962.
JD152494 - Sequence 133518 from Patent EP1572962.
JD390678 - Sequence 371702 from Patent EP1572962.
BC137394 - Homo sapiens synovial sarcoma, X breakpoint 4B, mRNA (cDNA clone MGC:169015 IMAGE:9021392), complete cds.
BC137395 - Homo sapiens synovial sarcoma, X breakpoint 4B, mRNA (cDNA clone MGC:169016 IMAGE:9021393), complete cds.
AX740218 - Sequence 1 from Patent EP1300463.
U90841 - Homo sapiens SSX4 (SSX4) mRNA, complete cds.
BC153138 - Synthetic construct Homo sapiens clone IMAGE:100016472, MGC:184317 synovial sarcoma, X breakpoint 4B (SSX4B) mRNA, encodes complete protein.
CU675111 - Synthetic construct Homo sapiens gateway clone IMAGE:100016752 5' read SSX4 mRNA.
KJ897609 - Synthetic construct Homo sapiens clone ccsbBroadEn_07003 SSX4 gene, encodes complete protein.
BC148551 - Synthetic construct Homo sapiens clone IMAGE:100015511, MGC:183070 synovial sarcoma, X breakpoint 4B (SSX4B) mRNA, encodes complete protein.
EU446709 - Synthetic construct Homo sapiens clone IMAGE:100070116; IMAGE:100011918; FLH257409.01L synovial sarcoma, X breakpoint 4 (SSX4) gene, encodes complete protein.
AB464265 - Synthetic construct DNA, clone: pF1KB7434, Homo sapiens SSX4B gene for synovial sarcoma, X breakpoint 4B, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RPE3, NM_001034832, NP_005627, O60224, Q5JQZ0, Q9UJU9, SSX4, SSX4A, SSX4_HUMAN, uc004djh.1
UCSC ID: uc004djh.2
RefSeq Accession: NM_001034832
Protein: O60224 (aka SSX4_HUMAN)
CCDS: CCDS35241.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001034832.3
exon count: 8CDS single in 3' UTR: no RNA size: 1244
ORF size: 567CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 868.00frame shift in genome: no % Coverage: 98.71
has start codon: yes stop codon in genome: no # of Alignments: 2
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.