Human Gene SSX2B (uc004dra.1)
  Description: Homo sapiens synovial sarcoma, X breakpoint 2 (SSX2B), transcript variant 1, mRNA.
RefSeq Summary (NM_003147): 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 spontaneous humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. This gene, and also the SSX1 and SSX4 family members, have been involved in t(X;18)(p11.2;q11.2) translocations that are 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. The encoded hybrid proteins are likely responsible for transforming activity. Alternative splicing of this gene results in multiple transcript variants. This gene also has an identical duplicate, GeneID: 727837, located about 45 kb downstream in the opposite orientation on chromosome X. [provided by RefSeq, Jul 2013].
Transcript (Including UTRs)
   Position: hg19 chrX:52,780,308-52,790,617 Size: 10,310 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chrX:52,781,758-52,789,480 Size: 7,723 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersMalaCardsGene AllelesMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:52,780,308-52,790,617)mRNA (may differ from genome)Protein (223 aa)
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-  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: SSX2B
Diseases sorted by gene-association score: sarcoma (9), epithelioid cell synovial sarcoma (4), synovium cancer (4), kidney hemangiopericytoma (3), extraskeletal mesenchymal chondrosarcoma (3), connective tissue cancer (3), sarcoma, synovial (2), spindle cell synovial sarcoma (2), cellular congenital mesoblastic nephroma (2), lung sarcoma (1), n syndrome (1), malignant mesenchymoma (1)

+  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 -31.89108-0.295 Picture PostScript Text
3' UTR -161.04672-0.240 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
  Pfam Domains:
PF01352 - KRAB box

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

ModBase Predicted Comparative 3D Structure on Q16385-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC103863 - Homo sapiens synovial sarcoma, X breakpoint 2, mRNA (cDNA clone MGC:119055 IMAGE:40003337), complete cds.
JD378390 - Sequence 359414 from Patent EP1572962.
Z49105 - H.sapiens HD21 mRNA.
X86175 - H.sapiens mRNA for SSX2 protein.
BC016957 - Homo sapiens synovial sarcoma, X breakpoint 2, mRNA (cDNA clone MGC:21532 IMAGE:3916128), complete cds.
BC002818 - Homo sapiens synovial sarcoma, X breakpoint 2, mRNA (cDNA clone MGC:3884 IMAGE:3636268), complete cds.
BC007343 - Homo sapiens synovial sarcoma, X breakpoint 2, mRNA (cDNA clone MGC:15364 IMAGE:3615133), complete cds.
BC071827 - Homo sapiens synovial sarcoma, X breakpoint 2, mRNA (cDNA clone MGC:88485 IMAGE:4641362), complete cds.
JD240326 - Sequence 221350 from Patent EP1572962.
JD057997 - Sequence 39021 from Patent EP1572962.
JD488298 - Sequence 469322 from Patent EP1572962.
Z49106 - H.sapiens Mel-40 mRNA for B-cell antigen.
KJ892211 - Synthetic construct Homo sapiens clone ccsbBroadEn_01605 SSX2 gene, encodes complete protein.
CU675627 - Synthetic construct Homo sapiens gateway clone IMAGE:100017997 5' read SSX2 mRNA.
KJ897607 - Synthetic construct Homo sapiens clone ccsbBroadEn_07001 SSX2 gene, encodes complete protein.
AB464264 - Synthetic construct DNA, clone: pF1KB8334, Homo sapiens SSX2 gene for synovial sarcoma, X breakpoint 2, without stop codon, in Flexi system.
EU446707 - Synthetic construct Homo sapiens clone IMAGE:100070091; IMAGE:100011916; FLH258152.01L synovial sarcoma, X breakpoint 2 (SSX2) gene, encodes complete protein.
AM393802 - Synthetic construct Homo sapiens clone IMAGE:100002115 for hypothetical protein (SSX2 gene).
BC069313 - Homo sapiens synovial sarcoma, X breakpoint 2, transcript variant 2, mRNA (cDNA clone MGC:96920 IMAGE:7262129), complete cds.
JX014236 - Homo sapiens cell-line SKMEL28 SSX2 mRNA, complete cds, alternatively spliced.
S79894 - SYT...SSX {translocation breakpoint} [human, synovial sarcoma patient, tumor, mRNA Mutant, 3 genes, 165 nt].
S79332 - SYT...SSX2 {translocation breakpoint} [human, synovial sarcomas, mRNA Partial Mutant, 3 genes, 585 nt].
X79200 - Homo spaiens mRNA for SYT-SSX protein.
AF190791 - Homo sapiens SSX2 (SSX2) mRNA, partial cds, alternatively spliced.
JD349323 - Sequence 330347 from Patent EP1572962.
JD103483 - Sequence 84507 from Patent EP1572962.
JD330243 - Sequence 311267 from Patent EP1572962.
JD060165 - Sequence 41189 from Patent EP1572962.
JD445052 - Sequence 426076 from Patent EP1572962.
JD090320 - Sequence 71344 from Patent EP1572962.
JD267802 - Sequence 248826 from Patent EP1572962.
JD417283 - Sequence 398307 from Patent EP1572962.
JD333979 - Sequence 315003 from Patent EP1572962.
JD285863 - Sequence 266887 from Patent EP1572962.
JD411575 - Sequence 392599 from Patent EP1572962.
JD050238 - Sequence 31262 from Patent EP1572962.
JD053702 - Sequence 34726 from Patent EP1572962.
JD293037 - Sequence 274061 from Patent EP1572962.
JD426958 - Sequence 407982 from Patent EP1572962.
JD188073 - Sequence 169097 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_003147, NP_003138, Q16385-2, SSX2, SSX2A
UCSC ID: uc004dra.1
RefSeq Accession: NM_003147
Protein: Q16385-2, splice isoform of Q16385 CCDS: CCDS65267.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003147.4
exon count: 9CDS single in 3' UTR: no RNA size: 1466
ORF size: 672CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1539.50frame shift in genome: no % Coverage: 98.77
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
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.