U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    SSX2B SSX family member 2B [ Homo sapiens (human) ]

    Gene ID: 727837, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    SSX2Bprovided by HGNC
    Official Full Name
    SSX family member 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:22263
    See related
    Ensembl:ENSG00000268447 AllianceGenome:HGNC:22263
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SSX; CT5.2; CT5.2b; HOM-MEL-40
    Summary
    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: 6757, located about 45 kb upstream in the opposite orientation on chromosome X. [provided by RefSeq, Jul 2013]
    Expression
    Restricted expression toward testis (RPKM 18.4) See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See SSX2B in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (52751252..52761536)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (52036196..52046488)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (52780329..52790617)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ornithine aminotransferase pseudogene Neighboring gene ornithine aminotransferase pseudogene Neighboring gene S100A11 pseudogene 8 Neighboring gene SSX family member 21, pseudogene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. SS18-SSX Expression in a Contemporary Cohort of Primary Renal Synovial Sarcoma: A Multi-Institutional Experience of Fourteen Patients. Challa B, et al. Int J Surg Pathol, 2023 Oct. PMID 36591871
    2. Identification of two alternative fusion genes, SYT-SSX1 and SYT-SSX2, in t(X;18)(p11.2;q11.2)-positive synovial sarcomas. de Leeuw B, et al. Hum Mol Genet, 1995 Jun. PMID 7655467
    3. Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial sarcoma. Crew AJ, et al. EMBO J, 1995 May 15. PMID 7539744, Free PMC Article
    4. Molecular diagnosis of synovial sarcoma and characterization of a variant SYT-SSX2 fusion transcript. Fligman I, et al. Am J Pathol, 1995 Dec. PMID 7495284, Free PMC Article
    5. Heterogeneous expression of the SSX cancer/testis antigens in human melanoma lesions and cell lines. dos Santos NR, et al. Cancer Res, 2000 Mar 15. PMID 10749136

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SS18-SSX Expression in a Contemporary Cohort of Primary Renal Synovial Sarcoma: A Multi-Institutional Experience of Fourteen Patients.
      Title: SS18-SSX Expression in a Contemporary Cohort of Primary Renal Synovial Sarcoma: A Multi-Institutional Experience of Fourteen Patients.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC21532, MGC88485

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    protein SSX2
    Names
    cancer/testis antigen 5.2
    cancer/testis antigen family 5, member 2b
    synovial sarcoma, X breakpoint 2B
    tumor antigen HOM-MEL-40

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001164417.3 → NP_001157889.1  protein SSX2 isoform b

      See identical proteins and their annotated locations for NP_001157889.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) contains a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC244505, BC016957, BC071827
      Consensus CDS
      CCDS48129.1
      UniProtKB/Swiss-Prot
      Q16385, Q5JS26, Q96IP7, Q9BU88
      Related
      ENSP00000470740.2, ENST00000596480.6
      Conserved Domains (3) summary
      cd07765
      Location:24 → 61
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00349
      Location:23 → 82
      KRAB; krueppel associated box
      pfam09514
      Location:156 → 187
      SSXRD; SSXRD motif

    2. NM_001278701.2 → NP_001265630.1  protein SSX2 isoform a

      See identical proteins and their annotated locations for NP_001265630.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC244505, BC071827
      Consensus CDS
      CCDS65267.1
      UniProtKB/Swiss-Prot
      Q16385
      Related
      ENSP00000477922.1, ENST00000612490.1
      Conserved Domains (1) summary
      smart00349
      Location:23 → 82
      KRAB; krueppel associated box

    3. NM_001278702.2 → NP_001265631.1  protein SSX2 isoform c

      See identical proteins and their annotated locations for NP_001265631.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (c) contains a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC244505, BC016957, BC071827, BE391023
      UniProtKB/TrEMBL
      R9QTR3
      Conserved Domains (3) summary
      cd07765
      Location:24 → 61
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00349
      Location:23 → 82
      KRAB; krueppel associated box
      pfam09514
      Location:182 → 213
      SSXRD; SSXRD motif

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      52751252..52761536
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      52036196..52046488
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16385.2 GenPept UniProtKB/Swiss-Prot:Q16385

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools