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    SDCBP2 syndecan binding protein 2 [ Homo sapiens (human) ]

    Gene ID: 27111, updated on 27-Nov-2024

    Summary

    Official Symbol
    SDCBP2provided by HGNC
    Official Full Name
    syndecan binding protein 2provided by HGNC
    Primary source
    HGNC:HGNC:15756
    See related
    Ensembl:ENSG00000125775 MIM:617358; AllianceGenome:HGNC:15756
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ST2; ST-2; SITAC; SITAC18
    Summary
    The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2) and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. [provided by RefSeq, Sep 2011]
    Expression
    Biased expression in duodenum (RPKM 54.3), small intestine (RPKM 53.5) and 8 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SDCBP2 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (1309909..1329139, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (1359112..1378345, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (1290553..1309783, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12587 Neighboring gene RAD21 cohesin complex component like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12589 Neighboring gene MPRA-validated peak4117 silencer Neighboring gene syntaphilin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:1275655-1276546 Neighboring gene FKBP1A-SDCBP2 readthrough (NMD candidate) Neighboring gene uncharacterized LOC124904856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17457 Neighboring gene Sharpr-MPRA regulatory region 67 Neighboring gene SDCBP2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 14422 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:1358033-1359232 Neighboring gene FKBP prolyl isomerase 1A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:1371785-1372298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:1373090-1373590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12592 Neighboring gene uncharacterized LOC105372497 Neighboring gene microRNA 6869 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:1396577-1397776

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef inhibits the expression of syndecan binding protein (syntenin) in human podocyte PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ12256

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phosphatidylinositol-4,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intracellular transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nervous system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IC
    Inferred by Curator
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    syntenin-2
    Names
    syndecan binding protein (syntenin) 2

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_029926.2 RefSeqGene

      Range
      5097..24327
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001199784.2NP_001186713.1  syntenin-2 isoform a

      See identical proteins and their annotated locations for NP_001186713.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same isoform (a).
      Source sequence(s)
      AF159228, BM987490, BU684857
      Consensus CDS
      CCDS42848.1
      UniProtKB/Swiss-Prot
      O95892, Q5W0X1, Q9BZ42, Q9H190, Q9H567, Q9NRY8
      Related
      ENSP00000342935.3, ENST00000339987.7
      Conserved Domains (2) summary
      cd00136
      Location:117185
      PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
      cd00992
      Location:191264
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    2. NM_015685.6NP_056500.2  syntenin-2 isoform b

      See identical proteins and their annotated locations for NP_056500.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AF131809, BC002727, BI599848, BM987490, BU684857
      Consensus CDS
      CCDS13013.1
      UniProtKB/Swiss-Prot
      Q9H190
      Related
      ENSP00000371229.3, ENST00000381808.7
      Conserved Domains (2) summary
      cd00136
      Location:32100
      PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
      cd00992
      Location:106179
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    3. NM_080489.5NP_536737.3  syntenin-2 isoform a

      See identical proteins and their annotated locations for NP_536737.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Both variants 1 and 3 encode the same isoform (a).
      Source sequence(s)
      BC002727, BM987490, BU684857
      Consensus CDS
      CCDS42848.1
      UniProtKB/Swiss-Prot
      O95892, Q5W0X1, Q9BZ42, Q9H190, Q9H567, Q9NRY8
      Related
      ENSP00000354013.3, ENST00000360779.4
      Conserved Domains (2) summary
      cd00136
      Location:117185
      PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
      cd00992
      Location:191264
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      1309909..1329139 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      1359112..1378345 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)