Format

Send to:

Choose Destination

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

Gene ID: 27111, updated on 1-Jun-2020

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
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

Genomic context

See SDCBP2 in Genome Data Viewer
Location:
20p13
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (1309909..1329139, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (1290553..1309879, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RAD21 cohesin complex component like 1 Neighboring gene syntaphilin Neighboring gene FKBP1A-SDCBP2 readthrough (NMD candidate) Neighboring gene SDCBP2 antisense RNA 1 Neighboring gene FKBP prolyl isomerase 1A Neighboring gene uncharacterized LOC105372497 Neighboring gene microRNA 6869

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

Homology

Clone Names

  • FLJ12256

Gene Ontology Provided by GOA

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

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_001199784.1NP_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
    Q9H190
    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_015685.5NP_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
    Q9H190
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

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