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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
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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)

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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)