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

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: mouse all
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Genomic context

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Targeting SDCBP2 in acute myeloid leukemia.
Title: Targeting SDCBP2 in acute myeloid leukemia.
These results identified syntenin-2 as the first PDZ domain protein controlled by HPV8 and HPV16 at the mRNA level.
Title: Human papillomavirus type 8 E6 oncoprotein inhibits transcription of the PDZ protein syntenin-2.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Z94646 (e-PCR)
- UniSTS:37644

SHGC-37152 (e-PCR)
- UniSTS:31364

D5S1597E (e-PCR)
- UniSTS:151019

Readthrough FKBP1A-SDCBP2

Readthrough gene: FKBP1A-SDCBP2, Included gene: FKBP1A

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 more info	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

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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

NG_029926.2 RefSeqGene

Range

5097..24327

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001199784.2 → NP_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:117 → 185

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:191 → 264

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) ...
NM_015685.6 → NP_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:32 → 100

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:106 → 179

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) ...
NM_080489.5 → NP_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:117 → 185

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:191 → 264

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) ...