Sdcbp syndecan binding protein [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sdcbpprovided by MGI
Official Full Name: syndecan binding proteinprovided by MGI
Primary source: MGI:MGI:1337026
See related: Ensembl:ENSMUSG00000028249 AllianceGenome:MGI:1337026
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Sycl; MDA-9; syntenin-1
Summary: Enables interleukin-5 receptor binding activity. Involved in positive regulation of cell growth; positive regulation of cell migration; and positive regulation of cell population proliferation. Acts upstream of or within Ras protein signal transduction. Part of interleukin-5 receptor complex. Is expressed in several structures, including central nervous system; heart; nose; skin; and urinary system. Orthologous to human SDCBP (syndecan binding protein). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in placenta adult (RPKM 62.3), bladder adult (RPKM 56.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4; 4 A1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (6365654..6396122)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (6365680..6396122)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker.
Title: Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker.
Binding of syntenin-1 requires phosphorylation of UNC93B1 and provides a mechanism for dynamic regulation of TLR7 activation and signalling
Title: UNC93B1 recruits syntenin-1 to dampen TLR7 signalling and prevent autoimmunity.
High Sdcbp expression is associated with B16 melanoma invasion.
Title: MicroRNA-23a inhibits melanoma cell proliferation, migration, and invasion in mice through a negative feedback regulation of sdcbp and the MAPK/ERK signaling pathway.
Our results suggest that syntenin-1 plays an important role in extinction of cued fear memory by modulating neuronal activity in the basolateral amygdala and infralimbic cortex.
Title: Impairment in extinction of cued fear memory in syntenin-1 knockout mice.
These findings demonstrate that syntenin promotes VEGF signaling and, through its PDZ-dependent interaction with ephrin-B2, enhances VEGF-mediated VEGFR2 endocytosis and subsequent downstream signaling and angiogenesis in endothelial cells
Title: Syntenin promotes VEGF-induced VEGFR2 endocytosis and angiogenesis by increasing ephrin-B2 function in endothelial cells.
Present study is the first demonstration of the relevance of MDA-9/Syntenin expression in regulating inflammation and immunosuppression in the microenvironment thereby impacting tumor growth and metastasis in mouse melanoma model.
Title: Knockout of MDA-9/Syntenin (SDCBP) expression in the microenvironment dampens tumor-supporting inflammation and inhibits melanoma metastasis.
Syntenin-1 negatively regulates the intestinal immunoglobulin production and has a function to maintain the intestinal homeostasis in vivo.
Title: Increased production of intestinal immunoglobulins in Syntenin-1-deficient mice.
ALCAM stably interacts with actin by binding to syntenin-1 and ezrin.
Title: Syntenin-1 and ezrin proteins link activated leukocyte cell adhesion molecule to the actin cytoskeleton.
Angiopoietin-2 secretion by endothelial cell exosomes: regulation by the phosphatidylinositol 3-kinase (PI3K)/Akt/endothelial nitric oxide synthase (eNOS) and syndecan-4/syntenin pathways.
Title: Angiopoietin-2 secretion by endothelial cell exosomes: regulation by the phosphatidylinositol 3-kinase (PI3K)/Akt/endothelial nitric oxide synthase (eNOS) and syndecan-4/syntenin pathways.
MDA-9/syntenin may play a prominent role during normal mouse development in the context of cell proliferation as well as differentiation through modulating multiple signaling pathways as a crucial adaptor protein.
Title: Expression patterns of MDA-9/syntenin during development of the mouse embryo.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (3) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU015268 (e-PCR)
- UniSTS:207592

AA959567 (e-PCR)
- UniSTS:159210

Homology

Homologs of the Sdcbp gene: The Sdcbp gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, mosquito, and frog.
Orthologs from Annotation Pipeline: 396 organisms have orthologs with human gene Sdcbp
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	ISO Inferred from Sequence Orthology more info
enables ephrin receptor binding	ISO Inferred from Sequence Orthology more info
enables frizzled binding	ISO Inferred from Sequence Orthology more info
enables growth factor binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables interleukin-5 receptor binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ionotropic glutamate receptor binding	ISO Inferred from Sequence Orthology more info
enables lipid binding	IEA Inferred from Electronic Annotation more info
enables metalloendopeptidase activity	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol-4,5-bisphosphate binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables syndecan binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables syndecan binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Ras protein signal transduction	IPI Inferred from Physical Interaction more info	PubMed
involved_in actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in intracellular signal transduction	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of receptor internalization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exosomal secretion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of extracellular exosome assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of pathway-restricted SMAD protein phosphorylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of pathway-restricted SMAD protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transforming growth factor beta receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of transforming growth factor beta receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in presynapse assembly	ISO Inferred from Sequence Orthology more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cell junction	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
part_of interleukin-5 receptor complex	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nuclear membrane	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
is_active_in presynapse	ISO Inferred from Sequence Orthology more info
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: syntenin-1

Names: scaffold protein Pbp1; syndecan interacting protein; syndecan-binding protein 1; syntenin

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.

mRNA and Protein(s)

NM_001098227.1 → NP_001091697.1 syntenin-1 isoform 1

See identical proteins and their annotated locations for NP_001091697.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK150278, BB736053, BY387130, BY757323, BY779386, W65143

Consensus CDS

CCDS51110.1

UniProtKB/Swiss-Prot

O08992, Q544P5

Related

ENSMUSP00000029912.5, ENSMUST00000029912.11

Conserved Domains (1) summary

cd00992
Location:113 → 192

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_016807.2 → NP_058087.2 syntenin-1 isoform 2

See identical proteins and their annotated locations for NP_058087.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 2).

Source sequence(s)

AK150278, BB736053, BY387130, BY757323, BY779386, W65143

Consensus CDS

CCDS17951.1

UniProtKB/Swiss-Prot

O08992

UniProtKB/TrEMBL

Q3TMX0

Related

ENSMUSP00000100073.6, ENSMUST00000103008.12

Conserved Domains (1) summary

cd00992
Location:112 → 191

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: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

6365654..6396122

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036164236.1 → XP_036020129.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q544P5

Conserved Domains (1) summary

cd00992
Location:113 → 192

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) ...
XM_036164237.1 → XP_036020130.1 syntenin-1 isoform X2

UniProtKB/TrEMBL

Q3TMX0

Conserved Domains (1) summary

cd00992
Location:112 → 191

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) ...
XM_006538084.5 → XP_006538147.1 syntenin-1 isoform X1

See identical proteins and their annotated locations for XP_006538147.1

UniProtKB/Swiss-Prot

O08992, Q544P5

Related

ENSMUSP00000135777.2, ENSMUST00000175769.8

Conserved Domains (1) summary

cd00992
Location:113 → 192

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) ...
XM_030253672.2 → XP_030109532.1 syntenin-1 isoform X2

UniProtKB/TrEMBL

Q3TMX0

Conserved Domains (1) summary

cd00992
Location:112 → 191

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) ...