Sdcbp syndecan binding protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Sdcbpprovided by RGD
Full Name: syndecan binding proteinprovided by RGD
Primary source: RGD:621497
See related: Ensembl:ENSRNOG00000009683 AllianceGenome:RGD:621497
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: mda-9; TACIP18
Summary: Enables several functions, including protein C-terminus binding activity; signaling receptor binding activity; and syndecan binding activity. Involved in presynapse assembly. Predicted to be located in several cellular components, including extracellular exosome; membrane raft; and nucleus. Predicted to be part of interleukin-5 receptor complex. Predicted to be active in cytoplasm and plasma membrane. Orthologous to human SDCBP (syndecan binding protein). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 1386.7), Heart (RPKM 1097.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q12

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (24245279..24314712)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (19473499..19517188)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (19471664..19498499)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

syntenin-1 negatively regulates syndecan-4 function via oligomerization and/or syndecan-4 interaction, impacting cytoskeletal organization and cell migration.
Title: New structural insight of C-terminal region of Syntenin-1, enhancing the molecular dimerization and inhibitory function related on Syndecan-4 signaling.
Syntenin-1 may contribute to the molecular organization of presynaptic active zones by linking ERC2 and other cytoskeletal matrix components to diverse syntenin-1-associated synaptic proteins.
Title: Organization of the presynaptic active zone by ERC2/CAST1-dependent clustering of the tandem PDZ protein syntenin-1.
Syntenin is involved in controlling neuronal membrane organization, and by its interaction with kainate receptors, syntenin may play a role in determining the formation and maturation of synapses.
Title: Syntenin is involved in the developmental regulation of neuronal membrane architecture.
Syntenin-1 may be an in vivo binding partner of GlyT2 that regulates its trafficking and/or presynaptic localization in glycinergic neurons.
Title: The neuronal glycine transporter 2 interacts with the PDZ domain protein syntenin-1.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IPI Inferred from Physical Interaction more info	PubMed
enables ephrin receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables frizzled binding	ISO Inferred from Sequence Orthology more info
enables growth factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables interleukin-5 receptor binding	ISO Inferred from Sequence Orthology more info
enables interleukin-5 receptor binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables ionotropic glutamate receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables neurexin family protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables neurexin family protein binding	NAS Non-traceable Author Statement more info	PubMed
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 sequestering activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables syndecan binding	IBA Inferred from Biological aspect of Ancestor more info
enables syndecan binding	IPI Inferred from Physical Interaction 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	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 receptor internalization	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity 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 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
involved_in positive regulation of transforming growth factor beta receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transforming growth factor beta receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in presynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in presynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in adherens junction	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	ISO Inferred from Sequence Orthology more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
part_of interleukin-5 receptor complex	ISO Inferred from Sequence Orthology more info
part_of interleukin-5 receptor complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in membrane raft	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
located_in nuclear membrane	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: syntenin-1

Names: 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_031986.2 → NP_114192.1 syntenin-1

See identical proteins and their annotated locations for NP_114192.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Related

ENSRNOP00000081603.1, ENSRNOT00000115856.1

Conserved Domains (1) summary

cd00992
Location:114 → 193

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

24245279..24314712

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063288489.1 → XP_063144559.1 syntenin-1 isoform X2
XM_039110857.2 → XP_038966785.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Conserved Domains (1) summary

cd00992
Location:114 → 193

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_063288487.1 → XP_063144557.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92
XM_039110862.2 → XP_038966790.1 syntenin-1 isoform X2

UniProtKB/TrEMBL

A0A8L2Q6V7

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_039110855.2 → XP_038966783.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Conserved Domains (1) summary

cd00992
Location:114 → 193

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_039110858.2 → XP_038966786.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Conserved Domains (1) summary

cd00992
Location:114 → 193

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_039110860.2 → XP_038966788.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Related

ENSRNOP00000079793.1

Conserved Domains (1) summary

cd00992
Location:114 → 193

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_063288488.1 → XP_063144558.1 syntenin-1 isoform X2
XM_039110863.2 → XP_038966791.1 syntenin-1 isoform X2

UniProtKB/TrEMBL

A0A8L2Q6V7

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_063288490.1 → XP_063144560.1 syntenin-1 isoform X2
XM_039110861.2 → XP_038966789.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Conserved Domains (1) summary

cd00992
Location:114 → 193

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_063288491.1 → XP_063144561.1 syntenin-1 isoform X2
XM_039110864.2 → XP_038966792.1 syntenin-1 isoform X2

UniProtKB/TrEMBL

A0A8L2Q6V7

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_039110859.2 → XP_038966787.1 syntenin-1 isoform X1

UniProtKB/Swiss-Prot

Q9JI92

UniProtKB/TrEMBL

A0A8L2Q6V7

Conserved Domains (1) summary

cd00992
Location:114 → 193

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) ...