Vcl vinculin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vclprovided by RGD
Official Full Name: vinculinprovided by RGD
Primary source: RGD:1311217
See related: Ensembl:ENSRNOG00000010765 AllianceGenome:RGD:1311217
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables small GTPase binding activity. Predicted to be involved in several processes, including cell-cell junction assembly; platelet aggregation; and protein localization to cell surface. Predicted to act upstream of or within cell adhesion; plasma membrane bounded cell projection organization; and regulation of cell migration. Located in Z disc; intercalated disc; and sarcolemma. Colocalizes with actin filament; focal adhesion; and stress fiber. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1W; hypertrophic cardiomyopathy; and hypertrophic cardiomyopathy 15. Orthologous to human VCL (vinculin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 714.6), Lung (RPKM 578.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p16

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (3315069..3404891, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (3265776..3355586, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (3455211..3544738, complement)

Chromosome 15 - NC_086033.1 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?

Integrin engagement during cell attachment activates Poldip2/Nox4 to oxidize actin, which modulates filamentous actin assembly and its interaction with vinculin.
Title: NOX4 (NADPH Oxidase 4) and Poldip2 (Polymerase δ-Interacting Protein 2) Induce Filamentous Actin Oxidation and Promote Its Interaction With Vinculin During Integrin-Mediated Cell Adhesion.
The vinculin-mediated mecahnotransduction mechanism in synthetic vascular smooth muscle cells may be more complex than those proposed for non-muscle cells.
Title: The role of extracellular matrix stiffness in regulating cytoskeletal remodeling via vinculin in synthetic smooth muscle cells.
Host anti-Cytolethal distending toxin antibodies cross-react with vinculin in model of Campylobacter jejuni gastroenteritis.
Title: Autoimmunity Links Vinculin to the Pathophysiology of Chronic Functional Bowel Changes Following Campylobacter jejuni Infection in a Rat Model.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH139160 (e-PCR)
- UniSTS:221246

VCL (e-PCR)
- UniSTS:266571

RH137914 (e-PCR)
- UniSTS:220001

BARC0060 (e-PCR)
- UniSTS:255337

RH133946 (e-PCR)
- UniSTS:217229

D15Got5 (e-PCR)
- UniSTS:112294

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
NOT enables actin binding	ISO Inferred from Sequence Orthology more info
enables actin binding	ISO Inferred from Sequence Orthology more info
enables actin filament binding	IEA Inferred from Electronic Annotation more info
enables alpha-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables alpha-catenin binding	IEA Inferred from Electronic Annotation more info
enables alpha-catenin binding	ISO Inferred from Sequence Orthology more info
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables dystroglycan binding	IEA Inferred from Electronic Annotation more info
enables dystroglycan binding	ISO Inferred from Sequence Orthology more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in adherens junction assembly	IEA Inferred from Electronic Annotation more info
involved_in adherens junction assembly	ISO Inferred from Sequence Orthology more info
involved_in apical junction assembly	IEA Inferred from Electronic Annotation more info
involved_in apical junction assembly	ISO Inferred from Sequence Orthology more info
involved_in axon extension	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon extension	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in epithelial cell-cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in lamellipodium assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lamellipodium assembly	ISO Inferred from Sequence Orthology more info
involved_in morphogenesis of an epithelium	IEA Inferred from Electronic Annotation more info
involved_in morphogenesis of an epithelium	ISO Inferred from Sequence Orthology more info
involved_in platelet aggregation	ISO Inferred from Sequence Orthology more info	PubMed
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cell surface	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of establishment of endothelial barrier	IEA Inferred from Electronic Annotation more info
involved_in regulation of establishment of endothelial barrier	ISO Inferred from Sequence Orthology more info
involved_in regulation of focal adhesion assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of focal adhesion assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to adherens junction	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein localization to adherens junction	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in actin filament	IDA Inferred from Direct Assay more info	PubMed
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	IEA Inferred from Electronic Annotation more info
located_in adherens junction	ISO Inferred from Sequence Orthology more info
located_in brush border	ISS Inferred from Sequence or Structural Similarity more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cell-cell contact zone	IBA Inferred from Biological aspect of Ancestor more info
located_in cell-cell contact zone	ISO Inferred from Sequence Orthology more info
located_in cell-cell junction	ISO Inferred from Sequence Orthology more info
located_in costamere	IEA Inferred from Electronic Annotation more info
located_in costamere	ISO Inferred from Sequence Orthology 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
is_active_in cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in fascia adherens	IEA Inferred from Electronic Annotation more info
located_in fascia adherens	ISO Inferred from Sequence Orthology more info
located_in focal adhesion	IDA Inferred from Direct Assay more info	PubMed
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in inner dense plaque of desmosome	ISS Inferred from Sequence or Structural Similarity more info
located_in intercalated disc	IDA Inferred from Direct Assay more info	PubMed
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in outer dense plaque of desmosome	ISS Inferred from Sequence or Structural Similarity 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
located_in podosome	IEA Inferred from Electronic Annotation more info
located_in podosome	ISO Inferred from Sequence Orthology more info
located_in podosome ring	IEA Inferred from Electronic Annotation more info
located_in podosome ring	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
located_in sarcolemma	IDA Inferred from Direct Assay more info	PubMed
located_in sarcolemma	IEA Inferred from Electronic Annotation more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info
located_in sarcolemma	ISS Inferred from Sequence or Structural Similarity more info
located_in stress fiber	IDA Inferred from Direct Assay more info	PubMed
located_in terminal web	ISS Inferred from Sequence or Structural Similarity more info
located_in zonula adherens	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: vinculin

Names: metavinculin

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_001107248.1 → NP_001100718.1 vinculin

See identical proteins and their annotated locations for NP_001100718.1

Status: PROVISIONAL

Source sequence(s)

CH474061

UniProtKB/Swiss-Prot

A6KKR4, P85972

UniProtKB/TrEMBL

R9PXU6

Related

ENSRNOP00000015179.6, ENSRNOT00000015179.8

Conserved Domains (1) summary

pfam01044
Location:66 → 1066

Vinculin; Vinculin family

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_086033.1 Reference GRCr8

Range

3315069..3404891 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006251639.5 → XP_006251701.3 vinculin isoform X1

UniProtKB/TrEMBL

A0A0G2K8V2, A6KKR3, R9PXU6

Related

ENSRNOP00000074748.2

Conserved Domains (1) summary

pfam01044
Location:66 → 1134

Vinculin; Vinculin family