vcla vinculin a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vclaprovided by ZNC
Official Full Name: vinculin aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050506-61
See related: Ensembl:ENSDARG00000044968 AllianceGenome:ZFIN:ZDB-GENE-050506-61
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: vcl; im:6902790; hm:zehn2160
Summary: Predicted to enable actin filament binding activity and structural molecule activity. Involved in heart contraction. Acts upstream of or within atrioventricular valve morphogenesis; membrane repolarization during cardiac muscle cell action potential; and sarcomere organization. Located in adherens junction. Is active in focal adhesion. Is expressed in several structures, including heart; lens; pectoral fin; solid lens vesicle; and somite. 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]
Orthologs: all
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Genomic context

Location:: chromosome: 13

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (25210344..25284395, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (25079891..25153936, complement)

Chromosome 13 - NC_007124.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Vinculin controls endothelial cell junction dynamics during vascular lumen formation.
Title: Vinculin controls endothelial cell junction dynamics during vascular lumen formation.
VCL recruits SSH1 and its effector, the actin depolymerizing factor cofilin (CFL), to regulate F-actin rearrangement and promote cardiomyocyte myofilament maturation
Title: Mechanical Forces Regulate Cardiomyocyte Myofilament Maturation via the VCL-SSH1-CFL Axis.
Study show that zebrafish contain two homologous vinculin isoforms, of which the sequence of key functional domains is conserved with several higher vertebrate. Loss of both zygotic vcla and maternal contribution of vcla did not result in notable defects, while the additional loss of zygotic vclb is lethal only after embryonic stages. These data indicate that embryonic development in zebrafish can occur without vinculin.
Title: Zygotic vinculin is not essential for embryonic development in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables actin binding	IEA Inferred from Electronic Annotation 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 beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within atrioventricular valve morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within membrane repolarization during cardiac muscle cell action potential	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sarcomere organization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IEA Inferred from Electronic Annotation more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
is_active_in cell-cell contact zone	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
is_active_in focal adhesion	IBA Inferred from Biological aspect of Ancestor more info
is_active_in focal adhesion	IDA Inferred from Direct Assay more info	PubMed
is_active_in focal adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in podosome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: vinculin a; vinculin

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_001128681.1 → NP_001122153.1 vinculin a

See identical proteins and their annotated locations for NP_001122153.1

Status: PROVISIONAL

Source sequence(s)

BC162980

UniProtKB/TrEMBL

B3DI32, F1REH0

Related

ENSDARP00000105799.2, ENSDART00000124167.4

Conserved Domains (1) summary

pfam01044
Location:66 → 1131

Vinculin; Vinculin family

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007124.7 Reference GRCz11 Primary Assembly

Range

25210344..25284395 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005156840.4 → XP_005156897.1 vinculin isoform X1

UniProtKB/TrEMBL

A0A8M2B3M1

Conserved Domains (1) summary

pfam01044
Location:66 → 1130

Vinculin; Vinculin family
XM_005156842.4 → XP_005156899.1 vinculin isoform X3

UniProtKB/TrEMBL

A0A8M2B2X1, F6NHA0

Related

ENSDARP00000039827.6, ENSDART00000039828.6

Conserved Domains (1) summary

pfam01044
Location:66 → 1066

Vinculin; Vinculin family
XM_021480576.1 → XP_021336251.1 vinculin isoform X2

UniProtKB/TrEMBL

A0A8M9QJN2

Conserved Domains (1) summary

pfam01044
Location:66 → 1067

Vinculin; Vinculin family