Vapb VAMP associated protein B and C [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vapbprovided by RGD
Official Full Name: VAMP associated protein B and Cprovided by RGD
Primary source: RGD:68326
See related: EnsemblRapid:ENSRNOG00000005331 AllianceGenome:RGD:68326
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: VAP-B; VAMP-B
Summary: Predicted to enable several functions, including FFAT motif binding activity; protein dimerization activity; and tubulin binding activity. Predicted to be involved in several processes, including IRE1-mediated unfolded protein response; endoplasmic reticulum organization; and modulation by host of viral genome replication. Is active in several cellular components, including endoplasmic reticulum; glutamatergic synapse; and postsynapse. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 8; autosomal dominant adult-onset proximal spinal muscular atrophy; and spinal muscular atrophy. Orthologous to human VAPB (VAMP associated protein B and C). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 191.4), Muscle (RPKM 190.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q42

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (182954247..182997018)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (162535974..162578747)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (171832558..171871042)

Chromosome 3 - NC_086021.1 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 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?

VAPB-PTPIP51 mitochondrial tethering proteins are present in synapses and regulate synaptic activity.
Title: The VAPB-PTPIP51 endoplasmic reticulum-mitochondria tethering proteins are present in neuronal synapses and regulate synaptic activity.
YIF1A interacts with VAPB via its transmembrane regions, recycles between the ER and Golgi and is mainly localized to the ER-Golgi intermediate compartments in hippocampal neurons.
Title: The ALS8 protein VAPB interacts with the ER-Golgi recycling protein YIF1A and regulates membrane delivery into dendrites.
The results suggested that neuronal cells have a particular requirement for VAPB proteolysis and that reduced levels of processed polypeptides may contribute to the neurodegeneration associated with amyotrophic lateral sclerosis type 8.
Title: The ALS8-associated mutant VAPB(P56S) is resistant to proteolysis in neurons.

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 FFAT motif binding	ISO Inferred from Sequence Orthology more info
enables beta-tubulin binding	ISO Inferred from Sequence Orthology more info
enables beta-tubulin binding	ISS Inferred from Sequence or Structural Similarity more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISS Inferred from Sequence or Structural Similarity more info
enables microtubule binding	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein-membrane adaptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle budding	ISO Inferred from Sequence Orthology more info
involved_in IRE1-mediated unfolded protein response	ISO Inferred from Sequence Orthology more info
involved_in IRE1-mediated unfolded protein response	ISS Inferred from Sequence or Structural Similarity more info
involved_in biological_process	ND No biological Data available more info
involved_in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum membrane organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum organization	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum unfolded protein response	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum unfolded protein response	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoplasmic reticulum-plasma membrane tethering	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in modulation by host of viral RNA genome replication	ISO Inferred from Sequence Orthology more info
involved_in negative regulation by host of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in negative regulation by virus of viral protein levels in host cell	ISO Inferred from Sequence Orthology more info
involved_in positive regulation by host of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral genome replication	ISS Inferred from Sequence or Structural Similarity more info
involved_in suppression of viral release by host	ISO Inferred from Sequence Orthology more info
involved_in viral release from host cell	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
NOT located_in endoplasmic reticulum exit site	ISO Inferred from Sequence Orthology more info
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vesicle-associated membrane protein-associated protein B

Names: VAMP (vesicle-associated membrane protein)-associated protein B and C; VAMP-associated protein B; vesicle-associated membrane protein, associated protein B and C

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_021847.4 → NP_068619.1 vesicle-associated membrane protein-associated protein B

See identical proteins and their annotated locations for NP_068619.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

Q9Z269

UniProtKB/TrEMBL

A6KL13

Related

ENSRNOP00000106660.1, ENSRNOT00000122080.1

Conserved Domains (2) summary

pfam00635
Location:8 → 111

Motile_Sperm; MSP (Major sperm protein) domain

cl19864
Location:65 → 222

Mu-like_Pro; Mu-like prophage I protein