Vps4b vacuolar protein sorting 4 homolog B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vps4bprovided by RGD
Official Full Name: vacuolar protein sorting 4 homolog Bprovided by RGD
Primary source: RGD:1305969
See related: Ensembl:ENSRNOG00000002705 AllianceGenome:RGD:1305969
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: Predicted to enable protein C-terminus binding activity and protein homodimerization activity. Predicted to be involved in several processes, including proteolysis involved in cellular protein catabolic process; regulation of cell cycle process; and regulation of exosomal secretion. Predicted to act upstream of or within several processes, including cholesterol transport; endosome organization; and potassium ion transport. Predicted to be located in several cellular components, including Flemming body; endosome membrane; and microtubule cytoskeleton. Orthologous to human VPS4B (vacuolar protein sorting 4 homolog B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 302.3), Kidney (RPKM 287.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13p11

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (23421758..23446848, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (22907105..22932200, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (26825261..26850460, complement)

Chromosome 13 - NC_086031.1 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: 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?

The up-regulation of VPS4B played an important role in the pathophysiology after middle cerebral artery occlusion.
Title: The expression changes of vacuolar protein sorting 4B (VPS4B) following middle cerebral artery occlusion (MCAO) in adult rats brain hippocampus.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in ESCRT III complex disassembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endosomal transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endosome organization	ISO Inferred from Sequence Orthology more info
involved_in endosome to lysosome transport via multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of blood-brain barrier	ISO Inferred from Sequence Orthology more info
involved_in late endosomal microautophagy	ISO Inferred from Sequence Orthology more info
involved_in midbody abscission	ISO Inferred from Sequence Orthology more info
involved_in mitotic metaphase chromosome alignment	ISO Inferred from Sequence Orthology more info
involved_in multivesicular body assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of exosomal secretion	ISO Inferred from Sequence Orthology more info
involved_in nucleus organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of centriole elongation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exosomal secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within potassium ion transport	ISO Inferred from Sequence Orthology more info
involved_in protein depolymerization	ISO Inferred from Sequence Orthology more info
involved_in regulation of centrosome duplication	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitotic spindle assembly	ISO Inferred from Sequence Orthology more info
involved_in response to lipid	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within vacuolar transport	ISO Inferred from Sequence Orthology more info
involved_in vacuole organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in viral budding from plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in viral budding via host ESCRT complex	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Flemming body	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in spindle pole	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 4B

Names: vacuolar protein sorting 4b

NP_001020887.1

EC 3.6.4.6

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_001025716.1 → NP_001020887.1 vacuolar protein sorting-associated protein 4B

See identical proteins and their annotated locations for NP_001020887.1

Status: PROVISIONAL

Source sequence(s)

BC099128

UniProtKB/TrEMBL

A0A8I6GH80, Q4KLL7

Related

ENSRNOP00000003715.4, ENSRNOT00000003715.5

Conserved Domains (4) summary

cd02678
Location:7 → 69

MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.

pfam09336
Location:381 → 441

Vps4_C; Vps4 C terminal oligomerization domain

pfam17862
Location:325 → 366

AAA_lid_3; AAA+ lid domain

cd19521
Location:128 → 298

RecA-like_VPS4; ATPase domain of vacuolar protein sorting-associated protein 4