Vps18 VPS18 core subunit of CORVET and HOPS complexes [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vps18provided by RGD
Official Full Name: VPS18 core subunit of CORVET and HOPS complexesprovided by RGD
Primary source: RGD:1311556
See related: Ensembl:ENSRNOG00000013689 AllianceGenome:RGD:1311556
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 several functions, including actin binding activity; syntaxin binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including endosome to lysosome transport; negative regulation of intracellular estrogen receptor signaling pathway; and vesicle docking involved in exocytosis. Predicted to act upstream of or within viral entry into host cell. Is active in presynapse. Orthologous to human VPS18 (VPS18 core subunit of CORVET and HOPS complexes). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 74.9), Spleen (RPKM 73.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q35

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (126733276..126744130)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (106279444..106290298)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (111097352..111108206)

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
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?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH131084 (e-PCR)
- UniSTS:214367

RH139583 (e-PCR)
- UniSTS:214367

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables actin binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in endosome organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endosome organization	ISO Inferred from Sequence Orthology more info
involved_in endosome organization	ISO Inferred from Sequence Orthology more info
involved_in endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosome to lysosome transport	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysosome organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of intracellular estrogen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in organelle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within symbiont entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in vesicle docking involved in exocytosis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of AP-3 adaptor complex	ISO Inferred from Sequence Orthology more info
part_of CORVET complex	ISO Inferred from Sequence Orthology more info
part_of HOPS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HOPS complex	ISO Inferred from Sequence Orthology more info
located_in actin filament	ISO Inferred from Sequence Orthology more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 18 homolog

Names: VPS18 CORVET/HOPS core subunit; vacuolar protein sorting 18 homolog

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_001106499.2 → NP_001099969.1 vacuolar protein sorting-associated protein 18 homolog

See identical proteins and their annotated locations for NP_001099969.1

Status: PROVISIONAL

Source sequence(s)

BC169083

UniProtKB/TrEMBL

B5DFJ4, F7F0E9

Related

ENSRNOP00000018717.4, ENSRNOT00000018717.6

Conserved Domains (3) summary

cd16462
Location:851 → 952

RING-H2_Pep3p_like; RING finger, H2 subclass, found in Saccharomyces cerevisiae vacuolar membrane protein PEP3 (Pep3p) and similar proteins

pfam00637
Location:615 → 743

Clathrin; Region in Clathrin and VPS

pfam05131
Location:291 → 434

Pep3_Vps18; Pep3/Vps18/deep orange family