Vps52 VPS52 subunit of GARP complex [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vps52provided by RGD
Official Full Name: VPS52 subunit of GARP complexprovided by RGD
Primary source: RGD:3618
See related: EnsemblRapid:ENSRNOG00000000470 AllianceGenome:RGD:3618
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: Are1; Sacm2l
Summary: Predicted to enable syntaxin binding activity. Predicted to be involved in several processes, including cytosolic transport; endocytic recycling; and vacuolar transport. Predicted to act upstream of or within ectodermal cell differentiation and embryonic ectodermal digestive tract development. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Predicted to be part of EARP complex and GARP complex. Predicted to be active in postsynapse and presynapse. Orthologous to human VPS52 (VPS52 subunit of GARP complex). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 264.5), Thymus (RPKM 262.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (4922599..4933458, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4920715..4931685, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (5431997..5441736, complement)

Chromosome 20 - NC_086038.1 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

D20Yum82 (e-PCR)
- UniSTS:526126

UniSTS:463437 (e-PCR)
- UniSTS:463437

Vps52 (e-PCR), detects polymorphism
- UniSTS:463437

RH141313 (e-PCR)
- UniSTS:223309

RH141868 (e-PCR)
- UniSTS:223860

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Golgi to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ectodermal cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic ectodermal digestive tract development	ISO Inferred from Sequence Orthology more info
involved_in endocytic recycling	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytic recycling	ISO Inferred from Sequence Orthology more info
involved_in endocytic recycling	ISS Inferred from Sequence or Structural Similarity more info
involved_in lysosomal transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lysosomal transport	ISO Inferred from Sequence Orthology more info
involved_in protein targeting	ISO Inferred from Sequence Orthology more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle-mediated cholesterol transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of EARP complex	ISO Inferred from Sequence Orthology more info
part_of EARP complex	ISS Inferred from Sequence or Structural Similarity more info
part_of GARP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of GARP complex	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in postsynapse	ISO Inferred from Sequence Orthology more info
is_active_in presynapse	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 52 homolog

Names: SAC2 suppressor of actin mutations 2-like protein; VPS52 GARP complex subunit; vacuolar protein sorting 52 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_033097.2 → NP_149088.1 vacuolar protein sorting-associated protein 52 homolog

See identical proteins and their annotated locations for NP_149088.1

Status: VALIDATED

Source sequence(s)

BC166419

UniProtKB/Swiss-Prot

O55166

UniProtKB/TrEMBL

A0A8I6A724, B2GUV2

Related

ENSRNOP00000098201.1, ENSRNOT00000120560.2

Conserved Domains (1) summary

pfam04129
Location:94 → 601

Vps52; Vps52 / Sac2 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_086038.1 Reference GRCr8

Range

4922599..4933458 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008772707.3 → XP_008770929.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

UniProtKB/TrEMBL

A0A8I6A724

Conserved Domains (1) summary

pfam04129
Location:94 → 618

Vps52; Vps52 / Sac2 family
XM_063278973.1 → XP_063135043.1 vacuolar protein sorting-associated protein 52 homolog isoform X3

UniProtKB/TrEMBL

A0A8I6A724
XM_039098438.2 → XP_038954366.1 vacuolar protein sorting-associated protein 52 homolog isoform X2

UniProtKB/TrEMBL

A0A8I6A724

Conserved Domains (1) summary

pfam04129
Location:94 → 618

Vps52; Vps52 / Sac2 family
XM_039098440.2 → XP_038954368.1 vacuolar protein sorting-associated protein 52 homolog isoform X4

Conserved Domains (1) summary

cl19950
Location:94 → 380

Sec3_C; Exocyst complex component Sec3