Vps54 VPS54 subunit of GARP complex [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vps54provided by RGD
Official Full Name: VPS54 subunit of GARP complexprovided by RGD
Primary source: RGD:628718
See related: EnsemblRapid:ENSRNOG00000007125 AllianceGenome:RGD:628718
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: Vsp54
Summary: Predicted to enable syntaxin binding activity. Predicted to be involved in Golgi to vacuole transport and retrograde transport, endosome to Golgi. Predicted to act upstream of or within several processes, including homeostasis of number of cells within a tissue; musculoskeletal movement; and neurofilament cytoskeleton organization. Located in membrane and trans-Golgi network. Orthologous to human VPS54 (VPS54 subunit of GARP complex). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 174.5), Thymus (RPKM 159.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14q22

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (99580120..99657178)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (95378821..95455871)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (106153407..106207715)

Chromosome 14 - NC_086032.1 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?

Submit: New GeneRIF Correction

General gene information

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Markers

AI454148 (e-PCR)
- UniSTS:261137

RH138139 (e-PCR)
- UniSTS:220226

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

Process	Evidence Code	Pubs
involved_in Golgi to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-glutamate import	IEA Inferred from Electronic Annotation more info
involved_in L-glutamate import	ISO Inferred from Sequence Orthology more info
involved_in apoptotic DNA fragmentation	IEA Inferred from Electronic Annotation more info
involved_in apoptotic DNA fragmentation	ISO Inferred from Sequence Orthology more info
involved_in astrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in astrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to progesterone stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to progesterone stimulus	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
involved_in homeostasis of number of cells	ISO Inferred from Sequence Orthology more info
involved_in homeostasis of number of cells within a tissue	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within homeostasis of number of cells within a tissue	ISO Inferred from Sequence Orthology more info
involved_in homeostasis of number of cells within a tissue	ISO Inferred from Sequence Orthology more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in limb development	ISO Inferred from Sequence Orthology more info
involved_in limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lysosomal transport	ISO Inferred from Sequence Orthology more info
involved_in microglia differentiation	IEA Inferred from Electronic Annotation more info
involved_in microglia differentiation	ISO Inferred from Sequence Orthology more info
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	ISO Inferred from Sequence Orthology more info
involved_in motor behavior	IEA Inferred from Electronic Annotation more info
involved_in motor behavior	ISO Inferred from Sequence Orthology more info
involved_in motor neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in motor neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in musculoskeletal movement	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within musculoskeletal movement	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of motor neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of motor neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in neural tissue regeneration	IEA Inferred from Electronic Annotation more info
involved_in neural tissue regeneration	ISO Inferred from Sequence Orthology more info
involved_in neurofilament cytoskeleton organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neurofilament cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in neuroinflammatory response	IEA Inferred from Electronic Annotation more info
involved_in neuroinflammatory response	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in neuron projection morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in neuron projection morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in post-embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cell surface	ISO Inferred from Sequence Orthology more info
involved_in protein targeting to ER	IEA Inferred from Electronic Annotation more info
involved_in protein targeting to ER	ISO Inferred from Sequence Orthology more info
involved_in protein targeting to lysosome	IEA Inferred from Electronic Annotation more info
involved_in protein targeting to lysosome	ISO Inferred from Sequence Orthology more info
involved_in protein targeting to vacuole	ISO Inferred from Sequence Orthology more info
involved_in regulation of growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of growth	ISO Inferred from Sequence Orthology more info
involved_in respiratory electron transport chain	IEA Inferred from Electronic Annotation more info
involved_in respiratory electron transport chain	ISO Inferred from Sequence Orthology more info
involved_in response to antibiotic	IEA Inferred from Electronic Annotation more info
involved_in response to antibiotic	ISO Inferred from Sequence Orthology more info
involved_in response to calcium ion	IEA Inferred from Electronic Annotation more info
involved_in response to calcium ion	ISO Inferred from Sequence Orthology more info
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle tissue growth	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle tissue growth	ISO Inferred from Sequence Orthology more info
involved_in spermatid differentiation	IEA Inferred from Electronic Annotation more info
involved_in spermatid differentiation	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in sphingolipid catabolic process	ISO Inferred from Sequence Orthology more info
involved_in striated muscle contraction	IEA Inferred from Electronic Annotation more info
involved_in striated muscle contraction	ISO Inferred from Sequence Orthology more info
involved_in synaptic transmission, GABAergic	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, GABAergic	ISO Inferred from Sequence Orthology more info
involved_in synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info
involved_in thrombin-activated receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in thrombin-activated receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin recycling	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin recycling	ISO Inferred from Sequence Orthology more info
involved_in vacuole organization	IEA Inferred from Electronic Annotation more info
involved_in vacuole organization	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated cholesterol transport	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated cholesterol transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of GARP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of GARP complex	IEA Inferred from Electronic Annotation more info
part_of GARP complex	ISO Inferred from Sequence Orthology more info
part_of GARP complex	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
is_active_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in synapse	IEA Inferred from Electronic Annotation more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network	IEA Inferred from Electronic Annotation more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 54

Names: VPS54 GARP complex subunit; vacuolar protein sorting 54 homolog; vps54-like protein

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_173147.2 → NP_775170.2 vacuolar protein sorting-associated protein 54

Status: VALIDATED

Source sequence(s)

JAXUCZ010000014

UniProtKB/Swiss-Prot

Q9JMK8

Conserved Domains (1) summary

pfam07928
Location:727 → 855

Vps54; Vps54-like protein

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_086032.1 Reference GRCr8

Range

99580120..99657178

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039091649.2 → XP_038947577.1 vacuolar protein sorting-associated protein 54 isoform X1

UniProtKB/Swiss-Prot

Q9JMK8

UniProtKB/TrEMBL

A6JQ37, G3V6Z1

Conserved Domains (1) summary

pfam07928
Location:739 → 867

Vps54; Vps54-like protein
XM_039091650.2 → XP_038947578.1 vacuolar protein sorting-associated protein 54 isoform X2

UniProtKB/Swiss-Prot

Q9JMK8

Related

ENSRNOP00000010264.6, ENSRNOT00000010264.8

Conserved Domains (1) summary

pfam07928
Location:727 → 855

Vps54; Vps54-like protein
XM_063272889.1 → XP_063128959.1 vacuolar protein sorting-associated protein 54 isoform X1

UniProtKB/Swiss-Prot

Q9JMK8

UniProtKB/TrEMBL

A6JQ37, G3V6Z1