Vps13a vacuolar protein sorting 13 homolog A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vps13aprovided by RGD
Official Full Name: vacuolar protein sorting 13 homolog Aprovided by RGD
Primary source: RGD:1311340
See related: EnsemblRapid:ENSRNOG00000025539 AllianceGenome:RGD:1311340
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: RGD1311340
Summary: Predicted to be involved in autophagy; lysosomal protein catabolic process; and protein localization to organelle. Predicted to act upstream of or within several processes, including brain-derived neurotrophic factor receptor signaling pathway; long-term synaptic depression; and myeloid cell differentiation. Predicted to be located in several cellular components, including bounding membrane of organelle; neuronal dense core vesicle lumen; and sperm midpiece. Predicted to be active in several cellular components, including endoplasmic reticulum; mitochondrion; and neuronal cell body. Human ortholog(s) of this gene implicated in choreaacanthocytosis and choreatic disease. Orthologous to human VPS13A (vacuolar protein sorting 13 homolog A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 223.6), Spleen (RPKM 181.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 73

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (223328784..223555500, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (213901999..214128638, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (235352513..235813597, complement)

Chromosome 1 - NC_086019.1 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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General gene information

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Markers

D1Got216 (e-PCR)
- UniSTS:112128

RH127917 (e-PCR)
- UniSTS:211227

D1Got218 (e-PCR)
- UniSTS:115056

RH128324 (e-PCR)
- UniSTS:211632

D1Got207 (e-PCR)
- UniSTS:112595

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in autophagy	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within autophagy	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within brain-derived neurotrophic factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to osmotic stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within exploration behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within flagellated sperm motility	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gene expression	ISO Inferred from Sequence Orthology more info
involved_in lipid transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within locomotory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within long-term synaptic depression	ISO Inferred from Sequence Orthology more info
involved_in lysosomal protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within microglia differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within motor behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuroinflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuromuscular process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuromuscular process controlling balance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection arborization	ISO Inferred from Sequence Orthology more info
involved_in protein retention in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein secretion	ISO Inferred from Sequence Orthology more info
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of synaptic plasticity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to environmental enrichment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within social behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sperm mitochondrion organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in dense core granule	ISO Inferred from Sequence Orthology more info
is_active_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in lipid droplet	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondria-associated endoplasmic reticulum membrane contact site	ISO Inferred from Sequence Orthology more info
located_in mitochondrial membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrial outer membrane	ISO Inferred from Sequence Orthology more info
is_active_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info	PubMed
is_active_in neuron projection	ISO Inferred from Sequence Orthology more info
is_active_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in neuronal dense core vesicle lumen	ISO Inferred from Sequence Orthology more info
located_in sperm midpiece	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: intermembrane lipid transfer protein VPS13A

Names: chorein; vacuolar protein sorting 13A; vacuolar protein sorting-associated protein 13A

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_001100975.2 → NP_001094445.2 intermembrane lipid transfer protein VPS13A

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I6A4A2

Related

ENSRNOP00000085879.1, ENSRNOT00000102736.2

Conserved Domains (7) summary

COG5043
Location:4 → 2005

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2202 → 2445

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam09333
Location:2939 → 3018

ATG_C; Autophagy-related protein C terminal domain

pfam12624
Location:4 → 113

Chorein_N; N-terminal region of Chorein or VPS13

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:2759 → 2936

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:568 → 791

VPS13_mid_rpt; Repeating coiled region of VPS13

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_086019.1 Reference GRCr8

Range

223328784..223555500 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039079915.2 → XP_038935843.1 intermembrane lipid transfer protein VPS13A isoform X4

Conserved Domains (4) summary

COG5043
Location:1928 → 2392

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:1503 → 1746

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16909
Location:2060 → 2237

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:1 → 92

VPS13_mid_rpt; Repeating coiled region of VPS13
XM_039079911.2 → XP_038935839.1 intermembrane lipid transfer protein VPS13A isoform X1

Related

ENSRNOP00000103448.1, ENSRNOT00000168353.1

Conserved Domains (3) summary

COG5043
Location:4 → 2005

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2202 → 2445

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16909
Location:2759 → 2936

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
XM_039079914.2 → XP_038935842.1 intermembrane lipid transfer protein VPS13A isoform X2

UniProtKB/TrEMBL

A0A8I5ZJJ9

Conserved Domains (3) summary

COG5043
Location:4 → 2005

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2202 → 2445

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16909
Location:2759 → 2936

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
XM_063264468.1 → XP_063120538.1 intermembrane lipid transfer protein VPS13A isoform X3

Related

ENSRNOP00000099419.1, ENSRNOT00000142855.1
XM_039079920.2 → XP_038935848.1 intermembrane lipid transfer protein VPS13A isoform X5

UniProtKB/TrEMBL

D4A899

Related

ENSRNOP00000014800.7, ENSRNOT00000014800.9

Conserved Domains (2) summary

COG5043
Location:4 → 1919

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal