Atp13a2 ATPase cation transporting 13A2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Atp13a2provided by RGD
Official Full Name: ATPase cation transporting 13A2provided by RGD
Primary source: RGD:1307977
See related: Ensembl:ENSRNOG00000008052 AllianceGenome:RGD:1307977
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
Also known as: RGD1307977
Summary: Predicted to enable ABC-type polyamine transporter activity; phosphatidic acid binding activity; and phosphatidylinositol-3,5-bisphosphate binding activity. Involved in regulation of autophagosome size and regulation of mitochondrion organization. Predicted to be located in several cellular components, including cytoplasmic vesicle; neuronal cell body; and vacuole. Predicted to be integral component of lysosomal membrane. Human ortholog(s) of this gene implicated in Kufor-Rakeb syndrome; Parkinson's disease; and hereditary spastic paraplegia. Orthologous to human ATP13A2 (ATPase cation transporting 13A2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 107.9), Spleen (RPKM 107.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (158575727..158595157)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (153292722..153312143)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (159512208..159531631)

Chromosome 5 - NC_086023.1 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?

Pink1 -/- rats show significantly decreased levels of Atp13a2, a transmembrane lysosomal P5-type ATPase suggesting a potential mechanism for the observed abnormal aggregation.
Title: Atp13a2 expression in the periaqueductal gray is decreased in the Pink1 -/- rat model of Parkinson disease.
Regulation of intracellular manganese homeostasis by Kufor-Rakeb syndrome-associated ATP13A2 protein.
Title: Regulation of intracellular manganese homeostasis by Kufor-Rakeb syndrome-associated ATP13A2 protein.

Submit: New GeneRIF Correction

General gene information

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Markers

RH134640 (e-PCR)
- UniSTS:217919

Atp13a2 (e-PCR), detects polymorphism
- UniSTS:527259

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATPase-coupled monoatomic cation transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables P-type ion transporter activity	IEA Inferred from Electronic Annotation more info
enables phosphatidic acid binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol-3,5-bisphosphate binding	ISO Inferred from Sequence Orthology more info
enables polyamine transmembrane transporter activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in autophagosome organization	ISO Inferred from Sequence Orthology more info
involved_in autophagosome-lysosome fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome-lysosome fusion	ISO Inferred from Sequence Orthology more info
involved_in autophagy	ISO Inferred from Sequence Orthology more info
involved_in cellular response to manganese ion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to oxidative stress	ISO Inferred from Sequence Orthology more info
involved_in extracellular exosome biogenesis	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular iron ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular zinc ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in lipid homeostasis	ISO Inferred from Sequence Orthology more info
involved_in lysosomal transport	ISO Inferred from Sequence Orthology more info
involved_in monoatomic cation transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in polyamine transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exosomal secretion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein secretion	ISO Inferred from Sequence Orthology more info
involved_in protein localization to lysosome	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagosome size	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of autophagosome size	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of autophagosome size	ISO Inferred from Sequence Orthology more info
involved_in regulation of lysosomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitochondrion organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitochondrion organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to nucleus	ISO Inferred from Sequence Orthology more info
involved_in spermine transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in autophagosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in multivesicular body	ISO Inferred from Sequence Orthology more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in transport vesicle	ISO Inferred from Sequence Orthology more info
located_in vesicle	ISO Inferred from Sequence Orthology more info
located_in vesicle membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: polyamine-transporting ATPase 13A2

Names: ATPase 13A2; ATPase type 13A2; probable cation-transporting ATPase 13A2

NP_001166903.1

EC 7.2.2.10

XP_006239308.1

EC 7.2.2.10

XP_006239309.1

EC 7.2.2.10

XP_006239312.1

EC 7.2.2.10

XP_006239313.1

EC 7.2.2.10

XP_063144147.1

EC 7.2.2.10

XP_063144148.1

EC 7.2.2.10

XP_063144149.1

EC 7.2.2.10

XP_063144150.1

EC 7.2.2.10

XP_063144151.1

EC 7.2.2.10

XP_063144152.1

EC 7.2.2.10

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_001173432.1 → NP_001166903.1 polyamine-transporting ATPase 13A2

See identical proteins and their annotated locations for NP_001166903.1

Status: PROVISIONAL

Source sequence(s)

BC168672

UniProtKB/TrEMBL

A0A8I5ZTP8, B5DEH6

Related

ENSRNOP00000082003.1, ENSRNOT00000114069.1

Conserved Domains (5) summary

COG4087
Location:843 → 892

COG4087; Soluble P-type ATPase [General function prediction only]

TIGR01657
Location:39 → 1071

P-ATPase-V; P-type ATPase of unknown pump specificity (type V)

pfam00122
Location:258 → 493

E1-E2_ATPase; E1-E2 ATPase

pfam12409
Location:39 → 110

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:621 → 658

Cation_ATPase; Cation transport ATPase (P-type)

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_086023.1 Reference GRCr8

Range

158575727..158595157

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063288078.1 → XP_063144148.1 polyamine-transporting ATPase 13A2 isoform X5
XM_006239250.5 → XP_006239312.1 polyamine-transporting ATPase 13A2 isoform X3

UniProtKB/TrEMBL

A0A8I5ZTP8

Related

ENSRNOP00000070096.2

Conserved Domains (6) summary

COG4087
Location:843 → 892

COG4087; Soluble P-type ATPase [General function prediction only]

TIGR01657
Location:39 → 1071

P-ATPase-V; P-type ATPase of unknown pump specificity (type V)

pfam00122
Location:258 → 493

E1-E2_ATPase; E1-E2 ATPase

pfam12409
Location:39 → 110

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:621 → 658

Cation_ATPase; Cation transport ATPase (P-type)

cl02930
Location:188 → 260

Cation_ATPase_N; Cation transporter/ATPase, N-terminus
XM_063288077.1 → XP_063144147.1 polyamine-transporting ATPase 13A2 isoform X2
XM_063288081.1 → XP_063144151.1 polyamine-transporting ATPase 13A2 isoform X8

UniProtKB/TrEMBL

A0A0G2JX15
XM_063288080.1 → XP_063144150.1 polyamine-transporting ATPase 13A2 isoform X7
XM_006239247.5 → XP_006239309.1 polyamine-transporting ATPase 13A2 isoform X10

UniProtKB/TrEMBL

A0A8I5ZTP8

Conserved Domains (5) summary

COG4087
Location:842 → 891

COG4087; Soluble P-type ATPase [General function prediction only]

TIGR01657
Location:39 → 1115

P-ATPase-V; P-type ATPase of unknown pump specificity (type V)

pfam00122
Location:257 → 492

E1-E2_ATPase; E1-E2 ATPase

pfam12409
Location:39 → 110

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:620 → 657

Cation_ATPase; Cation transport ATPase (P-type)
XM_006239251.5 → XP_006239313.1 polyamine-transporting ATPase 13A2 isoform X4

UniProtKB/TrEMBL

A0A8I5ZTP8

Conserved Domains (6) summary

COG4087
Location:842 → 891

COG4087; Soluble P-type ATPase [General function prediction only]

TIGR01657
Location:39 → 1070

P-ATPase-V; P-type ATPase of unknown pump specificity (type V)

pfam00122
Location:257 → 492

E1-E2_ATPase; E1-E2 ATPase

pfam12409
Location:39 → 110

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:620 → 657

Cation_ATPase; Cation transport ATPase (P-type)

cl02930
Location:187 → 259

Cation_ATPase_N; Cation transporter/ATPase, N-terminus
XM_063288082.1 → XP_063144152.1 polyamine-transporting ATPase 13A2 isoform X9
XM_006239246.5 → XP_006239308.1 polyamine-transporting ATPase 13A2 isoform X1

UniProtKB/TrEMBL

A0A8I5ZTP8, F1MAA4

Related

ENSRNOP00000010884.7

Conserved Domains (5) summary

COG4087
Location:843 → 892

COG4087; Soluble P-type ATPase [General function prediction only]

TIGR01657
Location:39 → 1116

P-ATPase-V; P-type ATPase of unknown pump specificity (type V)

pfam00122
Location:258 → 493

E1-E2_ATPase; E1-E2 ATPase

pfam12409
Location:39 → 110

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:621 → 658

Cation_ATPase; Cation transport ATPase (P-type)
XM_063288079.1 → XP_063144149.1 polyamine-transporting ATPase 13A2 isoform X6