Atp13a4 ATPase type 13A4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Atp13a4provided by MGI
Official Full Name: ATPase type 13A4provided by MGI
Primary source: MGI:MGI:1924456
See related: Ensembl:ENSMUSG00000038094 AllianceGenome:MGI:1924456
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 4832416L12; 4631413J11Rik; 9330174J19Rik
Summary: Predicted to enable ATPase-coupled monoatomic cation transmembrane transporter activity and polyamine transmembrane transporter activity. Acts upstream of or within intracellular calcium ion homeostasis. Located in endoplasmic reticulum membrane and endosome membrane. Is expressed in brain and embryo. Orthologous to human ATP13A4 (ATPase 13A4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in genital fat pad adult (RPKM 4.5), cerebellum adult (RPKM 2.4) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 B2; 16 20.24 cM

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (29208685..29363682, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (29389103..29544864, complement)

Chromosome 16 - NC_000082.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data suggest that ATP13A4 may play a vital role in the developing nervous system and its impairment can contribute to the symptoms seen in autism spectrum disorder.
Title: The E646D-ATP13A4 mutation associated with autism reveals a defect in calcium regulation.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)

General gene information

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Markers

BE136099 (e-PCR)
- UniSTS:209199

Atp13a4 (e-PCR), detects polymorphism
- UniSTS:530873

D16Mit57 (e-PCR), detects polymorphism
- UniSTS:116447

Gene Ontology Provided by MGI

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 ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone 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 DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables P-type calcium transporter activity	IC Inferred by Curator more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables polyamine transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular calcium ion homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in polyamine transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in late endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: probable cation-transporting ATPase 13A4

Names: P5-ATPase; type V P-type ATPase

NP_001158084.1

EC 3.6.3.-

NP_001158085.1

EC 3.6.3.-

NP_766201.3

EC 3.6.3.-

XP_006522114.1

EC 3.6.3.-

XP_006522116.1

EC 3.6.3.-

XP_006522117.1

EC 3.6.3.-

XP_006522118.1

EC 3.6.3.-

XP_017172444.1

EC 3.6.3.-

XP_017172445.1

EC 3.6.3.-

XP_030104933.1

EC 3.6.3.-

XP_036015780.1

EC 3.6.3.-

XP_036015781.1

EC 3.6.3.-

XP_036015782.1

EC 3.6.3.-

XP_036015783.1

EC 3.6.3.-

XP_036015784.1

EC 3.6.3.-

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_001164612.1 → NP_001158084.1 probable cation-transporting ATPase 13A4 isoform 1

See identical proteins and their annotated locations for NP_001158084.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC175464

Consensus CDS

CCDS49816.1

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

UniProtKB/TrEMBL

S4R234

Related

ENSMUSP00000138479.2, ENSMUST00000182627.8

Conserved Domains (6) summary

COG4087
Location:821 → 870

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

TIGR01657
Location:18 → 1115

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

pfam00122
Location:228 → 472

E1-E2_ATPase; E1-E2 ATPase

pfam00690
Location:170 → 218

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:596 → 635

Cation_ATPase; Cation transport ATPase (P-type)
NM_001164613.1 → NP_001158085.1 probable cation-transporting ATPase 13A4 isoform 3

See identical proteins and their annotated locations for NP_001158085.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and 3' coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AK028776, BE955453

Consensus CDS

CCDS49817.1

UniProtKB/TrEMBL

A0A0R4J0M2

Related

ENSMUSP00000048753.8, ENSMUST00000039090.9

Conserved Domains (2) summary

cd07542
Location:174 → 762

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter
NM_172613.4 → NP_766201.3 probable cation-transporting ATPase 13A4 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC175464

Consensus CDS

CCDS59623.1

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

UniProtKB/TrEMBL

E9QPP7

Related

ENSMUSP00000060987.9, ENSMUST00000057018.15

Conserved Domains (6) summary

COG4087
Location:802 → 851

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

TIGR01657
Location:18 → 1096

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

pfam00122
Location:228 → 453

E1-E2_ATPase; E1-E2 ATPase

pfam00690
Location:170 → 218

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter

pfam13246
Location:577 → 616

Cation_ATPase; Cation transport ATPase (P-type)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

29208685..29363682 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017316955.3 → XP_017172444.1 probable cation-transporting ATPase 13A4 isoform X3

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (2) summary

cd07542
Location:174 → 1001

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter
XM_006522051.5 → XP_006522114.1 probable cation-transporting ATPase 13A4 isoform X4

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (2) summary

cd07542
Location:174 → 931

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter
XM_036159889.1 → XP_036015782.1 probable cation-transporting ATPase 13A4 isoform X2

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (2) summary

cd07542
Location:174 → 956

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:17 → 142

P5-ATPase; P5-type ATPase cation transporter
XM_036159887.1 → XP_036015780.1 probable cation-transporting ATPase 13A4 isoform X1

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (2) summary

cd07542
Location:143 → 970

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:48 → 111

P5-ATPase; P5-type ATPase cation transporter
XM_036159890.1 → XP_036015783.1 probable cation-transporting ATPase 13A4 isoform X5

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (1) summary

cd07542
Location:82 → 909

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
XM_036159891.1 → XP_036015784.1 probable cation-transporting ATPase 13A4 isoform X6

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (1) summary

cd07542
Location:1 → 769

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
XM_036159888.1 → XP_036015781.1 probable cation-transporting ATPase 13A4 isoform X1

UniProtKB/Swiss-Prot

Q5XF90, Q80V28, Q8C105, Q8C184

Conserved Domains (2) summary

cd07542
Location:143 → 970

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:48 → 111

P5-ATPase; P5-type ATPase cation transporter
XM_030249073.1 → XP_030104933.1 probable cation-transporting ATPase 13A4 isoform X9

Conserved Domains (1) summary

cd07542
Location:1 → 471

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
XM_006522055.4 → XP_006522118.1 probable cation-transporting ATPase 13A4 isoform X9

Conserved Domains (1) summary

cd07542
Location:1 → 471

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
XM_006522053.5 → XP_006522116.1 probable cation-transporting ATPase 13A4 isoform X7

Conserved Domains (2) summary

cd07542
Location:174 → 948

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter
XM_006522054.4 → XP_006522117.1 probable cation-transporting ATPase 13A4 isoform X8

Conserved Domains (2) summary

cd07542
Location:174 → 915

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter
XM_017316956.3 → XP_017172445.1 probable cation-transporting ATPase 13A4 isoform X10

UniProtKB/TrEMBL

A0A0R4J0M2

Conserved Domains (2) summary

cd07542
Location:174 → 762

P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

pfam12409
Location:18 → 137

P5-ATPase; P5-type ATPase cation transporter