Atp6v1d ATPase, H+ transporting, lysosomal V1 subunit D [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Atp6v1dprovided by MGI
Official Full Name: ATPase, H+ transporting, lysosomal V1 subunit Dprovided by MGI
Primary source: MGI:MGI:1921084
See related: Ensembl:ENSMUSG00000021114 AllianceGenome:MGI:1921084
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: VATD; Vma8; Atp6m; 1110004P10Rik
Summary: Predicted to enable proton-transporting ATPase activity, rotational mechanism. Involved in synaptic vesicle lumen acidification. Part of proton-transporting V-type ATPase complex. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; integumental system; and sensory organ. Orthologous to human ATP6V1D (ATPase H+ transporting V1 subunit D). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in cortex adult (RPKM 56.2), frontal lobe adult (RPKM 53.1) and 22 other tissues See more
Orthologs: human all
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Genomic context

Location:: 12 C3; 12 35.51 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (78889756..78908810, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (78842982..78862008, complement)

Chromosome 12 - NC_000078.7 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?

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Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12Wsu1e (e-PCR), detects polymorphism
- UniSTS:141862

Atp6m (e-PCR), detects polymorphism
- UniSTS:228480

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables proton-transporting ATPase activity, rotational mechanism	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to cilium	ISO Inferred from Sequence Orthology more info
involved_in protein localization to cilium	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic vesicle lumen acidification	EXP Inferred from Experiment more info	PubMed
involved_in synaptic vesicle lumen acidification	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle lumen acidification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of ATPase complex	ISO Inferred from Sequence Orthology more info	PubMed
colocalizes_with centrosome	ISO Inferred from Sequence Orthology more info
colocalizes_with centrosome	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with cilium	ISO Inferred from Sequence Orthology more info
colocalizes_with cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in extrinsic component of synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in extrinsic component of synaptic vesicle membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	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 plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of proton-transporting V-type ATPase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of proton-transporting V-type ATPase complex	IDA Inferred from Direct Assay more info	PubMed
part_of proton-transporting V-type ATPase complex	ISO Inferred from Sequence Orthology more info
part_of proton-transporting V-type ATPase, V1 domain	ISO Inferred from Sequence Orthology more info	PubMed
part_of vacuolar proton-transporting V-type ATPase, V1 domain	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: V-type proton ATPase subunit D

Names: ATPase, H+ transporting lysosomal (vacuolar proton pump); ATPase, H+ transporting, V1 subunit D; ATPase, H+ transporting, lysosomal 34kD, V1 subunit D; V-ATPase 28 kDa accessory protein; V-ATPase subunit D; lysosomal 34kDa; vacuolar proton pump subunit D

NP_076210.1

EC 7.1.2.2

XP_030102816.1

EC 7.1.2.2

XP_036013525.1

EC 7.1.2.2

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_023721.2 → NP_076210.1 V-type proton ATPase subunit D

See identical proteins and their annotated locations for NP_076210.1

Status: VALIDATED

Source sequence(s)

AK147910, BY096594

Consensus CDS

CCDS26002.1

UniProtKB/Swiss-Prot

P57746

UniProtKB/TrEMBL

Q3U684, Q3U861, Q3UJH5

Related

ENSMUSP00000021536.8, ENSMUST00000021536.9

Conserved Domains (1) summary

pfam01813
Location:17 → 202

ATP-synt_D; ATP synthase subunit D

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_000078.7 Reference GRCm39 C57BL/6J

Range

78889756..78908810 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157632.1 → XP_036013525.1 V-type proton ATPase subunit D isoform X2

UniProtKB/TrEMBL

Q3U684, Q3UJH5

Conserved Domains (1) summary

pfam01813
Location:1 → 184

ATP-synt_D; ATP synthase subunit D
XM_030246956.2 → XP_030102816.1 V-type proton ATPase subunit D isoform X1

UniProtKB/Swiss-Prot

P57746

UniProtKB/TrEMBL

Q3U684, Q3U861, Q3UJH5

Conserved Domains (1) summary

pfam01813
Location:17 → 202

ATP-synt_D; ATP synthase subunit D