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    Atp9a ATPase, class II, type 9A [ Mus musculus (house mouse) ]

    Gene ID: 11981, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Atp9aprovided by MGI
    Official Full Name
    ATPase, class II, type 9Aprovided by MGI
    Primary source
    MGI:MGI:1330826
    See related
    Ensembl:ENSMUSG00000027546 AllianceGenome:MGI:1330826
    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
    IIa
    Summary
    Predicted to enable ATPase-coupled intramembrane lipid transporter activity and protease binding activity. Involved in neuron projection morphogenesis. Located in early endosome and late endosome. Is expressed in several structures, including alimentary system; central nervous system; hemolymphoid system gland; peripheral nervous system; and retina. Used to study specific developmental disorder. Human ortholog(s) of this gene implicated in neurodevelopmental disorder with poor growth and behavioral abnormalities. Orthologous to human ATP9A (ATPase phospholipid transporting 9A (putative)). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in colon adult (RPKM 66.0), CNS E18 (RPKM 56.7) and 25 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Atp9a in Genome Data Viewer
    Location:
    2 H3; 2 88.99 cM
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (168476358..168584290, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (168634438..168742370, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 33413 Neighboring gene nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2 Neighboring gene STARR-seq mESC enhancer starr_06462 Neighboring gene STARR-positive B cell enhancer mm9_chr2:168365341-168365641 Neighboring gene STARR-seq mESC enhancer starr_06463 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:168421294-168421477 Neighboring gene STARR-seq mESC enhancer starr_06464 Neighboring gene STARR-seq mESC enhancer starr_06465 Neighboring gene microRNA 7004 Neighboring gene VISTA enhancer mm1375 Neighboring gene STARR-seq mESC enhancer starr_06468 Neighboring gene STARR-seq mESC enhancer starr_06472 Neighboring gene spalt like transcription factor 4 Neighboring gene predicted gene 14261 Neighboring gene predicted gene, 25214

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. ATP9A deficiency causes ADHD and aberrant endosomal recycling via modulating RAB5 and RAB11 activity. Meng T, et al. Mol Psychiatry, 2023 Mar. PMID 36604604, Free PMC Article
    2. Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. Zhang Y, et al. PLoS Genet, 2008 Feb 29. PMID 18454193, Free PMC Article
    3. Multiple members of a third subfamily of P-type ATPases identified by genomic sequences and ESTs. Halleck MS, et al. Genome Res, 1998 Apr. PMID 9548971
    4. The type 4 subfamily of P-type ATPases, putative aminophospholipid translocases with a role in human disease. Paulusma CC, et al. Biochim Biophys Acta, 2005 Jun 30. PMID 15919184
    5. Multipotent genetic suppression of retrotransposon-induced mutations by Nxf1 through fine-tuning of alternative splicing. Concepcion D, et al. PLoS Genet, 2009 May. PMID 19436707, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0611

    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 ATPase-coupled intramembrane lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATPase-coupled intramembrane lipid transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protease binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lipid translocation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of exosomal secretion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of exosomal secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron projection morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phospholipid translocation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phospholipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of endocytic recycling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of retrograde transport, endosome to Golgi ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in recycling endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    probable phospholipid-transporting ATPase IIA
    Names
    ATPase 9A, class II
    ATPase 9A, p type
    ATPase, class 2
    NP_001276374.1
    NP_001276375.1
    NP_001341906.1
    NP_001341907.1
    NP_056546.2
    XP_006498666.1
    XP_017170555.1
    XP_017170556.1
    XP_030102742.1

    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)

    1. NM_001289445.1 → NP_001276374.1  probable phospholipid-transporting ATPase IIA isoform 2

      See identical proteins and their annotated locations for NP_001276374.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK082271, AL844575, AL929248, BC094551, BE989200, BY123191
      Consensus CDS
      CCDS71202.1
      UniProtKB/TrEMBL
      Q505G9, Q8C288
      Related
      ENSMUSP00000104804.3, ENSMUST00000109175.9
      Conserved Domains (2) summary
      cd07541
      Location:39 → 951
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      cl26237
      Location:449 → 557
      Cation_ATPase; Cation transport ATPase (P-type)

    2. NM_001289446.1 → NP_001276375.1  probable phospholipid-transporting ATPase IIA isoform 3

      See identical proteins and their annotated locations for NP_001276375.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 3, which has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK082271, AL844575, BE989200, BY240030, BY293759
      Consensus CDS
      CCDS71203.1
      UniProtKB/TrEMBL
      Q505G9, Q8C4G3
      Related
      ENSMUSP00000104806.2, ENSMUST00000109177.8
      Conserved Domains (2) summary
      cd07541
      Location:37 → 949
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      cl26237
      Location:447 → 555
      Cation_ATPase; Cation transport ATPase (P-type)

    3. NM_001354977.2 → NP_001341906.1  probable phospholipid-transporting ATPase IIA isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL844575, AL929248
      UniProtKB/TrEMBL
      Q505G9
      Conserved Domains (2) summary
      cd07541
      Location:33 → 945
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      pfam13246
      Location:443 → 551
      Cation_ATPase; Cation transport ATPase (P-type)

    4. NM_001354978.1 → NP_001341907.1  probable phospholipid-transporting ATPase IIA isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL844575, AL929248
      UniProtKB/TrEMBL
      Q505G9
      Conserved Domains (2) summary
      cd07541
      Location:1 → 871
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      pfam13246
      Location:369 → 477
      Cation_ATPase; Cation transport ATPase (P-type)

    5. NM_015731.3 → NP_056546.2  probable phospholipid-transporting ATPase IIA isoform 1

      See identical proteins and their annotated locations for NP_056546.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL844575, AL929248
      Consensus CDS
      CCDS38345.1
      UniProtKB/Swiss-Prot
      O70228, Q8VDI5, Q922L9
      UniProtKB/TrEMBL
      Q505G9
      Related
      ENSMUSP00000029060.5, ENSMUST00000029060.11
      Conserved Domains (6) summary
      cd01427
      Location:652 → 802
      HAD_like; Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, ...
      TIGR01652
      Location:53 → 1045
      ATPase-Plipid; phospholipid-translocating P-type ATPase, flippase
      pfam00122
      Location:109 → 337
      E1-E2_ATPase; E1-E2 ATPase
      pfam13246
      Location:499 → 573
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16209
      Location:40 → 104
      PhoLip_ATPase_N; Phospholipid-translocating ATPase N-terminal
      pfam16212
      Location:811 → 1039
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal

    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

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      168476358..168584290 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017315066.1 → XP_017170555.1  probable phospholipid-transporting ATPase IIA isoform X2

      UniProtKB/TrEMBL
      Q505G9
      Conserved Domains (2) summary
      cd07541
      Location:1 → 871
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      pfam13246
      Location:369 → 477
      Cation_ATPase; Cation transport ATPase (P-type)

    2. XM_030246882.1 → XP_030102742.1  probable phospholipid-transporting ATPase IIA isoform X2

      UniProtKB/TrEMBL
      Q505G9
      Conserved Domains (2) summary
      cd07541
      Location:1 → 871
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      pfam13246
      Location:369 → 477
      Cation_ATPase; Cation transport ATPase (P-type)

    3. XM_006498603.1 → XP_006498666.1  probable phospholipid-transporting ATPase IIA isoform X1

      UniProtKB/TrEMBL
      Q505G9
      Conserved Domains (2) summary
      cd07541
      Location:34 → 946
      P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B
      pfam13246
      Location:444 → 552
      Cation_ATPase; Cation transport ATPase (P-type)

    4. XM_017315067.1 → XP_017170556.1  probable phospholipid-transporting ATPase IIA isoform X3

      Conserved Domains (2) summary
      pfam13246
      Location:14 → 122
      Cation_ATPase; Cation transport ATPase (P-type)
      cl21460
      Location:73 → 516
      HAD_like; Haloacid Dehalogenase-like Hydrolases
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O70228.3 GenPept UniProtKB/Swiss-Prot:O70228

    Gene LinkOut

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