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    Ap3d1 adaptor related protein complex 3 subunit delta 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314633, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Ap3d1provided by RGD
    Official Full Name
    adaptor related protein complex 3 subunit delta 1provided by RGD
    Primary source
    RGD:1308659
    See related
    Ensembl:ENSRNOG00000018977 AllianceGenome:RGD:1308659
    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
    Ap3d
    Summary
    Involved in synaptic vesicle budding from endosome. Predicted to be located in axon and postsynapse. Predicted to be part of AP-3 adaptor complex. Predicted to be active in endosome; glutamatergic synapse; and terminal bouton. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome. Orthologous to human AP3D1 (adaptor related protein complex 3 subunit delta 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 201.8), Brain (RPKM 185.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ap3d1 in Genome Data Viewer
    Location:
    7q11
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (9620909..9656350)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (8970249..9005651)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (11838639..11873992)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene pleckstrin homology domain containing J1 Neighboring gene DOT1 like histone lysine methyltransferase Neighboring gene uncharacterized LOC134479808 Neighboring gene uncharacterized LOC120093774 Neighboring gene IZUMO family member 4 Neighboring gene MOB kinase activator 3A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Adaptor protein complexes 1 and 3 are essential for generation of synaptic vesicles from activity-dependent bulk endosomes. Cheung G, et al. J Neurosci, 2012 Apr 25. PMID 22539861, Free PMC Article
    2. Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway. Asensio CS, et al. Dev Cell, 2013 Nov 25. PMID 24210660, Free PMC Article
    3. The neuronal form of adaptor protein-3 is required for synaptic vesicle formation from endosomes. Blumstein J, et al. J Neurosci, 2001 Oct 15. PMID 11588176, Free PMC Article
    4. Hermansky-Pudlak protein complexes, AP-3 and BLOC-1, differentially regulate presynaptic composition in the striatum and hippocampus. Newell-Litwa K, et al. J Neurosci, 2010 Jan 20. PMID 20089890, Free PMC Article
    5. Vglut1 and ZnT3 co-targeting mechanisms regulate vesicular zinc stores in PC12 cells. Salazar G, et al. J Cell Sci, 2005 May 1. PMID 15860731

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in anterograde axonal transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in anterograde synaptic vesicle transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in anterograde synaptic vesicle transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within antigen processing and presentation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within antigen processing and presentation, exogenous lipid antigen via MHC class Ib ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosome to melanosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within intracellular protein transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neurotransmitter receptor transport, postsynaptic endosome to lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neurotransmitter receptor transport, postsynaptic endosome to lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of NK T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_positive_effect positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein localization to organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein targeting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein targeting to vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle budding from endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle budding from endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic vesicle budding from endosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synaptic vesicle budding from endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synaptic vesicle membrane organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within synaptic vesicle membrane organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle-mediated transport in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in zinc ion import into lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in axon cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in postsynapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynaptic endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynaptic endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in terminal bouton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in terminal bouton ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    AP-3 complex subunit delta-1
    Names
    adaptor-related protein complex 3, delta 1 subunit
    adaptor-related protein complex 3, delta subunit

    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_001100719.1 → NP_001094189.1  AP-3 complex subunit delta-1

      See identical proteins and their annotated locations for NP_001094189.1

      Status: PROVISIONAL

      Source sequence(s)
      BC169097
      UniProtKB/TrEMBL
      A0A8I6AM24, B5DFK6, F7F0K5
      Related
      ENSRNOP00000025878.5, ENSRNOT00000025878.6
      Conserved Domains (4) summary
      pfam01602
      Location:32 → 581
      Adaptin_N; Adaptin N terminal region
      pfam06375
      Location:661 → 803
      BLVR; Bovine leukaemia virus receptor (BLVR)
      pfam12717
      Location:155 → 265
      Cnd1; non-SMC mitotic condensation complex subunit 1
      sd00044
      Location:151 → 172
      HEAT; HEAT repeat [structural motif]

    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

    1. NC_086025.1 Reference GRCr8

      Range
      9620909..9656350
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263422.1 → XP_063119492.1  AP-3 complex subunit delta-1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AM24

    2. XM_039079008.2 → XP_038934936.1  AP-3 complex subunit delta-1 isoform X3

      UniProtKB/TrEMBL
      A6K8H3
      Conserved Domains (3) summary
      sd00044
      Location:151 → 172
      HEAT; HEAT repeat [structural motif]
      pfam01602
      Location:32 → 581
      Adaptin_N; Adaptin N terminal region
      pfam06375
      Location:661 → 803
      AP3D1; AP-3 complex subunit delta-1

    3. XM_063263423.1 → XP_063119493.1  AP-3 complex subunit delta-1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AM24
    Nucleotide Protein Strain
    Heading Accession and Version

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