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    AP3S2 adaptor related protein complex 3 subunit sigma 2 [ Homo sapiens (human) ]

    Gene ID: 10239, updated on 27-Nov-2024

    Summary

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    Official Symbol
    AP3S2provided by HGNC
    Official Full Name
    adaptor related protein complex 3 subunit sigma 2provided by HGNC
    Primary source
    HGNC:HGNC:571
    See related
    Ensembl:ENSG00000157823 MIM:602416; AllianceGenome:HGNC:571
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AP3S3; sigma3b
    Summary
    Predicted to be involved in anterograde synaptic vesicle transport and vesicle-mediated transport. Located in intracellular membrane-bounded organelle. Part of AP-3 adaptor complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 10.1), thyroid (RPKM 9.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See AP3S2 in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (89830599..89893994, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87586470..87650001, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (90373831..90437226, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90327618-90328280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90335518-90336018 Neighboring gene alanyl aminopeptidase, membrane Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:90347169-90348368 Neighboring gene ANPEP proximal promoter Neighboring gene FOXA motif-containing MPRA enhancer 170 Neighboring gene ANPEP distal promoter Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90365008-90365508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90365509-90366009 Neighboring gene uncharacterized LOC124903551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90367927-90368600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90370583-90371474 Neighboring gene ARPIN-AP3S2 readthrough Neighboring gene uncharacterized LOC124903552 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:90380077-90381276 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:90391438-90392637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10057 Neighboring gene microRNA 5094 Neighboring gene arginine and serine rich coiled-coil 2 pseudogene Neighboring gene RNA, U6 small nuclear 1111, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90435515-90436264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10058 Neighboring gene microRNA 5009 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90437761-90438508 Neighboring gene RNA, U7 small nuclear 111 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90452345-90452529 Neighboring gene actin related protein 2/3 complex inhibitor Neighboring gene zinc finger and SCAN domain containing 5A pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Role of adaptor complex AP-3 in targeting wild-type and mutated CD63 to lysosomes. Rous BA, et al. Mol Biol Cell, 2002 Mar. PMID 11907283, Free PMC Article
    2. Genomewide linkage and peakwide association analyses of carotid plaque in Caribbean Hispanics. Dong C, et al. Stroke, 2010 Dec. PMID 20966410, Free PMC Article
    3. AP-3: an adaptor-like protein complex with ubiquitous expression. Dell'Angelica EC, et al. EMBO J, 1997 Mar 3. PMID 9118953, Free PMC Article
    4. Beta3A-adaptin, a subunit of the adaptor-like complex AP-3. Dell'Angelica EC, et al. J Biol Chem, 1997 Jun 13. PMID 9182526
    5. Specific regulation of the adaptor protein complex AP-3 by the Arf GAP AGAP1. Nie Z, et al. Dev Cell, 2003 Sep. PMID 12967569

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genomewide linkage and peakwide association analyses of carotid plaque in Caribbean Hispanics.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel loci for type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
    EBI GWAS Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed
    Pr55(Gag) gag In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed
    matrix gag In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough ARPIN-AP3S2

    Readthrough gene: ARPIN-AP3S2, Included gene: ARPIN

    Homology

    Clone Names

    • FLJ35955

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in anterograde axonal transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in anterograde synaptic vesicle transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in clathrin-coated vesicle cargo loading, AP-3-mediated NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in melanosome assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in platelet dense granule organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic vesicle coating NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic vesicle recycling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of AP-3 adaptor complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in axon cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in synaptic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    AP-3 complex subunit sigma-2
    Names
    AP-3 complex subunit sigma-3B
    adapter-related protein complex 3 subunit sigma-2
    adaptor complex sigma3B
    adaptor related protein complex 3 sigma 2 subunit
    clathrin-associated/assembly/adaptor protein, small 4, 22-kD
    sigma-3B-adaptin
    sigma-adaptin 3b

    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_005829.5 → NP_005820.1  AP-3 complex subunit sigma-2

      See identical proteins and their annotated locations for NP_005820.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript but encodes the supported protein.
      Source sequence(s)
      AC018988, BC002785, BC010020, DA268327, DA464242, DA752479, X99459
      Consensus CDS
      CCDS10357.1
      UniProtKB/Swiss-Prot
      B2R677, B4DGQ3, O09077, O09149, P59780, Q53H83, Q99589
      UniProtKB/TrEMBL
      Q6PK37
      Related
      ENSP00000338777.4, ENST00000336418.9
      Conserved Domains (1) summary
      cd14834
      Location:1 → 146
      AP3_sigma; AP-3 complex subunit sigma

    RNA

    1. NR_023361.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes an additional exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018988, AW402906, BX098014, DA337392, DB322370, DC340463, DR158459

    2. NR_037582.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018988, BC010615, DA777624

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      89830599..89893994 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      87586470..87650001 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P59780.1 GenPept UniProtKB/Swiss-Prot:P59780

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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