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

Gene ID: 10239, updated on 5-Mar-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, Apr 2022]
Expression
Ubiquitous expression in kidney (RPKM 10.1), thyroid (RPKM 9.4) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (89830599..89893994, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87586470..87650001, complement)
105.20220307 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. Beta3A-adaptin, a subunit of the adaptor-like complex AP-3. Dell'Angelica EC, et al. J Biol Chem, 1997 Jun 13. PMID 9182526
  4. 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
  5. Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Kooner JS, et al. Nat Genet, 2011 Aug 28. PMID 21874001, Free PMC Article

See all (36) 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)

Genotypes

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 presynapse 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_2023_10

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

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