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    AP3S1 adaptor related protein complex 3 subunit sigma 1 [ Homo sapiens (human) ]

    Gene ID: 1176, updated on 28-Oct-2024

    Summary

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    Official Symbol
    AP3S1provided by HGNC
    Official Full Name
    adaptor related protein complex 3 subunit sigma 1provided by HGNC
    Primary source
    HGNC:HGNC:2013
    See related
    Ensembl:ENSG00000177879 MIM:601507; AllianceGenome:HGNC:2013
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CLAPS3; Sigma3A
    Summary
    This gene encodes a subunit of the AP3 adaptor complex. This complex functions in the formation of subcellular vesicles budded from the Golgi body. Several related pseudogenes of this gene have been found. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 9.7), small intestine (RPKM 6.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See AP3S1 in Genome Data Viewer
    Location:
    5q22.3-q23.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (115841935..115914081)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (116354331..116426478)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (115177632..115249778)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14872 Neighboring gene uncharacterized LOC124901049 Neighboring gene cysteine dioxygenase type 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115176125-115176625 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:115176629-115177530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22939 Neighboring gene autophagy related 12 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:115216191-115216388 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:115265650-115266849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22940 Neighboring gene lincRNA adipogenesis and lipogenesis associated Neighboring gene laeverin Neighboring gene DEAD-box helicase 43 pseudogene 1

    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 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. Cloning, expression pattern and mapping to 12p 13.2 --> p13.1 of CLAPS3, a gene encoding a novel clathrin-adaptor small chain. Watanabe TK, et al. Cytogenet Cell Genet, 1996. PMID 8697810
    2. Downregulation of genes encoding for subunits of adaptor complex-3 in cervical carcinomas. Petrenko AA, et al. Biochemistry (Mosc), 2006 Oct. PMID 17125464
    3. Structural requirements for interactions between leucine-sorting signals and clathrin-associated adaptor protein complex AP3. Rodionov DG, et al. J Biol Chem, 2002 Dec 6. PMID 12370188
    4. Interaction of insulin receptor substrate-1 with the sigma3A subunit of the adaptor protein complex-3 in cultured adipocytes. VanRenterghem B, et al. J Biol Chem, 1998 Nov 6. PMID 9792713
    5. RNF13 Dileucine Motif Variants L311S and L312P Interfere with Endosomal Localization and AP-3 Complex Association. Cabana VC, et al. Cells, 2021 Nov 6. PMID 34831286, Free PMC Article

    See all (81) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. KCNQ and AP3S1, but not MAN2A1 or ALDH7A1 have a role in risk of type 2 diabetes in the Chinese Northern Han population
      Title: Variants in KCNQ1, AP3S1, MAN2A1, and ALDH7A1 and the risk of type 2 diabetes in the Chinese Northern Han population: a case-control study and meta-analysis.
    2. Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Variants in KCNQ1, AP3S1, MAN2A1, and ALDH7A1 and the risk of type 2 diabetes in the Chinese Northern Han population: a case-control study and meta-analysis.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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 gp120 env Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    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
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    gag AP3S1 deficiency in HPS2 fibroblasts inhibits HIV-1 Gag assembly and release PubMed
    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

    Homology

    Gene Ontology Provided by GOA

    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 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 insulin receptor signaling pathway TAS
    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 
    part_of AP-type membrane coat adaptor complex TAS
    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
    		  
    located_in transport vesicle TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    AP-3 complex subunit sigma-1
    Names
    adapter-related protein complex 3 subunit sigma-1
    adaptor related protein complex 3 sigma 1 subunit
    clathrin adaptor complex AP3, sigma-3A subunit
    clathrin-associated/assembly/adapter protein, small 3
    clathrin-associated/assembly/adaptor protein, small 3 (22kD)
    sigma-adaptin 3a

    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_001002924.3 → NP_001002924.2  AP-3 complex subunit sigma-1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' region, lacks an alternate in-frame exon in the 3' end, and initiates translation at an alternate start codon compared to variant 7. The encoded isoform (2) has a shorter N-terminus and lacks an alternate C-terminal segment compared to isoform 7.
      Source sequence(s)
      BC000804, BC012614, BP368651, BX647735
      UniProtKB/TrEMBL
      B2R4I8
      Related
      ENST00000395548.6
      Conserved Domains (1) summary
      COG5030
      Location:1 → 130
      APS2; Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]

    2. NM_001284.4 → NP_001275.1  AP-3 complex subunit sigma-1 isoform 1

      See identical proteins and their annotated locations for NP_001275.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon in the 3' end compared to variant 7. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 7.
      Source sequence(s)
      BC000804, BP368651, BX647735
      Consensus CDS
      CCDS4123.1
      UniProtKB/Swiss-Prot
      O00647, O00676, O00721, O00727, Q53XL4, Q6ICQ2, Q92572
      UniProtKB/TrEMBL
      B2R4I8
      Related
      ENSP00000325369.7, ENST00000316788.12
      Conserved Domains (1) summary
      cd14834
      Location:1 → 146
      AP3_sigma; AP-3 complex subunit sigma

    3. NM_001318090.2 → NP_001305019.1  AP-3 complex subunit sigma-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate in-frame exons compared to variant 7. The encoded isoform (3) is shorter than isoform 7.
      Source sequence(s)
      BC000804, DB483797
      UniProtKB/Swiss-Prot
      Q92572
      Conserved Domains (1) summary
      cl38905
      Location:1 → 78
      longin-like; Longin-like domains

    4. NM_001318091.2 → NP_001305020.1  AP-3 complex subunit sigma-1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 7. The encoded isoform (4) is shorter than isoform 7.
      Source sequence(s)
      BC000804, CN411347
      UniProtKB/TrEMBL
      B2R4I8
      Conserved Domains (1) summary
      cd14834
      Location:1 → 122
      AP3_sigma; AP-3 complex subunit sigma

    5. NM_001318093.2 → NP_001305022.1  AP-3 complex subunit sigma-1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon and contains another alternate exon, which results in a frameshift, compared to variant 7. The encoded isoform (5) has a shorter, distinct C-terminus compared to isoform 7.
      Source sequence(s)
      AC010282, BC000804, BI757703, BP368651, BX647735
      Consensus CDS
      CCDS83021.1
      UniProtKB/TrEMBL
      B2R4I8, F5H459
      Related
      ENSP00000446179.1, ENST00000506430.2
      Conserved Domains (1) summary
      cd14834
      Location:1 → 146
      AP3_sigma; AP-3 complex subunit sigma

    6. NM_001318094.2 → NP_001305023.1  AP-3 complex subunit sigma-1 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks two alternate in-frame exons compared to variant 7. The encoded isoform (6) is shorter than isoform 7.
      Source sequence(s)
      BC000804, BP368651, BX394598, BX647735
      UniProtKB/TrEMBL
      B2R4I8
      Conserved Domains (1) summary
      cd14834
      Location:1 → 115
      AP3_sigma; AP-3 complex subunit sigma

    7. NM_001364119.1 → NP_001351048.1  AP-3 complex subunit sigma-1 isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) encodes the longest isoform (7).
      Source sequence(s)
      AC010282, AC026449
      UniProtKB/TrEMBL
      B2R4I8
      Conserved Domains (1) summary
      cd14834
      Location:1 → 146
      AP3_sigma; AP-3 complex subunit sigma

    8. NM_001364120.1 → NP_001351049.1  AP-3 complex subunit sigma-1 isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) contains an alternate exon and lacks two other alternate exons compared to variant 7. The resulting isoform (8) has a shorter and distinct C-terminus compared to isoform 7.
      Source sequence(s)
      AC010282, AC026449
      Conserved Domains (1) summary
      cd14834
      Location:1 → 122
      AP3_sigma; AP-3 complex subunit sigma

    9. NM_001364122.1 → NP_001351051.1  AP-3 complex subunit sigma-1 isoform 9

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks three alternate exons compared to variant 7. The resulting isoform (9) is shorter compared to isoform 7.
      Source sequence(s)
      AC010282, AC026449
      Conserved Domains (1) summary
      cl38905
      Location:1 → 91
      longin-like; Longin-like domains

    RNA

    1. NR_157084.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC010282, AC026449

    2. NR_157085.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC010282, AC026449

    3. NR_157086.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC010282, AC026449

    4. NR_157087.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC010282, AC026449

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      115841935..115914081
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416696.1 → XP_047272652.1  AP-3 complex subunit sigma-1 isoform X2

    2. XM_017009024.3 → XP_016864513.2  AP-3 complex subunit sigma-1 isoform X1

      UniProtKB/TrEMBL
      B2R4I8, F5H459
      Conserved Domains (1) summary
      cd14834
      Location:1 → 146
      AP3_sigma; AP-3 complex subunit sigma

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      116354331..116426478
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351566.1 → XP_054207541.1  AP-3 complex subunit sigma-1 isoform X2

    2. XM_054351565.1 → XP_054207540.1  AP-3 complex subunit sigma-1 isoform X1

      UniProtKB/TrEMBL
      F5H459
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92572.1 GenPept UniProtKB/Swiss-Prot:Q92572

    Gene LinkOut

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