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

Gene ID: 1176, updated on 5-Jul-2020

Summary

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
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

Genomic context

See AP3S1 in Genome Data Viewer
Location:
5q22.3-q23.1
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (115841606..115914081)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (115177303..115249778)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cysteine dioxygenase type 1 Neighboring gene autophagy related 12 Neighboring gene lincRNA adipogenesis and lipogenesis associated Neighboring gene laeverin Neighboring gene DEAD-box helicase 43 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
anterograde axonal transport ISS
Inferred from Sequence or Structural Similarity
more info
 
anterograde synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
 
insulin receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
AP-3 adaptor complex IDA
Inferred from Direct Assay
more info
PubMed 
AP-type membrane coat adaptor complex TAS
Traceable Author Statement
more info
PubMed 
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
axon cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
transport vesicle TAS
Traceable Author Statement
more info
PubMed 

General protein information

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)

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_001002924.3NP_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/Swiss-Prot
    Q92572
    Related
    ENST00000395548.6
    Conserved Domains (1) summary
    COG5030
    Location:1130
    APS2; Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
  2. NM_001284.4NP_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
    Q92572
    Related
    ENSP00000325369.7, ENST00000316788.12
    Conserved Domains (1) summary
    cd14834
    Location:1146
    AP3_sigma; AP-3 complex subunit sigma
  3. NM_001318090.2NP_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:178
    longin-like; Longin-like domains
  4. NM_001318091.2NP_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/Swiss-Prot
    Q92572
    Conserved Domains (1) summary
    cd14834
    Location:1122
    AP3_sigma; AP-3 complex subunit sigma
  5. NM_001318093.2NP_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/Swiss-Prot
    Q92572
    UniProtKB/TrEMBL
    F5H459
    Related
    ENSP00000446179.1, ENST00000506430.2
    Conserved Domains (1) summary
    cd14834
    Location:1146
    AP3_sigma; AP-3 complex subunit sigma
  6. NM_001318094.2NP_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/Swiss-Prot
    Q92572
    Conserved Domains (1) summary
    cd14834
    Location:1115
    AP3_sigma; AP-3 complex subunit sigma
  7. NM_001364119.1NP_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
    Conserved Domains (1) summary
    cd14834
    Location:1146
    AP3_sigma; AP-3 complex subunit sigma
  8. NM_001364120.1NP_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:1122
    AP3_sigma; AP-3 complex subunit sigma
  9. NM_001364122.1NP_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:191
    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_157087.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC010282, AC026449

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    115841606..115914081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009025.1XP_016864514.1  AP-3 complex subunit sigma-1 isoform X2

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

    Conserved Domains (1) summary
    cd14834
    Location:1146
    AP3_sigma; AP-3 complex subunit sigma
  3. XM_011543136.3XP_011541438.3  AP-3 complex subunit sigma-1 isoform X1

    Conserved Domains (1) summary
    cd14834
    Location:1146
    AP3_sigma; AP-3 complex subunit sigma
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