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AP5S1 adaptor related protein complex 5 subunit sigma 1 [ Homo sapiens (human) ]

Gene ID: 55317, updated on 5-Mar-2024

Summary

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Official Symbol
AP5S1provided by HGNC
Official Full Name
adaptor related protein complex 5 subunit sigma 1provided by HGNC
Primary source
HGNC:HGNC:15875
See related
Ensembl:ENSG00000125843 MIM:614824; AllianceGenome:HGNC:15875
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
C20orf29
Summary
Involved in double-strand break repair via homologous recombination and endosomal transport. Located in several cellular components, including late endosome; lysosome; and nucleoplasm. Part of AP-type membrane coat adaptor complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 4.9), thyroid (RPKM 3.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20p13
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3820547..3828838)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3851488..3859779)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (3801194..3809485)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3766794-3767503 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3775953-3776684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12630 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:3777341-3777548 Neighboring gene cell division cycle 25B Neighboring gene Sharpr-MPRA regulatory region 3723 Neighboring gene Sharpr-MPRA regulatory region 8683 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:3782484-3783683 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3787799-3788390 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3788391-3788981 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:3791796-3792995 Neighboring gene long intergenic non-protein coding RNA 1730 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3800994-3801697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12631 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3811623-3812123 Neighboring gene NFE2L2 motif-containing MPRA enhancer 155/156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12633 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3831491-3831992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3838319-3838818 Neighboring gene mitochondrial antiviral signaling protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3846659-3847160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3869109-3869660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12634 Neighboring gene PANK2 antisense RNA 1 Neighboring gene pantothenate kinase 2

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. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. Słabicki M, et al. PLoS Biol, 2010 Jun 29. PMID 20613862, Free PMC Article
  2. The fifth adaptor protein complex. Hirst J, et al. PLoS Biol, 2011 Oct. PMID 22022230, Free PMC Article
  3. The DNA sequence and comparative analysis of human chromosome 20. Deloukas P, et al. Nature, 2001 Dec 20-27. PMID 11780052
  4. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Aregger M, et al. Nat Metab, 2020 Jun. PMID 32694731, Free PMC Article
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: MAVS

Homology

Clone Names

  • FLJ11168

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 double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosomal transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of AP-5 adaptor complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of AP-type membrane coat adaptor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of AP-type membrane coat adaptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in late endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in late endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome NAS
Non-traceable Author Statement
more info
 PubMed 
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in lysosomal membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in lysosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
AP-5 complex subunit sigma-1
Names
adapter-related protein complex 5 sigma subunit
adaptor related protein complex 5 sigma 1 subunit
adaptor-related protein complex 5 sigma subunit
protein C20orf29
sigma5

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_001204446.2 → NP_001191375.1  AP-5 complex subunit sigma-1

    See identical proteins and their annotated locations for NP_001191375.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AK002030, AL109804, DA129391, DA253969
    Consensus CDS
    CCDS13070.1
    UniProtKB/Swiss-Prot
    B3KSD0, D3DVY7, Q9NUS5
    Related
    ENSP00000246041.2, ENST00000246041.6
    Conserved Domains (1) summary
    pfam15001
    Location:1 → 193
    AP-5_subunit_s1; AP-5 complex subunit sigma-1

  2. NM_001204447.2 → NP_001191376.1  AP-5 complex subunit sigma-1

    See identical proteins and their annotated locations for NP_001191376.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AI338486, AK093332, AL109804, DA253969, DB190907
    Consensus CDS
    CCDS13070.1
    UniProtKB/Swiss-Prot
    B3KSD0, D3DVY7, Q9NUS5
    Related
    ENSP00000368886.2, ENST00000379567.6
    Conserved Domains (1) summary
    pfam15001
    Location:1 → 193
    AP-5_subunit_s1; AP-5 complex subunit sigma-1

  3. NM_018347.3 → NP_060817.1  AP-5 complex subunit sigma-1

    See identical proteins and their annotated locations for NP_060817.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AK002030, AL109804, BC043344, DA253969
    Consensus CDS
    CCDS13070.1
    UniProtKB/Swiss-Prot
    B3KSD0, D3DVY7, Q9NUS5
    Related
    ENSP00000481750.1, ENST00000615891.2
    Conserved Domains (1) summary
    pfam15001
    Location:1 → 193
    AP-5_subunit_s1; AP-5 complex subunit sigma-1

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    3820547..3828838
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    3851488..3859779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NUS5.1 GenPept UniProtKB/Swiss-Prot:Q9NUS5

Gene LinkOut

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