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

    Gene ID: 55317, updated on 27-Nov-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, Nov 2024]
    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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    See AP5S1 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3820547..3828838)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3851488..3859779)
    RS_2024_09 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)

    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
      ENSP00000405487.2, ENST00000455742.6
      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_2024_08

    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

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

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