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    VPS9D1 VPS9 domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 9605, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VPS9D1provided by HGNC
    Official Full Name
    VPS9 domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:13526
    See related
    Ensembl:ENSG00000075399 MIM:619292; AllianceGenome:HGNC:13526
    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
    ATPBL; ATP-BL; C16orf7
    Summary
    Enables identical protein binding activity. Predicted to be involved in proton motive force-driven ATP synthesis. Predicted to be active in cytosol and endocytic vesicle. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in brain (RPKM 5.5), appendix (RPKM 5.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS9D1 in Genome Data Viewer
    Location:
    16q24.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89707134..89720898, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95791896..95805664, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89773542..89787306, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7919 Neighboring gene long intergenic non-protein coding RNA 2166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89765851-89766716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7920 Neighboring gene cyclin dependent kinase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89772795-89773295 Neighboring gene spermatogenesis associated 2 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89777095-89777658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11419 Neighboring gene VPS9D1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89795065-89795636 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46690 Neighboring gene zinc finger protein 276 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46706 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46707/46708 Neighboring gene MPRA-validated peak2667 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46713 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46714 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46718 Neighboring gene FA complementation group A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11421 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:89846248-89846785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89872952-89873474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7925 Neighboring gene Sharpr-MPRA regulatory region 3988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7927 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:89900233-89901432 Neighboring gene uncharacterized LOC124903760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89903444-89904066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89904067-89904688 Neighboring gene spire type actin nucleation factor 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 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. Isolation and mapping of a putative b subunit of human ATP synthase (ATP-BL) from human leukocytes. Sugimoto J, et al. DNA Res, 1999 Feb 26. PMID 10231027
    2. Vps9d1 regulates tubular endosome formation through specific activation of Rab22A. Nakashima S, et al. J Cell Sci, 2023 Mar 15. PMID 36762583
    3. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Choy KW, et al. Physiol Genomics, 2006 Mar 13. PMID 16368877
    4. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
    5. Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease. Viard J, et al. Life Sci Alliance, 2022 Aug 1. PMID 35914814, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Vps9d1 regulates tubular endosome formation through specific activation of Rab22A.
      Title: Vps9d1 regulates tubular endosome formation through specific activation of Rab22A.
    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

    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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in proton motive force-driven ATP synthesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    VPS9 domain-containing protein 1

    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_004913.3 → NP_004904.2  VPS9 domain-containing protein 1

      See identical proteins and their annotated locations for NP_004904.2

      Status: VALIDATED

      Source sequence(s)
      AB018551, AC010538, AI458261, BC052626, BM920493, BY795348, CA428853
      Consensus CDS
      CCDS42220.1
      UniProtKB/Swiss-Prot
      Q9Y2B5
      UniProtKB/TrEMBL
      H3BM58
      Related
      ENSP00000374037.3, ENST00000389386.8
      Conserved Domains (1) summary
      pfam02204
      Location:509 → 624
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      89707134..89720898 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434932.1 → XP_047290888.1  VPS9 domain-containing protein 1 isoform X5

    2. XM_011523476.4 → XP_011521778.1  VPS9 domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      H3BM58
      Conserved Domains (1) summary
      pfam02204
      Location:509 → 624
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    3. XM_047434931.1 → XP_047290887.1  VPS9 domain-containing protein 1 isoform X2

    4. XM_047434936.1 → XP_047290892.1  VPS9 domain-containing protein 1 isoform X9

    5. XM_005256329.6 → XP_005256386.1  VPS9 domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      H3BM58
      Conserved Domains (1) summary
      pfam02204
      Location:510 → 625
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    6. XM_047434935.1 → XP_047290891.1  VPS9 domain-containing protein 1 isoform X8

    7. XM_047434930.1 → XP_047290886.1  VPS9 domain-containing protein 1 isoform X1

    8. XM_047434937.1 → XP_047290893.1  VPS9 domain-containing protein 1 isoform X10

      Related
      ENSP00000454244.1, ENST00000561976.5

    9. XM_047434933.1 → XP_047290889.1  VPS9 domain-containing protein 1 isoform X6

    10. XM_047434934.1 → XP_047290890.1  VPS9 domain-containing protein 1 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      95791896..95805664 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314449.1 → XP_054170424.1  VPS9 domain-containing protein 1 isoform X5

    2. XM_054314448.1 → XP_054170423.1  VPS9 domain-containing protein 1 isoform X4

    3. XM_054314446.1 → XP_054170421.1  VPS9 domain-containing protein 1 isoform X2

    4. XM_054314453.1 → XP_054170428.1  VPS9 domain-containing protein 1 isoform X9

    5. XM_054314447.1 → XP_054170422.1  VPS9 domain-containing protein 1 isoform X3

    6. XM_054314451.1 → XP_054170426.1  VPS9 domain-containing protein 1 isoform X8

    7. XM_054314445.1 → XP_054170420.1  VPS9 domain-containing protein 1 isoform X1

    8. XM_054314450.1 → XP_054170425.1  VPS9 domain-containing protein 1 isoform X6

    9. XM_054314452.1 → XP_054170427.1  VPS9 domain-containing protein 1 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2B5.2 GenPept UniProtKB/Swiss-Prot:Q9Y2B5

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