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

Gene ID: 9605, updated on 27-Nov-2024

Summary

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, Nov 2024]
Expression
Ubiquitous expression in brain (RPKM 5.5), appendix (RPKM 5.3) and 25 other tissues See more
Orthologs
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Genomic context

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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_004913.3NP_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:509624
    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_047434932.1XP_047290888.1  VPS9 domain-containing protein 1 isoform X5

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

    UniProtKB/TrEMBL
    H3BM58
    Conserved Domains (1) summary
    pfam02204
    Location:509624
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
  3. XM_047434931.1XP_047290887.1  VPS9 domain-containing protein 1 isoform X2

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

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

    UniProtKB/TrEMBL
    H3BM58
    Conserved Domains (1) summary
    pfam02204
    Location:510625
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
  6. XM_047434935.1XP_047290891.1  VPS9 domain-containing protein 1 isoform X8

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

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

    Related
    ENSP00000454244.1, ENST00000561976.5
  9. XM_047434933.1XP_047290889.1  VPS9 domain-containing protein 1 isoform X6

  10. XM_047434934.1XP_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_054314449.1XP_054170424.1  VPS9 domain-containing protein 1 isoform X5

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

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

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

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

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

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

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

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