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VPS13D vacuolar protein sorting 13 homolog D [ Homo sapiens (human) ]

Gene ID: 55187, updated on 12-Oct-2019

Summary

Official Symbol
VPS13Dprovided by HGNC
Official Full Name
vacuolar protein sorting 13 homolog Dprovided by HGNC
Primary source
HGNC:HGNC:23595
See related
Ensembl:ENSG00000048707 MIM:608877
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
SCAR4
Summary
This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in skin (RPKM 12.9), thyroid (RPKM 9.2) and 25 other tissues See more
Orthologs

Genomic context

See VPS13D in Genome Data Viewer
Location:
1p36.22-p36.21
Exon count:
70
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (12230030..12512047)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (12290101..12572099)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TNF receptor superfamily member 1B Neighboring gene uncharacterized LOC107984917 Neighboring gene microRNA 4632 Neighboring gene ribosomal protein L10 pseudogene 17 Neighboring gene NFE2L2 motif-containing MPRA enhancer 265 Neighboring gene small nucleolar RNA, H/ACA box 59A Neighboring gene Sharpr-MPRA regulatory region 4366 Neighboring gene long intergenic non-protein coding RNA 2766

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ23066

Gene Ontology Provided by GOA

Process Evidence Code Pubs
mitochondrion organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mitophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein retention in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
extrinsic component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 13D
Names
vacuolar protein sorting 13D

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.

Genomic

  1. NG_056877.1 RefSeqGene

    Range
    4992..287009
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1213

mRNA and Protein(s)

  1. NM_015378.4NP_056193.2  vacuolar protein sorting-associated protein 13D isoform 1

    See identical proteins and their annotated locations for NP_056193.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ608774, AL031276, BC051804, BX682532, HY121734
    Consensus CDS
    CCDS30588.1
    UniProtKB/Swiss-Prot
    Q5THJ4
    Related
    ENSP00000478104.1, ENST00000620676.6
    Conserved Domains (6) summary
    cd14306
    Location:26422677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:32763559
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam12624
    Location:3112
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:139356
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:39844129
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:614894
    VPS13_mid_rpt; Repeating coiled region of VPS13
  2. NM_018156.4NP_060626.2  vacuolar protein sorting-associated protein 13D isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1
    Source sequence(s)
    AJ608775, AL031276, BC051804, BX682532, HY121734
    Consensus CDS
    CCDS30589.1
    UniProtKB/Swiss-Prot
    Q5THJ4
    Related
    ENSP00000482233.1, ENST00000613099.4
    Conserved Domains (6) summary
    cd14306
    Location:26422677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:32513534
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam12624
    Location:3112
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:139356
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:39594104
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:614894
    VPS13_mid_rpt; Repeating coiled region of VPS13

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    12230030..12512047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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