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VPS50 VPS50 subunit of EARP/GARPII complex [ Homo sapiens (human) ]

Gene ID: 55610, updated on 17-Jun-2019

Summary

Official Symbol
VPS50provided by HGNC
Official Full Name
VPS50 subunit of EARP/GARPII complexprovided by HGNC
Primary source
HGNC:HGNC:25956
See related
Ensembl:ENSG00000004766 MIM:616465
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
VPS54L; CCDC132
Expression
Ubiquitous expression in brain (RPKM 5.6), thyroid (RPKM 4.2) and 25 other tissues See more
Orthologs

Genomic context

See VPS50 in Genome Data Viewer
Location:
7q21.2-q21.3
Exon count:
31
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (93232340..93361123)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (92861653..92990435)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 9 like Neighboring gene HEPACAM family member 2 Neighboring gene calcitonin receptor Neighboring gene microRNA 653 Neighboring gene microRNA 489

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 FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20097, FLJ23581, KIAA1861, MGC176659

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SNARE binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
endocytic recycling IDA
Inferred from Direct Assay
more info
PubMed 
endocytic recycling IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
NOT retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
EARP complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
membrane HDA PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
syndetin
Names
EARP/GARPII complex subunit VPS50
VPS50, EARP/GARPII complex subunit
coiled-coil domain containing 132
coiled-coil domain-containing protein 132

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.

mRNA and Protein(s)

  1. NM_001257998.1NP_001244927.1  syndetin isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (c) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC002379, AC002453, AK126478, BC017888, BE671517
    Consensus CDS
    CCDS59065.1
    UniProtKB/Swiss-Prot
    Q96JG6
    Related
    ENSP00000443104.1, ENST00000544910.5
    Conserved Domains (2) summary
    pfam10474
    Location:696927
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:24315
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)
  2. NM_017667.4NP_060137.2  syndetin isoform a

    See identical proteins and their annotated locations for NP_060137.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AB100163, AC002379, BC017888, BC035984, BE671517
    Consensus CDS
    CCDS43617.1
    UniProtKB/Swiss-Prot
    Q96JG6
    Related
    ENSP00000307666.5, ENST00000305866.10
    Conserved Domains (2) summary
    pfam10474
    Location:726957
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:54345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)
  3. NM_024553.2NP_078829.1  syndetin isoform b

    See identical proteins and their annotated locations for NP_078829.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    BC017888
    Consensus CDS
    CCDS5630.1
    UniProtKB/Swiss-Prot
    Q96JG6
    Related
    ENSP00000251739.5, ENST00000251739.9
    Conserved Domains (1) summary
    cl19297
    Location:54314
    Dor1; Dor1-like family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    93232340..93361123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516395.2XP_011514697.1  syndetin isoform X1

    Conserved Domains (2) summary
    pfam10474
    Location:537768
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    cl19297
    Location:1156
    Dor1; Dor1-like family
  2. XM_011516396.3XP_011514698.1  syndetin isoform X3

    Conserved Domains (2) summary
    pfam10475
    Location:54345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)
    pfam13900
    Location:633671
    GVQW; Putative domain of unknown function
  3. XM_017012412.2XP_016867901.1  syndetin isoform X4

  4. XM_024446826.1XP_024302594.1  syndetin isoform X2

    Conserved Domains (2) summary
    pfam10474
    Location:457688
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    cl19297
    Location:176
    Dor1; Dor1-like family

RNA

  1. XR_001744835.2 RNA Sequence

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