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Vps50 VPS50 EARP/GARPII complex subunit [ Mus musculus (house mouse) ]

Gene ID: 73288, updated on 2-Nov-2024

Summary

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Official Symbol
Vps50provided by MGI
Official Full Name
VPS50 EARP/GARPII complex subunitprovided by MGI
Primary source
MGI:MGI:1920538
See related
Ensembl:ENSMUSG00000001376 AllianceGenome:MGI:1920538
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
BLM; Ccdc132; mKIAA1861; 1700034M03Rik; 8430415E05Rik
Summary
Predicted to enable SNARE binding activity. Acts upstream of or within endocytic recycling. Predicted to be located in membrane; perinuclear region of cytoplasm; and recycling endosome. Predicted to be part of EARP complex. Orthologous to human VPS50 (VPS50 subunit of EARP/GARPII complex). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in CNS E18 (RPKM 4.5), CNS E14 (RPKM 4.3) and 23 other tissues See more
Orthologs
human all
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Genomic context

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See Vps50 in Genome Data Viewer
Location:
6 A1; 6 1.81 cM
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (3498393..3603531)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (3498393..3603531)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_14988 Neighboring gene STARR-seq mESC enhancer starr_14989 Neighboring gene STARR-positive B cell enhancer mm9_chr6:3349393-3349694 Neighboring gene STARR-seq mESC enhancer starr_14990 Neighboring gene sterile alpha motif domain containing 9-like Neighboring gene STARR-seq mESC enhancer starr_14991 Neighboring gene STARR-positive B cell enhancer ABC_E6412 Neighboring gene HEPACAM family member 2 Neighboring gene STARR-positive B cell enhancer ABC_E9270 Neighboring gene STARR-seq mESC enhancer starr_14997 Neighboring gene predicted gene, 52885 Neighboring gene STARR-seq mESC enhancer starr_14998 Neighboring gene STARR-seq mESC enhancer starr_14999 Neighboring gene STARR-seq mESC enhancer starr_15001 Neighboring gene STARR-seq mESC enhancer starr_15002 Neighboring gene predicted gene, 53306 Neighboring gene calcitonin receptor Neighboring gene microRNA 653

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Deletion of VPS50 protein in mouse brain impairs synaptic function and behavior. Ahumada-Marchant C, et al. BMC Biol, 2024 Jun 26. PMID 38926759, Free PMC Article
  2. The Conserved VPS-50 Protein Functions in Dense-Core Vesicle Maturation and Acidification and Controls Animal Behavior. Paquin N, et al. Curr Biol, 2016 Apr 4. PMID 26948874, Free PMC Article
  3. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, et al. Nat Cell Biol, 2015 May. PMID 25799061, Free PMC Article
  4. Lack of periostin leads to suppression of Notch1 signaling and calcific aortic valve disease. Tkatchenko TV, et al. Physiol Genomics, 2009 Nov 6. PMID 19723774, Free PMC Article
  5. WDFY4 is required for cross-presentation in response to viral and tumor antigens. Theisen DJ, et al. Science, 2018 Nov 9. PMID 30409884, Free PMC Article

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

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 MGI

Function Evidence Code Pubs
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SNARE binding ISO
Inferred from Sequence Orthology
more info
 PubMed 
Process Evidence Code Pubs
involved_in endocytic recycling IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within endocytic recycling IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within endocytic recycling ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in endocytic recycling ISO
Inferred from Sequence Orthology
more info
  
involved_in endocytic recycling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in retrograde transport, endosome to Golgi ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of EARP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of EARP complex ISO
Inferred from Sequence Orthology
more info
  
part_of EARP complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane ISO
Inferred from Sequence Orthology
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in recycling endosome ISO
Inferred from Sequence Orthology
more info
 PubMed 
located_in recycling endosome ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
syndetin
Names
EARP/GARPII complex subunit VPS50
bcl2-like protein blm
coiled-coil domain containing 132
coiled-coil domain-containing protein 132

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_001167750.1 → NP_001161222.1  syndetin isoform 2

    See identical proteins and their annotated locations for NP_001161222.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC066688, AI551221, BC043092, BY100563
    Consensus CDS
    CCDS51713.1
    UniProtKB/Swiss-Prot
    Q8CI71
    Related
    ENSMUSP00000125872.2, ENSMUST00000164052.5
    Conserved Domains (2) summary
    pfam10474
    Location:726 → 929
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:54 → 345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)

  2. NM_001167751.1 → NP_001161223.1  syndetin isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC066688, AK042031, BC043092, BY100563
    Consensus CDS
    CCDS51714.1
    UniProtKB/Swiss-Prot
    Q8CI71
    Related
    ENSMUSP00000128323.2, ENSMUST00000170873.10
    Conserved Domains (2) summary
    pfam10474
    Location:726 → 925
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:54 → 345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)

  3. NM_024260.5 → NP_077222.4  syndetin isoform 1

    See identical proteins and their annotated locations for NP_077222.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI551221, AK129458, BY100563
    Consensus CDS
    CCDS39415.1
    UniProtKB/Swiss-Prot
    Q6ZPG9, Q7TSR5, Q80XR1, Q8C6D0, Q8C9I6, Q8CI71, Q99LN1
    Related
    ENSMUSP00000001412.9, ENSMUST00000001412.17
    Conserved Domains (2) summary
    pfam10474
    Location:726 → 957
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:54 → 345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    3498393..3603531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036152347.1 → XP_036008240.1  syndetin isoform X1

    Conserved Domains (2) summary
    pfam10474
    Location:454 → 688
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    cl19297
    Location:1 → 76
    Dor1; Dor1-like family
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8CI71.2 GenPept UniProtKB/Swiss-Prot:Q8CI71

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