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

    Gene ID: 73288, updated on 27-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
    • 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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