U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Vta1 vesicle (multivesicular body) trafficking 1 [ Mus musculus (house mouse) ]

    Gene ID: 66201, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Vta1provided by MGI
    Official Full Name
    vesicle (multivesicular body) trafficking 1provided by MGI
    Primary source
    MGI:MGI:1913451
    See related
    Ensembl:ENSMUSG00000019868 AllianceGenome:MGI:1913451
    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
    LIP5; SBP1; 1110001D18Rik; 1110059P08Rik
    Summary
    Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway. Located in cytoplasm. Is expressed in 1st branchial arch; cortical plate; fronto-nasal process; heart; and limb. Orthologous to human VTA1 (vesicle trafficking 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 23.2), whole brain E14.5 (RPKM 22.3) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Vta1 in Genome Data Viewer
    Location:
    10 A2; 10 5.5 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (14531077..14581233, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (14654760..14705542, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_25828 Neighboring gene predicted gene, 40603 Neighboring gene adhesion G protein-coupled receptor G6 Neighboring gene VISTA enhancer mm116 Neighboring gene STARR-seq mESC enhancer starr_25829 Neighboring gene STARR-seq mESC enhancer starr_25830 Neighboring gene STARR-seq mESC enhancer starr_25831 Neighboring gene ribosomal protein L23A pseudogene Neighboring gene STARR-seq mESC enhancer starr_25832 Neighboring gene STARR-seq mESC enhancer starr_25835 Neighboring gene STARR-seq mESC enhancer starr_25837 Neighboring gene predicted gene, 57851 Neighboring gene STARR-seq mESC enhancer starr_25839 Neighboring gene RIKEN cDNA 1700016L04 gene Neighboring gene STARR-positive B cell enhancer mm9_chr10:14425245-14425545 Neighboring gene gap junction protein, epsilon 1 Neighboring gene heat shock protein 8 pseudogene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. LIP5 interacts with aquaporin 2 and facilitates its lysosomal degradation. van Balkom BW, et al. J Am Soc Nephrol, 2009 May. PMID 19357255, Free PMC Article
    2. The lysosomal trafficking regulator interacting protein-5 localizes mainly in epithelial cells. Boone M, et al. J Mol Histol, 2010 Feb. PMID 20358264
    3. Mammalian class E Vps proteins, SBP1 and mVps2/CHMP2A, interact with and regulate the function of an AAA-ATPase SKD1/Vps4B. Fujita H, et al. J Cell Sci, 2004 Jun 15. PMID 15173323
    4. ESCRT-dependent control of craniofacial morphogenesis with concomitant perturbation of NOTCH signaling. Hermosilla Aguayo V, et al. Dev Biol, 2023 Nov. PMID 37573008
    5. Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Pilot-Storck F, et al. Mol Cell Proteomics, 2010 Jul. PMID 20368287, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LIP5 protein expression in a mouse tissue panel and various rodent and human tissues were studied.[LIP5]
      Title: The lysosomal trafficking regulator interacting protein-5 localizes mainly in epithelial cells.
    Submit: New GeneRIF Correction

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Readthrough Gm57851

    Readthrough gene: Gm57851, Included gene: Gje1

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in late endosome to vacuole transport via multivesicular body sorting pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in late endosome to vacuole transport via multivesicular body sorting pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in multivesicular body sorting pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in multivesicular body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    vacuolar protein sorting-associated protein VTA1 homolog
    Names
    SKD1-binding protein 1
    Vps20-associated 1 homolog
    lysosomal trafficking regulator interacting protein-5

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001429337.1 → NP_001416266.1  vacuolar protein sorting-associated protein VTA1 homolog isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC159336

    2. NM_001429338.1 → NP_001416267.1  vacuolar protein sorting-associated protein VTA1 homolog isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC159336

    3. NM_001429339.1 → NP_001416268.1  vacuolar protein sorting-associated protein VTA1 homolog isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC159336

    4. NM_001429340.1 → NP_001416269.1  vacuolar protein sorting-associated protein VTA1 homolog isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC159336

    5. NM_001429341.1 → NP_001416270.1  vacuolar protein sorting-associated protein VTA1 homolog isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC159336

    6. NM_025418.4 → NP_079694.2  vacuolar protein sorting-associated protein VTA1 homolog isoform 1

      See identical proteins and their annotated locations for NP_079694.2

      Status: VALIDATED

      Source sequence(s)
      AC159336
      Consensus CDS
      CCDS23705.1
      UniProtKB/Swiss-Prot
      Q9CR26
      UniProtKB/TrEMBL
      Q3V4B3
      Related
      ENSMUSP00000119829.2, ENSMUST00000154132.8
      Conserved Domains (2) summary
      pfam04652
      Location:22 → 152
      Vta1; Vta1 like
      cl28408
      Location:183 → 264
      UBQ; Ubiquitin homologues

    RNA

    1. NR_190724.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC159336

    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_000076.7 Reference GRCm39 C57BL/6J

      Range
      14531077..14581233 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9CR26.1 GenPept UniProtKB/Swiss-Prot:Q9CR26

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous