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    Plekhm1 pleckstrin homology domain containing, family M (with RUN domain) member 1 [ Mus musculus (house mouse) ]

    Gene ID: 353047, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Plekhm1provided by MGI
    Official Full Name
    pleckstrin homology domain containing, family M (with RUN domain) member 1provided by MGI
    Primary source
    MGI:MGI:2443207
    See related
    Ensembl:ENSMUSG00000034247 AllianceGenome:MGI:2443207
    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
    B2; AP162; D330036J23Rik
    Summary
    Predicted to enable metal ion binding activity. Involved in lysosome localization; positive regulation of bone resorption; and positive regulation of ruffle assembly. Predicted to be located in autolysosome and nucleolus. Used to study autosomal recessive osteopetrosis 6. Human ortholog(s) of this gene implicated in autosomal recessive osteopetrosis 6 and osteopetrosis. Orthologous to human PLEKHM1 (pleckstrin homology and RUN domain containing M1). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 17.4), mammary gland adult (RPKM 16.6) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Plekhm1 in Genome Data Viewer
    Location:
    11 E1; 11 67.09 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (103255101..103303531, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (103364275..103412705, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase kinase 14 Neighboring gene predicted gene, 34823 Neighboring gene STARR-positive B cell enhancer ABC_E10718 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:103128947-103129269 Neighboring gene STARR-seq mESC enhancer starr_30841 Neighboring gene STARR-seq mESC enhancer starr_30842 Neighboring gene STARR-positive B cell enhancer ABC_E3026 Neighboring gene Rho GTPase activating protein 27 Neighboring gene Rho GTPase activating protein 27, opposite strand 3 Neighboring gene STARR-positive B cell enhancer ABC_E8459 Neighboring gene STARR-seq mESC enhancer starr_30848 Neighboring gene STARR-positive B cell enhancer ABC_E9376 Neighboring gene STARR-positive B cell enhancer ABC_E3027 Neighboring gene predicted gene, 39397 Neighboring gene STARR-seq mESC enhancer starr_30849 Neighboring gene STARR-seq mESC enhancer starr_30850 Neighboring gene leucine rich repeat containing 37A Neighboring gene STARR-seq mESC enhancer starr_30851

    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. PLEKHM1: Adapting to life at the lysosome. McEwan DG, et al. Autophagy, 2015 Apr 3. PMID 25905573, Free PMC Article
    2. TRAFD1 (FLN29) Interacts with Plekhm1 and Regulates Osteoclast Acidification and Resorption. Witwicka H, et al. PLoS One, 2015. PMID 25992615, Free PMC Article
    3. PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins. McEwan DG, et al. Mol Cell, 2015 Jan 8. PMID 25498145
    4. LIS1 regulates osteoclast formation and function through its interactions with dynein/dynactin and Plekhm1. Ye S, et al. PLoS One, 2011. PMID 22073305, Free PMC Article
    5. PLEKHM1/DEF8/RAB7 complex regulates lysosome positioning and bone homeostasis. Fujiwara T, et al. JCI Insight, 2016 Oct 20. PMID 27777970, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRAFD1, in association with Plekhm1/Rab7-positive late endosomes-early lysosomes, has a previously unknown role in vesicle trafficking, acidification, and resorption in osteoclasts
      Title: TRAFD1 (FLN29) Interacts with Plekhm1 and Regulates Osteoclast Acidification and Resorption.
    2. identified PLEKHM1 as an endolysosomal adaptor platform that acts as a central hub to integrate endocytic and autophagic pathways at the lysosome
      Title: PLEKHM1: Adapting to life at the lysosome.
    3. results indicate that LIS1 is a previously unrecognized regulator of osteoclast formation, microtubule organization, and lysosomal secretion by virtue of its ability to modulate dynein function and Plekhm1
      Title: LIS1 regulates osteoclast formation and function through its interactions with dynein/dynactin and Plekhm1.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (5)  1 citation

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagosome-lysosome fusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagosome-lysosome fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in late endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in late endosome to lysosome transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lysosome localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosome localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of bone resorption IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of ruffle assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in autolysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in autolysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in autolysosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    pleckstrin homology domain-containing family M member 1
    Names
    PH domain-containing family M member 1

    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_183034.2 → NP_898855.1  pleckstrin homology domain-containing family M member 1

      See identical proteins and their annotated locations for NP_898855.1

      Status: VALIDATED

      Source sequence(s)
      AK048562, AL772325, BC053079, BP767414, BY203268
      Consensus CDS
      CCDS25518.1
      UniProtKB/Swiss-Prot
      Q3U3L2, Q7TSI1, Q8CHU5
      Related
      ENSMUSP00000047327.9, ENSMUST00000041272.10
      Conserved Domains (4) summary
      smart00233
      Location:703 → 795
      PH; Pleckstrin homology domain
      cd13321
      Location:529 → 646
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:48 → 181
      RUN; RUN domain
      pfam13901
      Location:864 → 1066
      zf-RING_9; Putative zinc-RING and/or ribbon

    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_000077.7 Reference GRCm39 C57BL/6J

      Range
      103255101..103303531 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7TSI1.1 GenPept UniProtKB/Swiss-Prot:Q7TSI1

    Gene LinkOut

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

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