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    PLEKHM3 pleckstrin homology domain containing M3 [ Homo sapiens (human) ]

    Gene ID: 389072, updated on 4-Jan-2025

    Summary

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    Official Symbol
    PLEKHM3provided by HGNC
    Official Full Name
    pleckstrin homology domain containing M3provided by HGNC
    Primary source
    HGNC:HGNC:34006
    See related
    Ensembl:ENSG00000178385 MIM:619186; AllianceGenome:HGNC:34006
    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
    DAPR; PLEKHM1L
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in myoblast differentiation. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Ubiquitous expression in brain (RPKM 3.2), thyroid (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLEKHM3 in Genome Data Viewer
    Location:
    2q33.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (207821288..208025527, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (208295515..208499792, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (208686012..208890251, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene cyclin Y like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208631909-208632465 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208632466-208633023 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208635695-208636515 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:208636987-208637462 Neighboring gene microRNA 4775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208647704-208648204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208660472-208661457 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208661458-208662442 Neighboring gene frizzled class receptor 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208666419-208666920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208666921-208667420 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208675729-208676550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17048 Neighboring gene HNF1 motif-containing MPRA enhancer 152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208713897-208714396 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:208772908-208774107 Neighboring gene Sharpr-MPRA regulatory region 2767 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:208835249-208835782 Neighboring gene RNA, U6 small nuclear 360, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17049 Neighboring gene ribosomal protein L9 pseudogene 14 Neighboring gene RNA, 5S ribosomal pseudogene 116

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. CircPLEKHM3 acts as a tumor suppressor through regulation of the miR-9/BRCA1/DNAJB6/KLF4/AKT1 axis in ovarian cancer. Zhang L, et al. Mol Cancer, 2019 Oct 17. PMID 31623606, Free PMC Article
    2. Identification and characterization of a novel gene, dapr, involved in skeletal muscle differentiation and protein kinase B signaling. Virtanen C, et al. J Biol Chem, 2009 Jan 16. PMID 19028694
    3. C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy. Yan BR, et al. Autophagy, 2022 Apr. PMID 34432599, Free PMC Article
    4. A central chaperone-like role for 14-3-3 proteins in human cells. Segal D, et al. Mol Cell, 2023 Mar 16. PMID 36931259
    5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircPLEKHM3 is down-regulated in ovarian cancer. Patients with a lower circPLEKHM3 expression have a worse prognosis. CircPLEKHM3 was found to act as a tumor suppressor that inhibits cell proliferation.
      Title: CircPLEKHM3 acts as a tumor suppressor through regulation of the miR-9/BRCA1/DNAJB6/KLF4/AKT1 axis in ovarian cancer.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. DAPR is a novel gene that binds to PKB/AKT and is a critical component for the differentiation of skeletal muscle myoblast cells into myotubes.
      Title: Identification and characterization of a novel gene, dapr, involved in skeletal muscle differentiation and protein kinase B signaling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ41210, AC083900.1, DKFZp686O04200

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in myoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pleckstrin homology domain-containing family M member 3
    Names
    PH domain-containing family M member 3
    differentiation associated protein

    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_001080475.3 → NP_001073944.1  pleckstrin homology domain-containing family M member 3

      Status: VALIDATED

      Source sequence(s)
      AC083900, AC093698, AC096772
      Consensus CDS
      CCDS42808.1
      UniProtKB/Swiss-Prot
      B9EKV2, Q6ZWE6, Q8WW68
      UniProtKB/TrEMBL
      C9J119
      Related
      ENSP00000417003.2, ENST00000427836.8
      Conserved Domains (4) summary
      cd13327
      Location:364 → 451
      PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
      cd14674
      Location:214 → 303
      PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
      pfam00169
      Location:362 → 454
      PH; PH domain
      pfam13901
      Location:529 → 729
      zf-RING_9; Putative zinc-RING and/or ribbon

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      207821288..208025527 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004073.2 → XP_016859562.1  pleckstrin homology domain-containing family M member 3 isoform X6

    2. XM_005246545.4 → XP_005246602.1  pleckstrin homology domain-containing family M member 3 isoform X4

      UniProtKB/TrEMBL
      C9J119
      Conserved Domains (4) summary
      cd13327
      Location:364 → 451
      PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
      cd14674
      Location:214 → 303
      PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
      pfam00169
      Location:362 → 454
      PH; PH domain
      pfam13901
      Location:529 → 651
      zf-RING_9; Putative zinc-RING and/or ribbon

    3. XM_011511160.3 → XP_011509462.1  pleckstrin homology domain-containing family M member 3 isoform X1

      UniProtKB/Swiss-Prot
      B9EKV2, Q6ZWE6, Q8WW68
      UniProtKB/TrEMBL
      C9J119
      Conserved Domains (4) summary
      cd13327
      Location:364 → 451
      PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
      cd14674
      Location:214 → 303
      PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
      pfam00169
      Location:362 → 454
      PH; PH domain
      pfam13901
      Location:529 → 729
      zf-RING_9; Putative zinc-RING and/or ribbon

    4. XM_017004072.3 → XP_016859561.1  pleckstrin homology domain-containing family M member 3 isoform X5

      UniProtKB/TrEMBL
      H7C0J9
      Related
      ENSP00000395354.1, ENST00000447645.5

    5. XM_006712521.5 → XP_006712584.1  pleckstrin homology domain-containing family M member 3 isoform X3

      UniProtKB/TrEMBL
      C9J119
      Conserved Domains (4) summary
      cd13327
      Location:364 → 451
      PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
      cd14674
      Location:214 → 303
      PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
      pfam00169
      Location:362 → 454
      PH; PH domain
      pfam13901
      Location:529 → 650
      zf-RING_9; Putative zinc-RING and/or ribbon

    6. XM_047444266.1 → XP_047300222.1  pleckstrin homology domain-containing family M member 3 isoform X3

      UniProtKB/TrEMBL
      C9J119

    7. XM_011511163.3 → XP_011509465.1  pleckstrin homology domain-containing family M member 3 isoform X2

      UniProtKB/TrEMBL
      C9J119
      Related
      ENSP00000400150.1, ENST00000457206.1
      Conserved Domains (4) summary
      cd13327
      Location:364 → 451
      PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
      cd14674
      Location:214 → 303
      PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
      pfam00169
      Location:362 → 454
      PH; PH domain
      pfam13901
      Location:529 → 652
      zf-RING_9; Putative zinc-RING and/or ribbon

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      208295515..208499792 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341972.1 → XP_054197947.1  pleckstrin homology domain-containing family M member 3 isoform X6

    2. XM_054341970.1 → XP_054197945.1  pleckstrin homology domain-containing family M member 3 isoform X4

      UniProtKB/TrEMBL
      C9J119

    3. XM_054341966.1 → XP_054197941.1  pleckstrin homology domain-containing family M member 3 isoform X1

      UniProtKB/Swiss-Prot
      B9EKV2, Q6ZWE6, Q8WW68
      UniProtKB/TrEMBL
      C9J119

    4. XM_054341971.1 → XP_054197946.1  pleckstrin homology domain-containing family M member 3 isoform X5

      UniProtKB/TrEMBL
      H7C0J9

    5. XM_054341968.1 → XP_054197943.1  pleckstrin homology domain-containing family M member 3 isoform X3

      UniProtKB/TrEMBL
      C9J119

    6. XM_054341969.1 → XP_054197944.1  pleckstrin homology domain-containing family M member 3 isoform X3

      UniProtKB/TrEMBL
      C9J119

    7. XM_054341967.1 → XP_054197942.1  pleckstrin homology domain-containing family M member 3 isoform X2

      UniProtKB/TrEMBL
      C9J119
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZWE6.2 GenPept UniProtKB/Swiss-Prot:Q6ZWE6

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