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    plod3 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 [ Danio rerio (zebrafish) ]

    Gene ID: 556077, updated on 9-Dec-2024

    Summary

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    Official Symbol
    plod3provided by ZNC
    Official Full Name
    procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-021031-4
    See related
    Ensembl:ENSDARG00000076317 AllianceGenome:ZFIN:ZDB-GENE-021031-4
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    cb479; cb816; diwanka; fb72h05; im:6912725; wu:fb72f10; wu:fb72h05
    Summary
    Predicted to enable procollagen glucosyltransferase activity and procollagen-lysine 5-dioxygenase activity. Acts upstream of or within motor neuron axon guidance and neural crest cell migration. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in several cellular components, including Golgi apparatus; endoplasmic reticulum; and extracellular space. Is expressed in several structures, including axis; eye; mesoderm; pectoral fin; and splanchnocranium. Orthologous to human PLOD3 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 3). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See plod3 in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (44843860..44879214, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (45131804..45167153, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 7.1 Neighboring gene ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 7.2 Neighboring gene asialoglycoprotein receptor 1a Neighboring gene formin-J

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Identification of Small Molecules for Prevention of Lens Epithelium-Derived Cataract Using Zebrafish. Taler K, et al. Cells, 2023 Oct 29. PMID 37947618, Free PMC Article
    2. Migration of zebrafish spinal motor nerves into the periphery requires multiple myotome-derived cues. Zeller J, et al. Dev Biol, 2002 Dec 15. PMID 12482713
    3. The myotomal diwanka (lh3) glycosyltransferase and type XVIII collagen are critical for motor growth cone migration. Schneider VA, et al. Neuron, 2006 Jun 1. PMID 16731508
    4. A novel role for Lh3 dependent ECM modifications during neural crest cell migration in zebrafish. Banerjee S, et al. PLoS One, 2013. PMID 23349938, Free PMC Article
    5. The lh3 Glycosyltransferase Directs Target-Selective Peripheral Nerve Regeneration. Isaacman-Beck J, et al. Neuron, 2015 Nov 18. PMID 26549330, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LH3 directs target-selective motor axon regeneration.
      Title: The lh3 Glycosyltransferase Directs Target-Selective Peripheral Nerve Regeneration.
    2. Together these data suggest that Lh3-Collagen18A1 dependent ECM modifications regulate the transition of trunk neural crest cells from a non-segmental sheet like migration mode to a segmental stream migration mode
      Title: A novel role for Lh3 dependent ECM modifications during neural crest cell migration in zebrafish.
    3. diwanka (lh3) acts through myotomal type XVIII collagen, a ligand for neural-receptor protein tyrosine phosphatases that guide motor axons
      Title: The myotomal diwanka (lh3) glycosyltransferase and type XVIII collagen are critical for motor growth cone migration.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC162023

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables procollagen glucosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables procollagen-lysine 5-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables procollagen-lysine 5-dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within lens development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within motor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neural crest cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
    Names
    diw
    lh3
    NP_001037808.2
    XP_005162484.2

    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_001044343.2 → NP_001037808.2  multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 precursor

      Status: VALIDATED

      Source sequence(s)
      BC133839, CU682622
      UniProtKB/TrEMBL
      A0A8M1N9F8, A3KNH4
      Related
      ENSDARP00000080199.5, ENSDART00000085764.7
      Conserved Domains (2) summary
      smart00702
      Location:565 → 728
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
      cl21455
      Location:61 → 148
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      44843860..44879214 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005162427.5 → XP_005162484.2  multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 isoform X1

      UniProtKB/TrEMBL
      A0A8M2B9A3
      Conserved Domains (2) summary
      smart00702
      Location:521 → 684
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
      cl21455
      Location:17 → 104
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395163.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      69337..99279 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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