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

Gene ID: 556077, updated on 2-Nov-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, Nov 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 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 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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