plod1a procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: plod1aprovided by ZNC
Official Full Name: procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-3165
See related: Ensembl:ENSDARG00000059746 AllianceGenome:ZFIN:ZDB-GENE-030131-3165
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: plod; plod1; fc95g08; fi18a05; wu:fc29c10; wu:fc95g08; wu:fi18a05; zgc:152876; ik:tdsubs_rzpd609-29b19
Summary: Predicted to enable procollagen-lysine 5-dioxygenase activity. Acts upstream of or within fin morphogenesis. Predicted to be located in rough 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 cranium; notochord; otic vesicle; pectoral fin; and shield. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome kyphoscoliotic type 1. Orthologous to human PLOD1 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 8

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	8	NC_007119.7 (47850075..47895817)
105	previous assembly	GRCz10 (GCF_000002035.5)	8	NC_007119.6 (47861083..47906825)

Chromosome 8 - NC_007119.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Zebrafish lysyl hydroxylases 1 and 2 were cloned and their patterns of expression during the first two days of embryonic development examined.
Title: Genomic structure and embryonic expression of zebrafish lysyl hydroxylase 1 and lysyl hydroxylase 2.

Submit: New GeneRIF Correction

General gene information

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Markers

fb94b12.x1 (e-PCR)
- UniSTS:203551

fj15f04.x1 (e-PCR)
- UniSTS:188455

AI629201 (e-PCR)
- UniSTS:206125

fi18a05.x1 (e-PCR)
- UniSTS:196947

fc29c10.y1 (e-PCR)
- UniSTS:193445

AI722604 (e-PCR)
- UniSTS:205999

fc95g08.x1 (e-PCR)
- UniSTS:204024

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-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 fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin morphogenesis	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
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in rough endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

Names: lh1; lysine hydroxylase; procollagen lysine 2-oxoglutarate 5-dioxygenase 1; procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1a

NP_001071210.2

EC 1.14.11.4

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)

NM_001077742.2 → NP_001071210.2 procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor

Status: VALIDATED

Source sequence(s)

BX548250

UniProtKB/TrEMBL

A0A8N1TQB9, A8WIN7

Related

ENSDARP00000077830.5, ENSDART00000083395.7

Conserved Domains (1) summary

smart00702
Location:565 → 728

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues