prkn parkin RBR E3 ubiquitin protein ligase [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: prknprovided by ZNC
Official Full Name: parkin RBR E3 ubiquitin protein ligaseprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050417-109
See related: Ensembl:ENSDARG00000021555 AllianceGenome:ZFIN:ZDB-GENE-050417-109
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: park2; zgc:112390; si:ch211-123f21.1
Summary: Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Acts upstream of or within several processes, including mitochondrial electron transport, NADH to ubiquinone; protein autoubiquitination; and response to oxidative stress. Located in cytoplasm. Is expressed in several structures, including digestive system; gill; heart; nervous system; and somite. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinson's disease 2; and ovarian cancer. Orthologous to human PRKN (parkin RBR E3 ubiquitin protein ligase). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information: Annotation category: partial on reference assembly
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 13

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (3354895..3474366, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (3221545..3341016, complement)

Chromosome 13 - NC_007124.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Melatonin, added together with MPTP or added once MPTP was removed, prevented and recovered, respectively, the parkinsonian phenotype once it was established, restoring gene expression and normal function of the parkin/PINK1/DJ-1/MUL1 loop and also the normal motor activity of the embryos.
Title: Melatonin rescues zebrafish embryos from the parkinsonian phenotype restoring the parkin/PINK1/DJ-1/MUL1 network.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin conjugating enzyme binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-protein transferase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within autophagy	IEA Inferred from Electronic Annotation more info
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in autophagy of mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mitochondrial electron transport, NADH to ubiquinone	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein phosphorylation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cellular response to oxidative stress	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitochondrion organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to oxidative stress	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to temperature stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
part_of ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase parkin

Names: Parkinson disease (autosomal recessive, juvenile) 2, parkin

NP_001017635.1

EC 2.3.2.31

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_001017635.1 → NP_001017635.1 E3 ubiquitin-protein ligase parkin

See identical proteins and their annotated locations for NP_001017635.1

Status: PROVISIONAL

Source sequence(s)

BC093281

UniProtKB/TrEMBL

Q561U2

Related

ENSDARP00000141580.2, ENSDART00000157437.3

Conserved Domains (4) summary

cd01798
Location:3 → 70

parkin_N; amino-terminal ubiquitin-like of parkin protein

smart00213
Location:1 → 71

UBQ; Ubiquitin homologues

smart00647
Location:305 → 368

IBR; In Between Ring fingers

pfam01485
Location:411 → 447

IBR; IBR domain, a half RING-finger domain
NM_001423707.1 → NP_001410636.1 E3 ubiquitin-protein ligase parkin

Status: VALIDATED

Source sequence(s)

CABZ01010736, CABZ01010738, CABZ01010740, CR318584, CU570981