pnkp polynucleotide kinase 3'-phosphatase [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pnkpprovided by ZNC
Official Full Name: polynucleotide kinase 3'-phosphataseprovided by ZNC
Primary source: ZFIN:ZDB-GENE-061013-433
See related: Ensembl:ENSDARG00000100455 AllianceGenome:ZFIN:ZDB-GENE-061013-433
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: fe48d04; wu:fe48d04; zgc:153084
Summary: Predicted to enable ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity; double-stranded DNA binding activity; and polynucleotide 3'-phosphatase activity. Predicted to be involved in DNA repair. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 2B2; ataxia-oculomotor apraxia type 4; and microcephaly, seizures, and developmental delay. Orthologous to human PNKP (polynucleotide kinase 3'-phosphatase). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 15

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	15	NC_007126.7 (14178721..14193928, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	15	NC_007126.6 (14242764..14257997, complement)

Chromosome 15 - NC_007126.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables polynucleotide 3'-phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables polynucleotide 3'-phosphatase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: bifunctional polynucleotide phosphatase/kinase

NP_001071046.1

EC 2.7.1.78

EC 3.1.3.32

XP_005173439.1

EC 2.7.1.78

EC 3.1.3.32

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_001077578.2 → NP_001071046.1 bifunctional polynucleotide phosphatase/kinase

See identical proteins and their annotated locations for NP_001071046.1

Status: PROVISIONAL

Source sequence(s)

BC124634

UniProtKB/TrEMBL

Q08BP0

Related

ENSDARP00000130085.1, ENSDART00000162707.2

Conserved Domains (4) summary

cd01427
Location:232 → 351

HAD_like; Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, ...

TIGR01663
Location:3 → 586

PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

cd00060
Location:3 → 95

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cl17190
Location:429 → 532

NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

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

NC_007126.7 Reference GRCz11 Primary Assembly

Range

14178721..14193928 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005173382.5 → XP_005173439.1 bifunctional polynucleotide phosphatase/kinase isoform X1

UniProtKB/TrEMBL

A0A0R4IRS4, A0A8M2BKP4

Related

ENSDARP00000139368.1, ENSDART00000165520.2

Conserved Domains (4) summary

cd01427
Location:234 → 353

HAD_like; Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, ...

TIGR01663
Location:1 → 588

PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

cd00060
Location:5 → 97

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cl17190
Location:431 → 534

NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...