Pnkp polynucleotide kinase 3'-phosphatase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pnkpprovided by RGD
Official Full Name: polynucleotide kinase 3'-phosphataseprovided by RGD
Primary source: RGD:1303331
See related: Ensembl:ENSRNOG00000020318 AllianceGenome:RGD:1303331
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including polydeoxyribonucleotide 5'-hydroxyl-kinase activity; polynucleotide 3'-phosphatase activity; and ubiquitin ligase-substrate adaptor activity. Predicted to be involved in several processes, including DNA repair; negative regulation of protein ADP-ribosylation; and positive regulation of DNA metabolic process. Located in mitochondrion. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 2B2 and microcephaly, seizures, and developmental delay. Orthologous to human PNKP (polynucleotide kinase 3'-phosphatase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 95.5), Thymus (RPKM 78.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q22

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (104476801..104483409)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (95341465..95346921)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (100853475..100859202)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables polynucleotide 3'-phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables polynucleotide 3'-phosphatase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-like ligase-substrate adaptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA ligation involved in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of telomere capping	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of telomere maintenance via telomerase	ISO Inferred from Sequence Orthology more info
involved_in protein K63-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in response to oxidative stress	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SCF ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
is_active_in site of double-strand break	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: bifunctional polynucleotide phosphatase/kinase

NP_001004259.1

EC 2.7.1.78

EC 3.1.3.32

XP_006229120.1

EC 2.7.1.78

EC 3.1.3.32

XP_017444627.1

EC 2.7.1.78

EC 3.1.3.32

XP_038967937.1

EC 2.7.1.78

EC 3.1.3.32

XP_063117997.1

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_001004259.1 → NP_001004259.1 bifunctional polynucleotide phosphatase/kinase

See identical proteins and their annotated locations for NP_001004259.1

Status: PROVISIONAL

Source sequence(s)

BC079307

UniProtKB/TrEMBL

A0A0G2JUH4, Q6AXV0

Related

ENSRNOP00000069099.2, ENSRNOT00000083551.2

Conserved Domains (1) summary

TIGR01663
Location:3 → 522

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

104476801..104483409

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063261927.1 → XP_063117997.1 bifunctional polynucleotide phosphatase/kinase isoform X1
XM_039112009.2 → XP_038967937.1 bifunctional polynucleotide phosphatase/kinase isoform X3

UniProtKB/TrEMBL

A0A0G2JUH4

Conserved Domains (1) summary

TIGR01663
Location:3 → 472

PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase
XM_006229058.5 → XP_006229120.1 bifunctional polynucleotide phosphatase/kinase isoform X2

UniProtKB/TrEMBL

A0A8I6AJP5, F7F4C1

Related

ENSRNOP00000039388.3

Conserved Domains (2) summary

TIGR01663
Location:3 → 476

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

cl17190
Location:320 → 396

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 ...
XM_017589138.2 → XP_017444627.1 bifunctional polynucleotide phosphatase/kinase isoform X4

UniProtKB/TrEMBL

A6JAT7

Conserved Domains (3) summary

TIGR01664
Location:1 → 110

DNA-3'-Pase; DNA 3'-phosphatase

pfam13671
Location:148 → 270

AAA_33; AAA domain

cl17190
Location:148 → 224

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 ...