Gene

pnkp

ID

ZDB-GENE-061013-433

Name

polynucleotide kinase 3'-phosphatase

Symbol

pnkp Nomenclature History

Previous Names

fe48d04
wu:fe48d04
zgc:153084

Type

protein_coding_gene

Location

Chr: 15 Mapping Details/Browsers

Description

Predicted to enable ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity and polynucleotide 3'-phosphatase activity. Predicted to be involved in DNA repair. Predicted to act upstream of or within DNA damage response. 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).

Genome Resources

Note

None

Comparative Information

Expression

All Expression Data

No data available

Cross-Species Comparison

High Throughput Data

GEO (1)

Expression Atlas

UO scRNA-seq (UCSC browser)

Single Cell Expression Atlas

Daniocell

Thisse Expression Data

No data available

Wild Type Expression Summary

Phenotype

All Phenotype Data: No data available
Cross-Species Comparison: Alliance

Phenotype Summary

Mutations

Mutants

Allele	Type	Localization	Consequence	Mutagen	Supplier
sa35823	Allele with one point mutation	Unknown	Splice Site	ENU	Zebrafish International Resource Center (ZIRC) (order this) European Zebrafish Resource Center (EZRC) (order this)

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Sequence Targeting Reagents

No data available

Human Disease

Associated With pnkp Human Ortholog

Disease Ontology Term	Multi-Species Data	OMIM Term	OMIM Phenotype ID
ataxia-oculomotor apraxia type 4	Alliance	Ataxia-oculomotor apraxia 4	616267
Charcot-Marie-Tooth disease type 2B2	Alliance	?Charcot-Marie-Tooth disease, type 2B2	605589
microcephaly, seizures, and developmental delay	Alliance	Microcephaly, seizures, and developmental delay	613402

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Associated With pnkp Via Experimental Models

No data available

Gene Ontology

Protein Domains

Domain, Family, and Site Summary

Type	InterPro ID	Name
Domain	IPR006549	HAD-superfamily hydrolase,subfamily IIIA
Domain	IPR006551	Polynucleotide 3'-phosphatase
Domain	IPR041388	PNK, FHA domain
Family	IPR006550	Bifunctional polynucleotide phosphatase/kinase PNKP
Family	IPR013954	Polynucleotide kinase 3 phosphatase

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Domain Details Per Protein

Protein	Additional Resources	Length
UniProtKB:A0A0R4IRS4	InterPro	588
UniProtKB:A0A8M6YSB6	InterPro	371
UniProtKB:Q08BP0	InterPro	586

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Transcripts

Genome Browsers

Genome Build: GRCz11Chromosome: 15

Type	Name	Annotation Method	Length (nt)	Analysis
mRNA	pnkp-201 (1) Ensembl	Ensembl	2,206 nt	Select Tool ZFIN BLAST
mRNA	pnkp-203 (1) Ensembl	Ensembl	3,351 nt	Select Tool ZFIN BLAST
mRNA	pnkp-204 (1) Ensembl	Ensembl	683 nt	Select Tool ZFIN BLAST
mRNA	pnkp-205 (1) Ensembl	Ensembl	3,680 nt	Select Tool ZFIN BLAST
mRNA	pnkp-206 (1) Ensembl	Ensembl	2,518 nt	Select Tool ZFIN BLAST

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Interactions and Pathways

No data available

Antibodies

No data available

Plasmids

No data available

Constructs

No data available

Marker Relationships

Relationship	Marker Type	Marker	Accession Numbers	Citations
Contained in	BAC	DKEY-243K1	CR925813	ZFIN Curated Data
Encodes	EST	fe48d04	AW058813
Encodes	cDNA	MGC:153084	BC124634	ZFIN Curated Data

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Sequences

Type	Accession #	Length (nt/aa)	Analysis
RNA	RefSeq:NM_001077578 (1)	2221 nt	Select Tool ZFIN BLAST NCBI BLAST Ensembl UCSC BLAT
Genomic	GenBank:CR925813 (1)	48715 nt	Select Tool MegaBLAST Ensembl
Polypeptide	UniProtKB:A0A0R4IRS4 (1)	588 aa	Select Tool ZFIN BLAST SIB BLAST Ensembl Protein Blast

Orthology

Comparative Orthology: Alliance
Gene Tree: Ensembl

Species	Symbol	Chromosome	Accession #	Evidence
Human	PNKP	19	Ensembl:ENSG00000039650 Gene:11284 HGNC:9154 OMIM:605610	Amino acid sequence comparison (1)
Mouse	Pnkp	7	Ensembl:ENSMUSG00000002963 Gene:59047 MGI:1891698	Amino acid sequence comparison (1)

Citations

Include unpublished citations

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

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