PNKP
polynucleotide kinase 3'-phosphatase | PNK

This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]

Member of: DE-6
Biological processes 42 terms
ATP binding (GO:0005524)ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)ATP-dependent polynucleotide 5'-hydroxyl-kinase activity (GO:0051734)DNA damage response (GO:0006974)DNA repair (GO:0006281)DNA repair (GO:0006281)DNA-templated DNA replication (GO:0006261)base-excision repair (GO:0006284)base-excision repair, gap-filling (GO:0006287)chromosome (GO:0005694)damaged DNA binding (GO:0003684)double-strand break repair via nonhomologous end joining (GO:0006303)double-strand break repair via nonhomologous end joining (GO:0006303)double-stranded DNA binding (GO:0003690)endonuclease activity (GO:0004519)membrane (GO:0016020)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleotide-excision repair (GO:0006289)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)polynucleotide 3'-phosphatase activity (GO:0046403)polynucleotide 3'-phosphatase activity (GO:0046403)polynucleotide 3'-phosphatase activity (GO:0046403)polynucleotide 3'-phosphatase activity (GO:0046403)positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)positive regulation of telomere maintenance (GO:0032206)protein binding (GO:0005515)purine nucleotide binding (GO:0017076)regulation of DNA repair (GO:0006282)response to oxidative stress (GO:0006979)response to radiation (GO:0009314)response to radiation (GO:0009314)single strand break repair (GO:0000012)site of DNA damage (GO:0090734)site of double-strand break (GO:0035861)site of double-strand break (GO:0035861)
Expression (TPM)
PNKP — as a Regulated Gene

TFs regulating PNKP 0 TFs

Transcription factors with Perturb-seq knockdown data for PNKP. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = PNKP upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to PNKP

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PNKP, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr19:49,580,125–49,580,813 287.0 kb Distal (>10kb) Multiome 848
chr19:49,589,601–49,594,008 274.0 kb Distal (>10kb) Multiome 994
chr19:49,638,063–49,638,728 229.3 kb Distal (>10kb) Multiome 237
chr19:49,639,671–49,642,787 227.1 kb Distal (>10kb) Multiome 1067
chr19:49,664,165–49,665,096 203.0 kb Distal (>10kb) Multiome 679
chr19:49,665,345–49,666,430 201.6 kb Distal (>10kb) Multiome 721
chr19:49,672,105–49,672,787 195.2 kb Distal (>10kb) Multiome 625
chr19:49,676,058–49,678,754 190.6 kb Distal (>10kb) Multiome 1033
chr19:49,680,433–49,681,147 186.8 kb Distal (>10kb) Multiome 435
chr19:49,690,485–49,691,761 176.4 kb Distal (>10kb) Multiome 327
chr19:49,746,188–49,746,748 121.1 kb Distal (>10kb) Multiome 283
chr19:49,766,231–49,767,440 100.9 kb Distal (>10kb) Multiome 718
chr19:49,802,146–49,802,787 65.1 kb Distal (>10kb) Multiome 200
chr19:49,805,226–49,805,871 62.0 kb Distal (>10kb) Multiome 245
chr19:49,808,201–49,809,746 58.6 kb Distal (>10kb) Multiome 509
chr19:49,812,926–49,813,834 54.1 kb Distal (>10kb) Multiome 650
chr19:49,817,356–49,818,721 49.3 kb Distal (>10kb) Multiome 784
chr19:49,850,394–49,852,067 16.7 kb Distal (>10kb) Multiome 862
chr19:49,865,368–49,865,584 1.4 kb Proximal (<10kb) 187
chr19:49,866,817–49,868,124 178 bp At TSS Multiome 874
chr19:49,869,068–49,870,398 2.1 kb Proximal (<10kb) Multiome 832
chr19:49,875,842–49,878,576 10.2 kb Distal (>10kb) Multiome 1153
chr19:49,889,853–49,891,381 22.9 kb Distal (>10kb) Multiome 640
chr19:49,928,884–49,930,473 62.4 kb Distal (>10kb) Multiome 1141
chr19:49,987,157–49,987,669 119.8 kb Distal (>10kb) Multiome 1095
chr19:50,024,875–50,026,285 158.1 kb Distal (>10kb) Multiome 1137
chr19:50,147,523–50,148,432 280.6 kb Distal (>10kb) Multiome 615

Genome Browser

Genomic view of the PNKP locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr19:49,570,125 – 50,158,432
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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