Gene Human Homo sapiens

PNKP

polynucleotide kinase 3'-phosphatase

gene with protein product

Human PNKPMouseRat

Reading the ortholog votes for mouse and rat.

Location: Cytogenetic band 19q13.33NCBI: 19:49,861,204-49,867,576 on the minus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000019.10, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 19:49,859,882-49,878,351 on the minus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as: PNK

Gene identity, from HGNC · HGNC 2026-09-29 · read 2026-09-30 ET · HGNC:9154

Silence this gene

The order page opens with PNKP and human filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for PNKP

sdASO, toASO or siRNA, chosen on the next page

Bring your own sequence Transcripts

For research use only. Not for use in diagnostic or therapeutic procedures.

Summary
Transcripts
Expression
Protein
Interactions
Pathways
Disease
Variants
Constraint
Orthologs
MicroRNAs
Long non-coding RNAs
Literature
Silencing this gene

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Ready in a moment

01 Summary and function

What PNKP does

This locus represents a gene involved in DNA repair.

NCBI Gene summary

Ready in a moment

02 Transcripts and isoforms

The RNA a design targets

1 RefSeq and 65 Ensembl transcripts on GRCh38.p14; MANE Select NM_007254.4.

NCBI Datasets · Ensembl

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03 Expression by tissue

Where PNKP is expressed

Reading GTEx and the Human Protein Atlas.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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04 Protein

The protein PNKP encodes

Reading UniProt, InterPro, AlphaFold DB and PDBe.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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05 Interactions

Proteins STRING associates with PNKP

The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; XRCC1, LIG3, POLB lead.

STRING v12.0

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06 Pathways

Where PNKP acts, as Reactome curates it

Reading UniProt and Reactome.Still reading. A first read of a gene can take a while; this page waits up to 60 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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07 Disease associations

Diseases linked to PNKP

Reading Open Targets and ClinGen.Still reading. A first read of a gene can take a while; this page waits up to 105 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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08 Variants

Classified variants of PNKP

Reading ClinVar.Still reading. A first read of a gene can take a while; this page waits up to 60 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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09 Constraint

How much variation PNKP tolerates

Reading gnomAD and Open Targets.Still reading. A first read of a gene can take a while; this page waits up to 45 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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10 Orthologs

The same gene in mouse, rat and human

Reading the Alliance, NCBI, Ensembl Compara and RGD.Still reading. A first read of a gene can take a while; this page waits up to 145 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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11 MicroRNAs

MicroRNAs hosted within PNKP

No annotated microRNA lies within PNKP in Ensembl release 116, on GRCh38.p14.

Ensembl · miRBase

Ready in a moment

12 Long non-coding RNAs

Long non-coding RNAs at the PNKP locus

No annotated long non-coding RNA overlaps PNKP in Ensembl release 116, on GRCh38.p14.

Ensembl

Ready in a moment

13 Literature

Papers that mention PNKP

Reading Europe PMC.Still reading. A first read of a gene can take a while; this page waits up to 55 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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14 Silencing this gene

From PNKP to a sequence that silences it

The AUMsilence platform designs the sequences against the human transcripts on this page. Six decisions are yours before it does. What is written under each is AUM's guidance; the timings and the concentrations are in the usage guide below.

01
Choose the region
A knockdown oligonucleotide can sit in the 5' untranslated region, the coding sequence or the 3' untranslated region, and all three are used. The coding sequence and the 3' untranslated region are the usual first choices for an RNase H design; the 5' end near the start codon suits a steric block. The map above shows where each region sits on the isoforms it draws.
02
Cover the isoforms you mean
An exon every isoform carries silences the whole gene; an exon only some isoforms carry silences those and spares the rest. Decide which you want before a sequence is chosen, and check the reference transcript (MANE Select in human; RefSeq Select and Ensembl canonical in mouse and rat) is the one your cells express.
03
Think across species early
The orthologs panel says whether mouse and rat carry the same gene. Whether one oligonucleotide can serve two species is a sequence question, settled at design by matching the candidate against each transcript, not by the protein identity shown there.
04
Check expression in your model
A transcript that is not expressed in your cells cannot show knockdown. Confirm the gene is expressed in the cell type and condition you will use, from your own data or a reference atlas, before the order. The expression panel above gives GTEx's median per tissue for a human gene; for mouse and rat it says that no atlas is on this page yet.
05
Run the controls
A scramble control of the same chemistry, a positive control against a gene known to knock down in your cells, untreated cells, and a mock condition where a transfection reagent is used. Read knockdown at the RNA level first, then at the protein; the usage guide gives the timing and the concentrations to start from.
06
Pick the product
AUMsilence sdASO needs no transfection reagent and works in the cells that resist one. AUMsilence toASO is the transfection-optimised version of the same design, and AUMsiRNA is the siRNA route. The selection guide compares them.

Order for PNKP Bring your own sequence The usage guide Selection guide

For research use only. Not for use in diagnostic or therapeutic procedures.

Gene Human Homo sapiens

PNKP

Reading the record for PNKP from HGNC, NCBI Gene and Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 115 seconds for it, and its scripts then bring in the page, or a line saying what did not arrive.

The full name, the identifiers, the location and the notes from the sources arrive with the record. Nothing is filled in ahead of it.

Order door

The door to order for PNKP opens with the record, which decides which product it carries. The order page itself is open now.

Bring your own sequence

For research use only. Not for use in diagnostic or therapeutic procedures.

This page is still reading the record. Its scripts replace this shell with the record when it arrives; with scripts off, it stays at this shell however long you wait.

01 Summary and function

What PNKP does

Waiting for the record before reading NCBI Gene and UniProt.

02 Transcripts and isoforms

The RNA a design targets

Waiting for the record before reading NCBI Datasets and Ensembl.

03 Expression by tissue

Where PNKP is expressed

Waiting for the record before reading GTEx and the Human Protein Atlas.

04 Protein

The protein PNKP encodes

Waiting for the record before reading UniProt, InterPro, AlphaFold DB and PDBe.

05 Interactions

Proteins STRING associates with PNKP

Waiting for the record before reading STRING.

06 Pathways

Where PNKP acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to PNKP

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of PNKP

Waiting for the record before reading ClinVar.

09 Constraint

How much variation PNKP tolerates

Waiting for the record before reading gnomAD and Open Targets.

10 Orthologs

The same gene in mouse, rat and human

Waiting for the record before reading the Alliance, NCBI, Ensembl Compara and RGD.

11 MicroRNAs

MicroRNAs hosted within PNKP

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the PNKP locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention PNKP

Waiting for the record before reading Europe PMC.

PNKP

What PNKP does

The RNA a design targets

Where PNKP is expressed

The protein PNKP encodes

Proteins STRING associates with PNKP

Where PNKP acts, as Reactome curates it

Diseases linked to PNKP

Classified variants of PNKP

How much variation PNKP tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PNKP

Long non-coding RNAs at the PNKP locus

Papers that mention PNKP

From PNKP to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

PNKP

What PNKP does

The RNA a design targets

Where PNKP is expressed

The protein PNKP encodes

Proteins STRING associates with PNKP

Where PNKP acts, as Reactome curates it

Diseases linked to PNKP

Classified variants of PNKP

How much variation PNKP tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PNKP

Long non-coding RNAs at the PNKP locus

Papers that mention PNKP

PNKP

What PNKP does

Gene summary

Protein function

The RNA a design targets

RefSeq 1 transcript

A window on one transcript

Ensembl 65 transcripts

A window on one transcript

Where PNKP is expressed

The protein PNKP encodes

Proteins STRING associates with PNKP

Where PNKP acts, as Reactome curates it

Diseases linked to PNKP

Classified variants of PNKP

How much variation PNKP tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PNKP

Long non-coding RNAs at the PNKP locus

Papers that mention PNKP

From PNKP to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

Gene summary

Protein function

RefSeq 1 transcript

A window on one transcript

Ensembl 65 transcripts

A window on one transcript