Polk polymerase (DNA directed), kappa [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Polkprovided by MGI
Official Full Name: polymerase (DNA directed), kappaprovided by MGI
Primary source: MGI:MGI:1349767
See related: Ensembl:ENSMUSG00000021668 AllianceGenome:MGI:1349767
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: DINP; Dinb1
Summary: Predicted to enable DNA-directed DNA polymerase activity. Acts upstream of or within DNA repair. Located in nucleus. Is expressed in several structures, including adrenal gland; eye; gonad; lung; and stomach. Orthologous to human POLK (DNA polymerase kappa). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in bladder adult (RPKM 3.8), testis adult (RPKM 3.6) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 D1; 13 50.56 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (96617195..96679087, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (96480687..96542579, complement)

Chromosome 13 - NC_000079.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The results indicate that Polkappa does not suppress benzo[a]pyrene -induced mutagenesis and carcinogenesis in the colon, but counteracts inflammation-induced mutagenesis in multiple organs.
Title: DNA polymerase kappa counteracts inflammation-induced mutagenesis in multiple organs of mice.
The results suggest that Polk has a limited ability to suppress BP-induced genotoxicity in the colon and bone marrow and also that the roles of specialized DNA polymerases in mutagenesis and carcinogenesis should be examined not only by in vitro assays but also by in vivo mouse studies. We also report the spontaneous mutagenesis in inactivated Polk KI mice at young and old ages.
Title: Limited ability of DNA polymerase kappa to suppress benzo[a]pyrene-induced genotoxicity in vivo.
the extreme N-terminal part of Polkappa is required for the processivity and fidelity of Polkappa during translesion synthesis of 10S(+)-trans-anti-benzo[a]pyrene diol epoxide-N(2)-deoxyguanine adducts lesions.
Title: Effects of the N terminus of mouse DNA polymerase κ on the bypass of a guanine-benzo[a]pyrenyl adduct.
Polk plays a predominant role in suppressing point mutations by carrying out error-free translesion DNA synthesis and contributes to the prevention of DNA strand breaks.
Title: In vivo evidence that DNA polymerase kappa is responsible for error-free bypass across DNA cross-links induced by mitomycin C.
The structural gap physically accommodates the bulky aromatic adduct and the N-clasp is essential for the structural integrity and flexibility of Polkappa during translesion synthesis.
Title: Variants of mouse DNA polymerase κ reveal a mechanism of efficient and accurate translesion synthesis past a benzo[a]pyrene dG adduct.
Polkappa accumulates at laser-induced sites of DNA damage.
Title: Mouse DNA polymerase kappa has a functional role in the repair of DNA strand breaks.
Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric polymerase (Pol) zeta, and Pol kappa
Title: Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric polymerase (Pol) ζ, and Pol κ.
Data suggest that DNA polymerase kappa Polkappa functions in DNA interstrand crosslinks (ICLs) repair in embryonic fibroblast cells (MEF), especially during the G0/G1 phases.
Title: Replication-independent repair of DNA interstrand crosslinks.
solution structure of the polymerase kappa-Rev1 complex
Title: Multifaceted recognition of vertebrate Rev1 by translesion polymerases ζ and κ.
in mammalian cells, both polymerases kappa and iota are necessary for the error-free bypass of N(2)-CEdG and N(2)-CMdG.
Title: The roles of DNA polymerases κ and ι in the error-free bypass of N2-carboxyalkyl-2'-deoxyguanosine lesions in mammalian cells.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Polk (e-PCR), detects polymorphism
- UniSTS:531507

Polk (e-PCR), detects polymorphism
- UniSTS:531508

Polk (e-PCR), detects polymorphism
- UniSTS:531509

Polk (e-PCR), detects polymorphism
- UniSTS:531510

D13Mit111 (e-PCR), detects polymorphism
- UniSTS:126937

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-directed DNA polymerase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-directed DNA polymerase activity	TAS Traceable Author Statement more info	PubMed
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables molecular adaptor activity	EXP Inferred from Experiment more info	PubMed
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA replication	IEA Inferred from Electronic Annotation more info
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in error-prone translesion synthesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in error-prone translesion synthesis	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair, DNA gap filling	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nuclear body	ISO Inferred from Sequence Orthology 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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
colocalizes_with site of DNA damage	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA polymerase kappa

Names: DINB protein; DNA damage-inducible protein b; DNA-directed DNA polymerase kappa; DinB homolog 1

NP_001334531.1

EC 2.7.7.7

NP_001334532.1

EC 2.7.7.7

NP_001334533.1

EC 2.7.7.7

NP_001334535.1

EC 2.7.7.7

NP_036178.1

EC 2.7.7.7

XP_006517743.1

EC 2.7.7.7

XP_030103145.1

EC 2.7.7.7

XP_036013953.1

EC 2.7.7.7

XP_036013954.1

EC 2.7.7.7

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_001347602.1 → NP_001334531.1 DNA polymerase kappa isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains lacks an alternate exon but contains a different in-frame exon in the central coding region, compared to variant a, resulting in an isoform (2) that is shorter than isoform a. The 5' UTR of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AC122828, AK014087, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080

Consensus CDS

CCDS84053.1

UniProtKB/TrEMBL

Q5Q9H7

Related

ENSMUSP00000088950.4, ENSMUST00000091387.4

Conserved Domains (2) summary

smart00734
Location:561 → 586

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:103 → 454

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa
NM_001347603.1 → NP_001334532.1 DNA polymerase kappa isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains lacks an alternate in-frame exon in the central coding region, compared to variant a, resulting in an isoform (3) that is shorter than isoform a. The 5' UTR of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080

Consensus CDS

CCDS88503.1

UniProtKB/TrEMBL

Q5Q9H6

Related

ENSMUSP00000152647.2, ENSMUST00000221899.2

Conserved Domains (2) summary

smart00734
Location:540 → 565

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:103 → 433

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa
NM_001347604.1 → NP_001334533.1 DNA polymerase kappa isoform 8

Status: VALIDATED

Description

Transcript Variant: This variant (8) contains lacks an alternate in-frame exon in the 3' coding region, compared to variant a, resulting in an isoform (8) that is shorter than isoform a. The 5' UTR of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, CN698108, DV656157, EH097080

Consensus CDS

CCDS88504.1

UniProtKB/TrEMBL

A0A1Y7VIV8, Q5Q9H1

Related

ENSMUSP00000152178.2, ENSMUST00000221645.2
NM_001347606.1 → NP_001334535.1 DNA polymerase kappa isoform 9

Status: VALIDATED

Description

Transcript Variant: This variant (9) contains lacks an alternate in-frame exon in both the central and 3' coding regions, compared to variant a, resulting in an isoform (9) that is shorter than isoform a. The 5' UTR of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, CN698108, DV656157, EH097080

Consensus CDS

CCDS88502.1

UniProtKB/TrEMBL

Q5Q9H0, Q5Q9H1

Related

ENSMUSP00000152192.2, ENSMUST00000222389.2
NM_012048.3 → NP_036178.1 DNA polymerase kappa isoform a

See identical proteins and their annotated locations for NP_036178.1

Status: VALIDATED

Description

Transcript Variant: This variant (a) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AK014087, AK042272, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080

Consensus CDS

CCDS26704.1

UniProtKB/Swiss-Prot

Q7TPY7, Q9QUG2

Related

ENSMUSP00000022172.5, ENSMUST00000022172.12

Conserved Domains (3) summary

smart00734
Location:620 → 645

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:103 → 513

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa

PRK02406
Location:107 → 521

PRK02406; DNA polymerase IV; Validated

RNA

NR_144622.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (1) uses an alternate splice site in the 3' region, compared to variant a. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant a, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). The 5' end of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080
NR_144623.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate exon in the central region and uses an alternate splice site in the 3' region, compared to variant a. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant a, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). The 5' end of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080
NR_144624.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks three alternate exons in the central region, compared to variant a. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant a, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). The 5' end of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080
NR_144625.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks three alternate exons in the central region, compared to variant a. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant a, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). The 5' end of this variant is incomplete because there are no 5'-complete transcripts representing it and there is splicing ambiguity at the 5' end.

Source sequence(s)

AK014087, AK138299, BG060790, BG061549, BY707241, CN698108, DV656157, EH097080

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000079.7 Reference GRCm39 C57BL/6J

Range

96617195..96679087 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036158060.1 → XP_036013953.1 DNA polymerase kappa isoform X3

UniProtKB/TrEMBL

Q5Q9H6

Conserved Domains (2) summary

smart00734
Location:540 → 565

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:103 → 433

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa
XM_030247285.1 → XP_030103145.1 DNA polymerase kappa isoform X1

UniProtKB/TrEMBL

Q5Q9H7

Conserved Domains (2) summary

smart00734
Location:561 → 586

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:103 → 454

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa
XM_006517680.5 → XP_006517743.1 DNA polymerase kappa isoform X2

Conserved Domains (2) summary

smart00734
Location:555 → 580

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:38 → 448

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa
XM_036158061.1 → XP_036013954.1 DNA polymerase kappa isoform X4

Conserved Domains (2) summary

smart00734
Location:531 → 556

ZnF_Rad18; Rad18-like CCHC zinc finger

cd03586
Location:14 → 424

PolY_Pol_IV_kappa; DNA Polymerase IV/Kappa