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POLB DNA polymerase beta [ Homo sapiens (human) ]

Gene ID: 5423, updated on 7-Apr-2024

Summary

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Official Symbol
POLBprovided by HGNC
Official Full Name
DNA polymerase betaprovided by HGNC
Primary source
HGNC:HGNC:9174
See related
Ensembl:ENSG00000070501 MIM:174760; AllianceGenome:HGNC:9174
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
The protein encoded by this gene is a DNA polymerase involved in base excision and repair, also called gap-filling DNA synthesis. The encoded protein, acting as a monomer, is normally found in the cytoplasm, but it translocates to the nucleus upon DNA damage. Several transcript variants of this gene exist, but the full-length nature of only one has been described to date. [provided by RefSeq, Sep 2011]
Expression
Broad expression in testis (RPKM 24.2), urinary bladder (RPKM 8.5) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See POLB in Genome Data Viewer
Location:
8p11.21
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (42338494..42371808)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (42608570..42642104)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42196012..42229326)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene IKBKB divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42127815-42128314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19154 Neighboring gene inhibitor of nuclear factor kappa B kinase subunit beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27305 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:42150166-42151365 Neighboring gene uncharacterized LOC105379395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42163399-42164071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42164072-42164743 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:42179455-42179956 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:42179957-42180456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42188156-42188656 Neighboring gene ribosomal protein L5 pseudogene 23 Neighboring gene H3K27ac hESC enhancers GRCh37_chr8:42248902-42249402 and GRCh37_chr8:42249403-42249903 Neighboring gene dickkopf WNT signaling pathway inhibitor 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:42258699-42258918 Neighboring gene voltage dependent anion channel 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The Impact of Human DNA Glycosylases on the Activity of DNA Polymerase β toward Various Base Excision Repair Intermediates. Bakman AS, et al. Int J Mol Sci, 2023 May 31. PMID 37298543, Free PMC Article
  2. The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain. Kladova OA, et al. Cells, 2023 May 2. PMID 37174699, Free PMC Article
  3. Targeting DNA polymerase β elicits synthetic lethality with mismatch repair deficiency in acute lymphoblastic leukemia. Teng JY, et al. Leukemia, 2023 Jun. PMID 37095208
  4. Human Polβ Natural Polymorphic Variants G118V and R149I Affects Substate Binding and Catalysis. Kladova OA, et al. Int J Mol Sci, 2023 Mar 20. PMID 36982964, Free PMC Article
  5. Defective DNA polymerase beta invoke a cytosolic DNA mediated inflammatory response. Zhao S, et al. Front Immunol, 2022. PMID 36624848, Free PMC Article

See all (267) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DNA polymerase beta connects tumorigenicity with the circadian clock in liver cancer through the epigenetic demethylation of Per1.
    Title: DNA polymerase beta connects tumorigenicity with the circadian clock in liver cancer through the epigenetic demethylation of Per1.
  2. Coordination between human DNA polymerase beta and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair.
    Title: Coordination between human DNA polymerase β and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair.
  3. The Impact of Human DNA Glycosylases on the Activity of DNA Polymerase beta toward Various Base Excision Repair Intermediates.
    Title: The Impact of Human DNA Glycosylases on the Activity of DNA Polymerase β toward Various Base Excision Repair Intermediates.
  4. Targeting DNA polymerase beta elicits synthetic lethality with mismatch repair deficiency in acute lymphoblastic leukemia.
    Title: Targeting DNA polymerase β elicits synthetic lethality with mismatch repair deficiency in acute lymphoblastic leukemia.
  5. The Activity of Natural Polymorphic Variants of Human DNA Polymerase beta Having an Amino Acid Substitution in the Transferase Domain.
    Title: The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain.
  6. Human Polbeta Natural Polymorphic Variants G118V and R149I Affects Substate Binding and Catalysis.
    Title: Human Polβ Natural Polymorphic Variants G118V and R149I Affects Substate Binding and Catalysis.
  7. Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase beta on the APE1-DNA interaction.
    Title: Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase β on the APE1-DNA interaction.
  8. Defective DNA polymerase beta invoke a cytosolic DNA mediated inflammatory response.
    Title: Defective DNA polymerase beta invoke a cytosolic DNA mediated inflammatory response.
  9. Polymorphic mutations in the polb gene promoter and their impact on transcriptional activity.
    Title: Polymorphic mutations in the polb gene promoter and their impact on transcriptional activity.
  10. Incorporation of 5',8-cyclo-2'deoxyadenosines by DNA repair polymerases via base excision repair.
    Title: Incorporation of 5',8-cyclo-2'deoxyadenosines by DNA repair polymerases via base excision repair.
Submit: New GeneRIF Correction See all GeneRIFs (174)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of polymerase (DNA directed), beta (POLB) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat is a potent inducer of the human DNA repair enzyme beta-polymerase, suggesting Tat may alter DNA stability in AIDS-related lymphomas PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC125976

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-deoxyribose-5-phosphate lyase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-(apurinic or apyrimidinic site) endonuclease activity TAS
Traceable Author Statement
more info
  
enables DNA-directed DNA polymerase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-directed DNA polymerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-directed DNA polymerase activity TAS
Traceable Author Statement
more info
  
enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables lyase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables microtubule binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA repair TAS
Traceable Author Statement
more info
 PubMed 
involved_in DNA-templated DNA replication TAS
Traceable Author Statement
more info
 PubMed 
involved_in base-excision repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in base-excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in base-excision repair TAS
Traceable Author Statement
more info
  
involved_in base-excision repair, gap-filling TAS
Traceable Author Statement
more info
  
involved_in double-strand break repair via nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homeostasis of number of cells IEA
Inferred from Electronic Annotation
more info
  
involved_in immunoglobulin heavy chain V-D-J recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in intrinsic apoptotic signaling pathway in response to DNA damage IEA
Inferred from Electronic Annotation
more info
  
involved_in lymph node development IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in nucleotide-excision repair, DNA gap filling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in pyrimidine dimer repair IEA
Inferred from Electronic Annotation
more info
  
involved_in response to ethanol IEA
Inferred from Electronic Annotation
more info
  
involved_in response to gamma radiation IEA
Inferred from Electronic Annotation
more info
  
involved_in response to hyperoxia IEA
Inferred from Electronic Annotation
more info
  
involved_in salivary gland morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in somatic hypermutation of immunoglobulin genes IEA
Inferred from Electronic Annotation
more info
  
involved_in spleen development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
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 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in spindle microtubule IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA polymerase beta
Names
5'-dRP lyase
5'-deoxyribose-phosphate lyase
AP lyase
DNA pol beta
DNA polymerase beta subunit
polymerase (DNA directed), beta
polymerase (DNA) beta
NP_002681.1
XP_005273592.1
XP_005273593.1
XP_005273594.1
XP_005273595.1
XP_005273596.1
XP_005273597.1
XP_016869072.1
XP_016869073.1
XP_047277856.1
XP_047277857.1
XP_054216680.1
XP_054216681.1
XP_054216682.1
XP_054216683.1
XP_054216684.1
XP_054216685.1
XP_054216686.1
XP_054216687.1
XP_054216688.1
XP_054216689.1

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)

  1. NM_002690.3 → NP_002681.1  DNA polymerase beta

    Status: REVIEWED

    Source sequence(s)
    BM678092, BP370570, D29013
    Consensus CDS
    CCDS6129.1
    UniProtKB/Swiss-Prot
    B2RC78, P06746, Q3KP48, Q6FI34
    UniProtKB/TrEMBL
    Q53EV2
    Related
    ENSP00000265421.4, ENST00000265421.9
    Conserved Domains (1) summary
    cd00141
    Location:15 → 333
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    42338494..42371808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005273535.5 → XP_005273592.1  DNA polymerase beta isoform X1

    UniProtKB/TrEMBL
    Q53EV2
    Conserved Domains (1) summary
    cd00141
    Location:15 → 368
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  2. XM_005273536.5 → XP_005273593.1  DNA polymerase beta isoform X2

    UniProtKB/TrEMBL
    Q53EV2
    Conserved Domains (2) summary
    cd00141
    Location:15 → 339
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
    smart00483
    Location:10 → 340
    POLXc; DNA polymerase X family

  3. XM_005273537.5 → XP_005273594.1  DNA polymerase beta isoform X3

    UniProtKB/TrEMBL
    Q53EV2
    Conserved Domains (1) summary
    cd00141
    Location:15 → 304
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  4. XM_005273538.3 → XP_005273595.1  DNA polymerase beta isoform X4

    Conserved Domains (1) summary
    cd00141
    Location:9 → 219
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  5. XM_005273539.3 → XP_005273596.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5
    Conserved Domains (1) summary
    cd00141
    Location:1 → 179
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  6. XM_017013583.2 → XP_016869072.1  DNA polymerase beta isoform X4

    Conserved Domains (1) summary
    cd00141
    Location:9 → 219
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  7. XM_017013584.2 → XP_016869073.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5
    Conserved Domains (1) summary
    cd00141
    Location:1 → 179
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  8. XM_005273540.5 → XP_005273597.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5
    Conserved Domains (1) summary
    cd00141
    Location:1 → 179
    NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

  9. XM_047421900.1 → XP_047277856.1  DNA polymerase beta isoform X4

  10. XM_047421901.1 → XP_047277857.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5

RNA

  1. XR_428311.4 RNA Sequence

    Related
    ENST00000518925.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    42608570..42642104
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360705.1 → XP_054216680.1  DNA polymerase beta isoform X1

  2. XM_054360706.1 → XP_054216681.1  DNA polymerase beta isoform X2

  3. XM_054360707.1 → XP_054216682.1  DNA polymerase beta isoform X3

  4. XM_054360708.1 → XP_054216683.1  DNA polymerase beta isoform X4

  5. XM_054360711.1 → XP_054216686.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5

  6. XM_054360709.1 → XP_054216684.1  DNA polymerase beta isoform X4

  7. XM_054360712.1 → XP_054216687.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5

  8. XM_054360714.1 → XP_054216689.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5

  9. XM_054360710.1 → XP_054216685.1  DNA polymerase beta isoform X4

  10. XM_054360713.1 → XP_054216688.1  DNA polymerase beta isoform X5

    UniProtKB/TrEMBL
    B7Z1W5

RNA

  1. XR_008487852.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P06746.3 GenPept UniProtKB/Swiss-Prot:P06746

Gene LinkOut

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