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    POLB DNA polymerase beta [ Homo sapiens (human) ]

    Gene ID: 5423, updated on 9-Dec-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (42338494..42371808)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (42608570..42642104)
    RS_2024_09 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. Enhancement of silencing DNA polymerase β on the radiotherapeutic sensitivity of human esophageal carcinoma cell lines. Wang Y, et al. Tumour Biol, 2014 Oct. PMID 25015190
    2. Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Sucato CA, et al. Biochemistry, 2007 Jan 16. PMID 17209556
    3. DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. Martínek V, et al. FEBS Lett, 2007 Feb 20. PMID 17286973, Free PMC Article
    4. The E295K DNA polymerase beta gastric cancer-associated variant interferes with base excision repair and induces cellular transformation. Lang T, et al. Mol Cell Biol, 2007 Aug. PMID 17526740, Free PMC Article
    5. Substrate-induced DNA polymerase β activation. Beard WA, et al. J Biol Chem, 2014 Nov 7. PMID 25261471, Free PMC Article

    See all (274) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polbeta Polymerase Activity.
      Title: SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polβ Polymerase Activity.
    2. Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase beta.
      Title: Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β.
    3. Impact of polbeta/XRCC1 Interaction Variants on the Efficiency of Nick Sealing by DNA Ligase IIIalpha in the Base Excision Repair Pathway.
      Title: Impact of polβ/XRCC1 Interaction Variants on the Efficiency of Nick Sealing by DNA Ligase IIIα in the Base Excision Repair Pathway.
    4. The Impact of SNP-Induced Amino Acid Substitutions L19P and G66R in the dRP-Lyase Domain of Human DNA Polymerase beta on Enzyme Activities.
      Title: The Impact of SNP-Induced Amino Acid Substitutions L19P and G66R in the dRP-Lyase Domain of Human DNA Polymerase β on Enzyme Activities.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (178)

    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)

    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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    NEW Try the new Transcript table

    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

      See identical proteins and their annotated locations for NP_002681.1

      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_2024_08

    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

      See identical proteins and their annotated locations for XP_005273592.1

      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

      See identical proteins and their annotated locations for XP_005273595.1

      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

      See identical proteins and their annotated locations for XP_005273596.1

      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

      See identical proteins and their annotated locations for XP_005273597.1

      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

      UniProtKB/TrEMBL
      Q53EV2

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

      UniProtKB/TrEMBL
      Q53EV2

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

      UniProtKB/TrEMBL
      Q53EV2

    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

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