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    POLB DNA polymerase beta [ Homo sapiens (human) ]

    Gene ID: 5423, updated on 17-Jun-2019

    Summary

    Official Symbol
    POLBprovided by HGNC
    Official Full Name
    DNA polymerase betaprovided by HGNC
    Primary source
    HGNC:HGNC:9174
    See related
    Ensembl:ENSG00000070501 MIM:174760
    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

    Genomic context

    See POLB in Genome Data Viewer
    Location:
    8p11.21
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (42338452..42371810)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42195973..42229331)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929897 Neighboring gene inhibitor of nuclear factor kappa B kinase subunit beta Neighboring gene uncharacterized LOC105379395 Neighboring gene ribosomal protein L5 pseudogene 23 Neighboring gene dickkopf WNT signaling pathway inhibitor 4 Neighboring gene voltage dependent anion channel 3

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

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

    HIV-1 interactions

    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 BioSystems

    • APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystem (from REACTOME)
      APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystemNEIL1 and NEIL2 have a dual DNA glycosylase and beta/delta lyase activity. The AP (apurinic/apyrimidinic) site-directed lyase activity of NEIL1 and NEIL2 is their major physiological role, as they ca...
    • Abasic sugar-phosphate removal via the single-nucleotide replacement pathway, organism-specific biosystem (from REACTOME)
      Abasic sugar-phosphate removal via the single-nucleotide replacement pathway, organism-specific biosystemAbasic sugar phosphate removal via the single nucleotide replacement pathway requires displacement of DNA glycosylase by APEX1, APEX1-mediated endonucleolytic cleavage at the 5' side of the base free...
    • BER complex, organism-specific biosystem (from KEGG)
      BER complex, organism-specific biosystemStructural complex; Genetic information processing; Repair system
    • BER complex, conserved biosystem (from KEGG)
      BER complex, conserved biosystemStructural complex; Genetic information processing; Repair system
    • Base Excision Repair, organism-specific biosystem (from REACTOME)
      Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
    • Base excision repair, organism-specific biosystem (from KEGG)
      Base excision repair, organism-specific biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
    • Base excision repair, conserved biosystem (from KEGG)
      Base excision repair, conserved biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
    • DNA Repair, organism-specific biosystem (from REACTOME)
      DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
    • Deubiquitination, organism-specific biosystem (from REACTOME)
      Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
    • HTLV-I infection, organism-specific biosystem (from KEGG)
      HTLV-I infection, organism-specific biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
    • HTLV-I infection, conserved biosystem (from KEGG)
      HTLV-I infection, conserved biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • Nucleotide Metabolism, organism-specific biosystem (from WikiPathways)
      Nucleotide Metabolism, organism-specific biosystemThe pathway outlined above focuses on purine metabolism and in particular that of guanine metabolism.
    • PCNA-Dependent Long Patch Base Excision Repair, organism-specific biosystem (from REACTOME)
      PCNA-Dependent Long Patch Base Excision Repair, organism-specific biosystemLong-patch base excision repair (BER) can proceed through PCNA-dependent DNA strand displacement synthesis by replicative DNA polymerases - DNA polymerase delta complex (POLD) or DNA polymerase epsil...
    • POLB-Dependent Long Patch Base Excision Repair, organism-specific biosystem (from REACTOME)
      POLB-Dependent Long Patch Base Excision Repair, organism-specific biosystemDuring POLB-dependent long patch base excision repair (BER), PARP1 and/or PARP2 is recruited to the BER site along with flap endonuclease FEN1. PARP1 and/or PARP2 and FEN1 facilitate POLB-mediated st...
    • Post-translational protein modification, organism-specific biosystem (from REACTOME)
      Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
    • Resolution of AP sites via the multiple-nucleotide patch replacement pathway, organism-specific biosystem (from REACTOME)
      Resolution of AP sites via the multiple-nucleotide patch replacement pathway, organism-specific biosystemWhile the single nucleotide replacement pathway appears to facilitate the repair of most damaged bases, an alternative BER pathway is evoked when the structure of the 5'-terminal sugar phosphate is s...
    • Resolution of AP sites via the single-nucleotide replacement pathway, organism-specific biosystem (from REACTOME)
      Resolution of AP sites via the single-nucleotide replacement pathway, organism-specific biosystemThe single nucleotide replacement pathway of base excision repair appears to facilitate the repair of most damaged bases. Following DNA glycosylase mediated cleavage of the damaged base, the endonucl...
    • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
      Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...
    • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
      Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...
    • Viral carcinogenesis, organism-specific biosystem (from KEGG)
      Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
    • Viral carcinogenesis, conserved biosystem (from KEGG)
      Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC125976

    Gene Ontology Provided by GOA

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

    General protein information

    Preferred Names
    DNA polymerase beta
    Names
    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_006716416.1
    XP_016869072.1
    XP_016869073.1

    NCBI Reference Sequences (RefSeq)

    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_002690.3NP_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
      P06746
      Related
      ENSP00000265421.4, ENST00000265421.9
      Conserved Domains (1) summary
      cd00141
      Location:15333
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

      Range
      42338452..42371810
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005273540.4XP_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:1179
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
    2. XM_017013583.1XP_016869072.1  DNA polymerase beta isoform X4

      Conserved Domains (1) summary
      cd00141
      Location:9219
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
    3. XM_017013584.1XP_016869073.1  DNA polymerase beta isoform X5

      UniProtKB/TrEMBL
      B7Z1W5
      Conserved Domains (1) summary
      cd00141
      Location:1179
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
    4. XM_005273538.2XP_005273595.1  DNA polymerase beta isoform X4

      See identical proteins and their annotated locations for XP_005273595.1

      Conserved Domains (1) summary
      cd00141
      Location:9219
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
    5. XM_005273539.2XP_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:1179
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
    6. XM_005273535.4XP_005273592.1  DNA polymerase beta isoform X1

      See identical proteins and their annotated locations for XP_005273592.1

      Conserved Domains (2) summary
      cd00141
      Location:15368
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
      smart00483
      Location:10369
      POLXc; DNA polymerase X family
    7. XM_005273536.4XP_005273593.1  DNA polymerase beta isoform X2

      Conserved Domains (2) summary
      cd00141
      Location:15339
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
      smart00483
      Location:10340
      POLXc; DNA polymerase X family
    8. XM_005273537.4XP_005273594.1  DNA polymerase beta isoform X3

      Conserved Domains (2) summary
      cd00141
      Location:15304
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases
      smart00483
      Location:10305
      POLXc; DNA polymerase X family
    9. XM_006716353.2XP_006716416.1  DNA polymerase beta isoform X5

      See identical proteins and their annotated locations for XP_006716416.1

      UniProtKB/TrEMBL
      B7Z1W5
      Conserved Domains (1) summary
      cd00141
      Location:1179
      NT_POLXc; Nucleotidyltransferase (NT) domain of family X DNA Polymerases

    RNA

    1. XR_001745544.2 RNA Sequence

      Related
      ENST00000522610.5
    2. XR_428311.3 RNA Sequence

      Related
      ENST00000518925.5
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