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POLB DNA polymerase beta [ Homo sapiens (human) ]

Gene ID: 5423, updated on 13-Jan-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 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (42338452..42371813)
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 
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
 
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, ENST00000265421.8
    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.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    42338452..42371813
    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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