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Aliases for POLB Gene

Aliases for POLB Gene

  • DNA Polymerase Beta 2 3 3 5
  • Polymerase (DNA Directed), Beta 2 3
  • Polymerase (DNA) Beta 2 3
  • DNA Polymerase Beta Subunit 3
  • DNA Pol Beta 3
  • EC 4.2.99.- 4
  • EC 2.7.7.7 4

External Ids for POLB Gene

Previous GeneCards Identifiers for POLB Gene

  • GC08M041722
  • GC08P042220
  • GC08P041936
  • GC08P042213
  • GC08P040719
  • GC08P042195

Summaries for POLB Gene

Entrez Gene Summary for POLB Gene

  • 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]

GeneCards Summary for POLB Gene

POLB (DNA Polymerase Beta) is a Protein Coding gene. Diseases associated with POLB include Werner Syndrome and Retinitis Pigmentosa, Y-Linked. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and HTLV-I infection. Gene Ontology (GO) annotations related to this gene include enzyme binding and damaged DNA binding. An important paralog of this gene is POLL.

UniProtKB/Swiss-Prot for POLB Gene

  • Repair polymerase that plays a key role in base-excision repair. Has 5-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5 sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3 end of the arising single-nucleotide gap. Conducts gap-filling DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.

Gene Wiki entry for POLB Gene

Additional gene information for POLB Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for POLB Gene

Genomics for POLB Gene

GeneHancer (GH) Regulatory Elements for POLB Gene

Promoters and enhancers for POLB Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J042337 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 711.6 +0.1 82 1.7 CLOCK ARNT ARID4B SIN3A YY1 SLC30A9 POLR2B E2F8 SP3 REST POLB ENSG00000254165 RPL5P23
GH08J042296 Enhancer 1.1 Ensembl ENCODE dbSUPER 76.3 -39.0 -39037 5.4 NCOA3 HDAC1 MXI1 JUN MAX FOSL1 ZNF121 GATA3 POLR2A SMC3 LOC105379395 POLB LOC101929897 IKBKB VDAC3 DKK4
GH08J042289 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 30.9 -46.4 -46389 5.6 HDGF PKNOX1 SMAD1 IRF4 ZNF207 ATF7 RUNX3 JUNB ZNF592 NBN POLB LOC101929897 IKBKB DKK4 ANK1 LOC105379395
GH08J042205 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 18.8 -130.5 -130489 4.9 PKNOX1 ZNF133 FEZF1 YY1 TCF12 ZNF213 FOS ATF7 KLF13 SP3 PLAT KAT6A POLB HGSNAT LOC101929897
GH08J042269 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 19.5 -67.4 -67389 2.9 PKNOX1 CLOCK SMAD1 ZFP64 ARID4B SIN3A DMAP1 E2F8 ZNF143 KLF13 IKBKB LOC101929897 KAT6A POLB ENSG00000254165 HGSNAT PLAT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around POLB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the POLB gene promoter:
  • HNF-4alpha1
  • HNF-4alpha2
  • deltaCREB
  • CREB
  • Nkx6-1
  • Egr-2
  • USF-1:USF-2
  • USF-1
  • USF1
  • USF2

Genomic Locations for POLB Gene

Genomic Locations for POLB Gene
chr8:42,338,454-42,371,813
(GRCh38/hg38)
Size:
33,360 bases
Orientation:
Plus strand
chr8:42,195,972-42,229,326
(GRCh37/hg19)
Size:
33,355 bases
Orientation:
Plus strand

Genomic View for POLB Gene

Genes around POLB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POLB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POLB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POLB Gene

Proteins for POLB Gene

  • Protein details for POLB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P06746-DPOLB_HUMAN
    Recommended name:
    DNA polymerase beta
    Protein Accession:
    P06746
    Secondary Accessions:
    • B2RC78
    • Q3KP48
    • Q6FI34

    Protein attributes for POLB Gene

    Size:
    335 amino acids
    Molecular mass:
    38178 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer. Interacts with APEX1, HUWE1/ARF-BP1, STUB1/CHIP and USP47. Interacts with FAM168A (PubMed:25260657).

    Three dimensional structures from OCA and Proteopedia for POLB Gene

neXtProt entry for POLB Gene

Post-translational modifications for POLB Gene

  • Methylation by PRMT6 stimulates the polymerase activity by enhancing DNA binding and processivity.
  • Ubiquitinated at Lys-41, Lys-61 and Lys-81: monoubiquitinated by HUWE1/ARF-BP1. Monoubiquitinated protein is then the target of STUB1/CHIP, which catalyzes polyubiquitination from monoubiquitin, leading to degradation by the proteasome. USP47 mediates the deubiquitination of monoubiquitinated protein, preventing polyubiquitination by STUB1/CHIP and its subsequent degradation.
  • Ubiquitination at posLast=8181, Lys61, and posLast=4141
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for POLB Gene

Domains & Families for POLB Gene

Gene Families for POLB Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • FDA approved drug targets
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for POLB Gene

Graphical View of Domain Structure for InterPro Entry

P06746

UniProtKB/Swiss-Prot:

DPOLB_HUMAN :
  • Residues 239-252 form a flexible loop which appears to affect the polymerase fidelity.
  • Belongs to the DNA polymerase type-X family.
Domain:
  • Residues 239-252 form a flexible loop which appears to affect the polymerase fidelity.
Family:
  • Belongs to the DNA polymerase type-X family.
genes like me logo Genes that share domains with POLB: view

Function for POLB Gene

Molecular function for POLB Gene

UniProtKB/Swiss-Prot Function:
Repair polymerase that plays a key role in base-excision repair. Has 5-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5 sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3 end of the arising single-nucleotide gap. Conducts gap-filling DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
UniProtKB/Swiss-Prot CatalyticActivity:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
GENATLAS Biochemistry:
polymerase (DNA directed),beta,39kDa,highly expressed (rat) in testis may be involved in DNA repair and in meiosis,not involved in DNA replication

Enzyme Numbers (IUBMB) for POLB Gene

Phenotypes From GWAS Catalog for POLB Gene

Gene Ontology (GO) - Molecular Function for POLB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003684 damaged DNA binding IEA --
GO:0003887 DNA-directed DNA polymerase activity IEA,TAS --
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity TAS --
GO:0005515 protein binding IPI 9207062
GO:0008017 microtubule binding IDA 15725623
genes like me logo Genes that share ontologies with POLB: view
genes like me logo Genes that share phenotypes with POLB: view

Animal Models for POLB Gene

MGI Knock Outs for POLB:
  • Polb Polb<tm1a(KOMP)Wtsi>
  • Polb Polb<tm1Koy>
  • Polb Polb<tm1.1Rsky>

Animal Model Products

miRNA for POLB Gene

miRTarBase miRNAs that target POLB

Clone Products

  • Addgene plasmids for POLB

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for POLB Gene

Localization for POLB Gene

Subcellular locations from UniProtKB/Swiss-Prot for POLB Gene

Nucleus. Cytoplasm. Note=Cytoplasmic in normal conditions. Translocates to the nucleus following DNA damage.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for POLB gene
Compartment Confidence
cytoskeleton 5
nucleus 5
plasma membrane 2
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for POLB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 19713937
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA,IEA 15725623
GO:0005874 microtubule IDA 15725623
GO:0005876 spindle microtubule IDA 15725623
genes like me logo Genes that share ontologies with POLB: view

Pathways & Interactions for POLB Gene

genes like me logo Genes that share pathways with POLB: view

Gene Ontology (GO) - Biological Process for POLB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication IEA --
GO:0006261 DNA-dependent DNA replication TAS 8168825
GO:0006281 DNA repair IEA,TAS 8168825
GO:0006284 base-excision repair IMP 21362556
GO:0006286 base-excision repair, base-free sugar-phosphate removal TAS --
genes like me logo Genes that share ontologies with POLB: view

No data available for SIGNOR curated interactions for POLB Gene

Drugs & Compounds for POLB Gene

(35) Drugs for POLB Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cytarabine Approved, Investigational Pharma inhibitor, Target 1166
Magnesium Approved Nutra 0
Iron Approved Pharma Target 1259
Carboplatin Approved Pharma Antitumor agent that forms platinum-DNA adducts., Platinum 2141
Phosphoric acid Approved Pharma 0

(46) Additional Compounds for POLB Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
14000-31-8
Thymidine 5'-triphosphate
  • 2'-Deoxythymidine triphosphate
  • 5'-TTP
  • Deoxy-TTP
  • Deoxythymidine 5'-triphosphate
  • Deoxythymidine triphosphate
365-08-2
genes like me logo Genes that share compounds with POLB: view

Transcripts for POLB Gene

Unigene Clusters for POLB Gene

Polymerase (DNA directed), beta:
Representative Sequences:

Clone Products

  • Addgene plasmids for POLB

Alternative Splicing Database (ASD) splice patterns (SP) for POLB Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15
SP1: - - - -
SP2: - -
SP3: - - - -
SP4: - - -
SP5: -
SP6:
SP7:

Relevant External Links for POLB Gene

GeneLoc Exon Structure for
POLB
ECgene alternative splicing isoforms for
POLB

Expression for POLB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for POLB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for POLB Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x7.5) and Brain - Cerebellum (x6.2).

Protein differential expression in normal tissues from HIPED for POLB Gene

This gene is overexpressed in CD4 Tcells (7.5) and Testis (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for POLB Gene



Protein tissue co-expression partners for POLB Gene

NURSA nuclear receptor signaling pathways regulating expression of POLB Gene:

POLB

SOURCE GeneReport for Unigene cluster for POLB Gene:

Hs.654484

Evidence on tissue expression from TISSUES for POLB Gene

  • Skin(4.3)
  • Nervous system(3.3)
  • Liver(2.2)
genes like me logo Genes that share expression patterns with POLB: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for POLB Gene

Orthologs for POLB Gene

This gene was present in the common ancestor of chordates.

Orthologs for POLB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia POLB 34 33
  • 99.6 (n)
OneToOne
dog
(Canis familiaris)
Mammalia POLB 34 33
  • 94.73 (n)
OneToOne
cow
(Bos Taurus)
Mammalia POLB 34 33
  • 93.43 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia POLB 34
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Polb 33
  • 89.45 (n)
mouse
(Mus musculus)
Mammalia Polb 16 34 33
  • 89.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia POLB 34
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves POLB 34 33
  • 79.6 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia POLB 34
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia polb 33
  • 75.45 (n)
Str.10890 33
African clawed frog
(Xenopus laevis)
Amphibia polB 33
zebrafish
(Danio rerio)
Actinopterygii polb 34 33
  • 73.73 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7184 33
sea squirt
(Ciona savignyi)
Ascidiacea Cin.6306 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6306 33
Species where no ortholog for POLB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for POLB Gene

ENSEMBL:
Gene Tree for POLB (if available)
TreeFam:
Gene Tree for POLB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for POLB: view image

Paralogs for POLB Gene

Paralogs for POLB Gene

(2) SIMAP similar genes for POLB Gene using alignment to 12 proteins:

  • DPOLB_HUMAN
  • B7Z1W5_HUMAN
  • E5RG65_HUMAN
  • E5RHZ4_HUMAN
  • E5RIJ0_HUMAN
  • E5RJ55_HUMAN
  • E7EW18_HUMAN
  • E9PIC6_HUMAN
  • H0YAV8_HUMAN
  • H0YB29_HUMAN
  • H0YBJ0_HUMAN
  • H0YBX1_HUMAN

Pseudogenes.org Pseudogenes for POLB Gene

genes like me logo Genes that share paralogs with POLB: view

Variants for POLB Gene

Sequence variations from dbSNP and Humsavar for POLB Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000021062 -- 42,366,839(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000062336 -- 42,363,477(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000078616 -- 42,370,857(+) C/A genic_downstream_transcript_variant, intron_variant
rs1000119191 -- 42,354,286(+) C/T intron_variant
rs1000243697 -- 42,357,686(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for POLB Gene

Variant ID Type Subtype PubMed ID
esv2661547 CNV deletion 23128226
esv3617009 CNV loss 21293372
nsv397871 CNV insertion 16902084
nsv508508 CNV deletion 20534489
nsv6169 CNV deletion 18451855
nsv831301 CNV loss 17160897
nsv967582 CNV duplication 23825009

Variation tolerance for POLB Gene

Residual Variation Intolerance Score: 52.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.72; 32.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for POLB Gene

Human Gene Mutation Database (HGMD)
POLB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
POLB

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for POLB Gene

Disorders for POLB Gene

MalaCards: The human disease database

(6) MalaCards diseases for POLB Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
werner syndrome
  • wrn
retinitis pigmentosa, y-linked
  • rpy
critical illness polyneuropathy
  • polyneuropathy, critical illness
external ear disease
  • preauricular cyst
inflammatory and toxic neuropathy
- elite association - COSMIC cancer census association via MalaCards
Search POLB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for POLB

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with POLB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for POLB Gene

Publications for POLB Gene

  1. Characterization of DNA polymerase beta splicing variants in gastric cancer: the most frequent exon 2-deleted isoform is a non-coding RNA. (PMID: 19635489) Simonelli V … Dogliotti E (Mutation research 2009) 3 22 44 58
  2. Covalent trapping of human DNA polymerase beta by the oxidative DNA lesion 2-deoxyribonolactone. (PMID: 11805079) DeMott MS … Demple B (The Journal of biological chemistry 2002) 3 4 22 58
  3. A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. (PMID: 8841119) Pelletier H … Kraut J (Biochemistry 1996) 3 4 22 58
  4. TCRP1 contributes to cisplatin resistance by preventing Pol β degradation in lung cancer cells. (PMID: 25260657) Liu X … He Z (Molecular and cellular biochemistry 2015) 3 4 58
  5. Comprehensive screen of genetic variation in DNA repair pathway genes and postmenopausal breast cancer risk. (PMID: 20496165) Monsees GM … Han J (Breast cancer research and treatment 2011) 3 44 58

Products for POLB Gene

Sources for POLB Gene

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