Polb (DNA polymerase beta) - Rat Genome Database

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Gene: Polb (DNA polymerase beta) Rattus norvegicus
Analyze
Symbol: Polb
Name: DNA polymerase beta
RGD ID: 3363
Description: Enables DNA-directed DNA polymerase activity; damaged DNA binding activity; and metal ion binding activity. Involved in several processes, including DNA repair; response to gamma radiation; and response to hyperoxia. Located in nucleus. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human POLB (DNA polymerase beta); PARTICIPATES IN base excision repair pathway; INTERACTS WITH (15Z)-tetracosenoic acid; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,3-dinitrobenzene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA pol beta; DNA-directed DNA polymerase beta; polymerase (DNA directed), beta; polymerase (DNA) beta; polymerase-beta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,379,438 - 69,402,710 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1674,237,001 - 74,260,271 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01674,237,001 - 74,260,272 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01673,869,828 - 73,893,106 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41673,864,702 - 73,888,011 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11673,864,971 - 73,890,378 (+)NCBI
Celera1667,272,411 - 67,295,648 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(15Z)-tetracosenoic acid  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
2'-deoxyadenosine  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
2-nitropropane  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (ISO)
4-hydroperoxycyclophosphamide  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-chlorouracil  (ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
cadmium dichloride  (EXP)
capsaicin  (EXP)
chlorpyrifos  (ISO)
chromium atom  (ISO)
cisplatin  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
diamminedichloroplatinum  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diepoxybutane  (ISO)
dioxygen  (ISO)
ethene  (EXP)
flutamide  (EXP)
folic acid  (ISO)
Honokiol  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
lithocholic acid  (EXP)
methyl methanesulfonate  (ISO)
mitomycin C  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
ochratoxin A  (EXP)
oxirane  (EXP)
paracetamol  (EXP)
paraquat  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
quercetin  (ISO)
rotenone  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
Soman  (EXP)
tamoxifen  (EXP)
taurine  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
transplatin  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Arndt JW, etal., Biochemistry. 2001 May 8;40(18):5368-75.
2. Bhupanapadu Sunkesula SR, etal., Neurochem Res. 2008 Jun;33(6):1117-28. Epub 2008 Feb 8.
3. Cortina MS, etal., Exp Eye Res. 2005 Dec;81(6):742-50. Epub 2005 Jun 24.
4. Cuneo MJ and London RE, Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6805-10. doi: 10.1073/pnas.0914077107. Epub 2010 Mar 29.
5. de Recondo AM and Abadiedebat J, Nucleic Acids Res. 1976 Aug;3(8):1823-37.
6. Gabel SA, etal., Structure. 2014 Dec 2;22(12):1754-63. doi: 10.1016/j.str.2014.09.012. Epub 2014 Nov 13.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Holmes EW, etal., Exp Mol Pathol 2002 Dec;73(3):209-19.
10. Jezewska MJ, etal., J Mol Biol 2001 Nov 9;313(5):977-1002.
11. Jinno S, etal., Mech Ageing Dev. 1995 Nov 24;85(2-3):95-107.
12. Jonason AS, etal., Chromosoma. 2001 Nov;110(6):402-10. Epub 2001 Sep 12.
13. Kaneko T, etal., Mech Ageing Dev. 2002 Sep;123(11):1521-8.
14. Konopinski R, etal., Acta Biochim Pol 1995;42(2):253-8.
15. Kotake M, etal., Mol Cell Endocrinol 2002 Jun 28;192(1-2):127-32.
16. Li D, etal., Int J Cancer. 2007 Apr 15;120(8):1748-54.
17. Li N, etal., DNA Repair (Amst). 2007 Sep 1;6(9):1297-306. Epub 2007 Apr 6.
18. Matsukage A, etal., J Biol Chem 1987 Jul 5;262(19):8960-2.
19. MGD data from the GO Consortium
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Pipeline to import KEGG annotations from KEGG into RGD
22. Prapurna DR and Rao KS, Int J Dev Neurosci. 1997 Feb;15(1):67-73.
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. Servant L, etal., J Biol Chem 2002 Dec 20;277(51):50046-53.
27. Zmudzka BZ, etal., Proc Natl Acad Sci U S A 1986 Jul;83(14):5106-10.
Additional References at PubMed
PMID:1408801   PMID:1420147   PMID:2036395   PMID:2198936   PMID:2404980   PMID:3042024   PMID:3600656   PMID:7516581   PMID:8137427   PMID:8639559   PMID:8841120   PMID:9207062  
PMID:10197627   PMID:10656829   PMID:12477932   PMID:12741854   PMID:14563842   PMID:15177179   PMID:15248749   PMID:15311928   PMID:15485914   PMID:15725623   PMID:15751954   PMID:15794655  
PMID:15901725   PMID:16001017   PMID:16042415   PMID:16600869   PMID:16996474   PMID:19013261   PMID:19231836   PMID:19421423   PMID:19713937   PMID:20108981   PMID:20227374   PMID:21362556  
PMID:22010960   PMID:22219134   PMID:22651551   PMID:23651085   PMID:24388753   PMID:25378300   PMID:27996060   PMID:33087265  


Genomics

Comparative Map Data
Polb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,379,438 - 69,402,710 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1674,237,001 - 74,260,271 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01674,237,001 - 74,260,272 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01673,869,828 - 73,893,106 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41673,864,702 - 73,888,011 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11673,864,971 - 73,890,378 (+)NCBI
Celera1667,272,411 - 67,295,648 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
POLB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl842,338,454 - 42,371,808 (+)EnsemblGRCh38hg38GRCh38
GRCh38842,338,452 - 42,371,810 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37842,196,012 - 42,229,326 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36842,315,187 - 42,348,470 (+)NCBINCBI36hg18NCBI36
Build 34842,315,186 - 42,348,470NCBI
Celera841,140,732 - 41,174,028 (+)NCBI
Cytogenetic Map8p11.21NCBI
HuRef840,719,534 - 40,752,550 (+)NCBIHuRef
CHM1_1842,242,875 - 42,276,239 (+)NCBICHM1_1
Polb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39823,118,135 - 23,143,482 (-)NCBIGRCm39mm39
GRCm39 Ensembl823,118,142 - 23,143,451 (-)Ensembl
GRCm38822,628,119 - 22,653,464 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl822,628,126 - 22,653,435 (-)EnsemblGRCm38mm10GRCm38
MGSCv37823,738,591 - 23,763,909 (-)NCBIGRCm37mm9NCBIm37
MGSCv36824,093,810 - 24,118,959 (-)NCBImm8
Celera824,118,302 - 24,143,706 (-)NCBICelera
Cytogenetic Map8A2NCBI
cM Map811.42NCBI
Polb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955536540,836 - 595,198 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955536542,179 - 595,198 (-)NCBIChiLan1.0ChiLan1.0
POLB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1839,026,991 - 39,060,464 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl839,026,991 - 39,060,464 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0841,582,370 - 41,615,950 (+)NCBIMhudiblu_PPA_v0panPan3
POLB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11623,306,359 - 23,335,352 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1623,306,367 - 23,335,322 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1623,810,815 - 23,839,790 (-)NCBI
ROS_Cfam_1.01625,054,877 - 25,083,907 (-)NCBI
UMICH_Zoey_3.11623,426,046 - 23,455,070 (-)NCBI
UNSW_CanFamBas_1.01623,988,955 - 24,018,019 (-)NCBI
UU_Cfam_GSD_1.01624,039,745 - 24,068,768 (-)NCBI
Polb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494346,368,259 - 46,394,119 (-)NCBI
SpeTri2.0NW_004936785324,655 - 350,496 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1711,356,129 - 11,388,821 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11711,356,130 - 11,388,122 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21713,109,577 - 13,131,807 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POLB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1840,332,165 - 40,368,065 (+)NCBI
ChlSab1.1 Ensembl840,332,208 - 40,372,582 (+)Ensembl
Vero_WHO_p1.0NW_0236660521,415,871 - 1,455,483 (-)NCBI
Polb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624780884,896 - 941,587 (-)NCBI

Position Markers
RH130718  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,404,421 - 69,404,619 (+)MAPPERmRatBN7.2
Rnor_6.01674,261,984 - 74,262,181NCBIRnor6.0
Rnor_5.01673,894,818 - 73,895,015UniSTSRnor5.0
RGSC_v3.41673,889,723 - 73,889,920UniSTSRGSC3.4
Celera1667,297,360 - 67,297,557UniSTS
RH 3.4 Map16664.21UniSTS
Cytogenetic Map16q12.5UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)167321963880115794Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:251
Count of miRNA genes:172
Interacting mature miRNAs:201
Transcripts:ENSRNOT00000026039
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 39 47 31 19 31 8 11 74 35 41 11 8
Low 4 10 10 10
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026039   ⟹   ENSRNOP00000026039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1674,237,001 - 74,260,271 (+)Ensembl
RefSeq Acc Id: NM_017141   ⟹   NP_058837
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,379,438 - 69,402,710 (+)NCBI
Rnor_6.01674,237,001 - 74,260,272 (+)NCBI
Rnor_5.01673,869,828 - 73,893,106 (+)NCBI
RGSC_v3.41673,864,702 - 73,888,011 (+)RGD
Celera1667,272,411 - 67,295,648 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058837   ⟸   NM_017141
- UniProtKB: P06766 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026039   ⟸   ENSRNOT00000026039

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700187
Promoter ID:EPDNEW_R10709
Type:multiple initiation site
Name:Polb_1
Description:DNA polymerase beta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01674,236,962 - 74,237,022EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3363 AgrOrtholog
Ensembl Genes ENSRNOG00000019150 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026039 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026039 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.150.110 UniProtKB/Swiss-Prot
  3.30.210.10 UniProtKB/Swiss-Prot
  3.30.460.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7386894 IMAGE-MGC_LOAD
InterPro DNA-dir_DNA_pol_X UniProtKB/Swiss-Prot
  DNA_pol-X_BS UniProtKB/Swiss-Prot
  DNA_pol_b-like_N UniProtKB/Swiss-Prot
  DNA_pol_B_palm_palm UniProtKB/Swiss-Prot
  DNA_pol_lambd_fingers_domain UniProtKB/Swiss-Prot
  DNA_pol_lamdba_lyase_dom_sf UniProtKB/Swiss-Prot
  DNA_Pol_thumb_sf UniProtKB/Swiss-Prot
  DNA_pol_X UniProtKB/Swiss-Prot
  DNA_pol_X_beta-like UniProtKB/Swiss-Prot
  Hlx-hairpin-Hlx_DNA-bd_motif UniProtKB/Swiss-Prot
  NT_sf UniProtKB/Swiss-Prot
  PolB_thumb UniProtKB/Swiss-Prot
KEGG Report rno:29240 UniProtKB/Swiss-Prot
MGC_CLONE MGC:112619 IMAGE-MGC_LOAD
NCBI Gene 29240 ENTREZGENE
Pfam DNA_pol_B_palm UniProtKB/Swiss-Prot
  DNA_pol_B_thumb UniProtKB/Swiss-Prot
  DNA_pol_lambd_f UniProtKB/Swiss-Prot
  HHH_8 UniProtKB/Swiss-Prot
PharmGKB POLB RGD
PhenoGen Polb PhenoGen
PRINTS DNAPOLX UniProtKB/Swiss-Prot
  DNAPOLXBETA UniProtKB/Swiss-Prot
PROSITE DNA_POLYMERASE_X UniProtKB/Swiss-Prot
SMART HhH1 UniProtKB/Swiss-Prot
  POLXc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47802 UniProtKB/Swiss-Prot
  SSF81301 UniProtKB/Swiss-Prot
UniProt DPOLB_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q64619_RAT UniProtKB/TrEMBL
UniProt Secondary Q4G081 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polb  DNA polymerase beta  Polb  polymerase (DNA) beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-09 Polb  polymerase (DNA) beta  Polb  polymerase (DNA directed), beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Polb  polymerase (DNA directed), beta    DNA polymerase beta  Name updated 1299863 APPROVED
2002-06-10 Polb  DNA polymerase beta      Name updated 70584 APPROVED