Polm (DNA polymerase mu) - Rat Genome Database
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Gene: Polm (DNA polymerase mu) Rattus norvegicus
Analyze
Symbol: Polm
Name: DNA polymerase mu
RGD ID: 1308247
Description: Predicted to have DNA-directed DNA polymerase activity. Predicted to be involved in B cell differentiation; double-strand break repair via nonhomologous end joining; and somatic hypermutation of immunoglobulin genes. Predicted to localize to nucleus. Orthologous to human POLM (DNA polymerase mu); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; 7,12-dimethyltetraphene; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA-directed DNA polymerase mu; DNA-directed DNA/RNA polymerase mu; LOC289757; polymerase (DNA directed), mu; polymerase (DNA) mu
Orthologs:
Homo sapiens (human) : POLM (DNA polymerase mu)  HGNC  Alliance
Mus musculus (house mouse) : Polm (polymerase (DNA directed), mu)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Polm (DNA polymerase mu)
Pan paniscus (bonobo/pygmy chimpanzee) : POLM (DNA polymerase mu)
Canis lupus familiaris (dog) : LOC100685589 (DNA-directed DNA/RNA polymerase mu-like)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Polm (DNA polymerase mu)
Sus scrofa (pig) : POLM (DNA polymerase mu)
Chlorocebus sabaeus (African green monkey) : POLM (DNA polymerase mu)
Heterocephalus glaber (naked mole-rat) : Polm (DNA polymerase mu)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01486,069,378 - 86,079,327 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,069,016 - 86,078,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01486,761,187 - 86,771,152 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,491,716 - 86,501,294 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11486,510,861 - 86,520,439 (-)NCBI
Celera1479,591,849 - 79,601,427 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:15789338  


Genomics

Comparative Map Data
Polm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01486,069,378 - 86,079,327 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,069,016 - 86,078,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01486,761,187 - 86,771,152 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,491,716 - 86,501,294 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11486,510,861 - 86,520,439 (-)NCBI
Celera1479,591,849 - 79,601,427 (-)NCBICelera
Cytogenetic Map14q21NCBI
POLM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl744,072,062 - 44,082,530 (-)EnsemblGRCh38hg38GRCh38
GRCh38744,072,062 - 44,082,530 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37744,111,846 - 44,122,129 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,078,371 - 44,088,607 (-)NCBINCBI36hg18NCBI36
Build 34743,885,085 - 43,895,322NCBI
Celera744,209,796 - 44,220,079 (-)NCBI
Cytogenetic Map7p13NCBI
HuRef743,997,135 - 44,007,419 (-)NCBIHuRef
CHM1_1744,115,540 - 44,126,017 (-)NCBICHM1_1
CRA_TCAGchr7v2744,151,339 - 44,161,618 (-)NCBI
Polm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39115,777,860 - 5,788,831 (-)NCBI
GRCm38115,827,860 - 5,838,832 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl115,827,860 - 5,838,016 (-)EnsemblGRCm38mm10GRCm38
MGSCv37115,727,863 - 5,738,019 (-)NCBIGRCm37mm9NCBIm37
MGSCv36115,727,863 - 5,737,763 (-)NCBImm8
Celera116,319,454 - 6,329,603 (-)NCBICelera
Cytogenetic Map11A1NCBI
Polm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554567,886,291 - 7,895,085 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554567,886,182 - 7,893,800 (+)NCBIChiLan1.0ChiLan1.0
POLM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1744,852,594 - 44,862,816 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0744,785,797 - 44,796,624 (-)NCBIMhudiblu_PPA_v0panPan3
LOC100685589
(Canis lupus familiaris - dog)
No map positions available.
Polm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647819,032,995 - 19,042,400 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11851,077,845 - 51,091,354 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21855,971,589 - 55,982,831 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POLM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2114,586,164 - 14,599,248 (+)Ensembl
ChlSab1.12114,585,912 - 14,596,127 (+)NCBI
Polm
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247407,932,179 - 7,939,133 (+)NCBI

Position Markers
RH130863  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01486,069,426 - 86,069,608NCBIRnor6.0
Rnor_5.01486,761,235 - 86,761,417UniSTSRnor5.0
RGSC_v3.41486,491,759 - 86,491,941UniSTSRGSC3.4
Celera1479,591,892 - 79,592,074UniSTS
Cytogenetic Map14q21UniSTS
RH 3.4 Map14574.6UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)1485307663106641756Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:302
Count of miRNA genes:190
Interacting mature miRNAs:226
Transcripts:ENSRNOT00000018319
Prediction methods:Microtar, Miranda, Rnahybrid, 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 2 4 7 4 7 3
Low 1 39 57 41 12 41 8 11 70 35 34 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018319   ⟹   ENSRNOP00000018320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1486,069,016 - 86,078,954 (-)Ensembl
RefSeq Acc Id: NM_001011912   ⟹   NP_001011912
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01486,069,383 - 86,078,959 (-)NCBI
Rnor_5.01486,761,187 - 86,771,152 (-)NCBI
RGSC_v3.41486,491,716 - 86,501,294 (-)RGD
Celera1479,591,849 - 79,601,427 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251211   ⟹   XP_006251273
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01486,069,378 - 86,079,326 (-)NCBI
Rnor_5.01486,761,187 - 86,771,152 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251212   ⟹   XP_006251274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01486,069,378 - 86,079,324 (-)NCBI
Rnor_5.01486,761,187 - 86,771,152 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251213   ⟹   XP_006251275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01486,069,378 - 86,079,327 (-)NCBI
Rnor_5.01486,761,187 - 86,771,152 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251214   ⟹   XP_006251276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01486,069,378 - 86,078,605 (-)NCBI
Rnor_5.01486,761,187 - 86,771,152 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001011912   ⟸   NM_001011912
- UniProtKB: Q66HH0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251273   ⟸   XM_006251211
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251274   ⟸   XM_006251212
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006251275   ⟸   XM_006251213
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006251276   ⟸   XM_006251214
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000018320   ⟸   ENSRNOT00000018319
Protein Domains
BRCT

Transcriptome

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

Promoters
RGD ID:13699463
Promoter ID:EPDNEW_R9987
Type:multiple initiation site
Name:Polm_1
Description:DNA polymerase mu
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_6.01486,078,968 - 86,079,028EPDNEW

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)
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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/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
SBN/Ygl (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: 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)
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
SHRSP/Gcrc (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
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)
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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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 86763404 86763405 G A snv SHR/NCrlPrin (KNAW), LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), SHRSP/Gcrc (KNAW), SHR/OlaIpcvPrin (KNAW), LE/Stm (KyushuU), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW)
14 86769111 86769112 C T snv WKY/NHsd (KNAW), SHR/OlaIpcvPrin (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), SHR/NCrlPrin (KNAW), WKY/NCrl (KNAW), SHR/NHsd (KNAW), SHRSP/Gcrc (KNAW), SHR/OlaIpcv (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 86071595 86071596 G A snv WKY/Gcrc (RGD), WKY/N (MCW), WKY/NCrl (RGD), SHR/NHsd (RGD), LE/Stm (RGD)
14 86077302 86077303 C T snv WKY/Gcrc (RGD), WKY/NCrl (RGD), WKY/NHsd (RGD), SHR/NHsd (RGD), WKY/N (MCW), SHRSP/Gcrc (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 86493931 86493932 G A snv SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), LE/Stm (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), WKY/NCrl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), LE/Stm (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308247 AgrOrtholog
Ensembl Genes ENSRNOG00000013647 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018320 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018319 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.110 UniProtKB/TrEMBL
  3.30.210.10 UniProtKB/TrEMBL
  3.30.460.10 UniProtKB/TrEMBL
  3.40.50.10190 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7096894 IMAGE-MGC_LOAD
InterPro BRCT UniProtKB/TrEMBL
  BRCT_dom_sf UniProtKB/TrEMBL
  DNA-dir_DNA_pol_X UniProtKB/TrEMBL
  DNA-dir_DNA_pol_X_beta-like_N UniProtKB/TrEMBL
  DNA-dir_DNA_pol_X_C UniProtKB/TrEMBL
  DNA/RNApol_mu UniProtKB/TrEMBL
  DNA_nucleotidylexotransferase UniProtKB/TrEMBL
  DNA_pol-X_BS UniProtKB/TrEMBL
  DNA_pol_B_palm_palm UniProtKB/TrEMBL
  DNA_pol_lambd_fingers_domain UniProtKB/TrEMBL
  DNA_Pol_thumb_sf UniProtKB/TrEMBL
  DNA_pol_X_lyase_dom UniProtKB/TrEMBL
  NT_sf UniProtKB/TrEMBL
  PolB_thumb UniProtKB/TrEMBL
KEGG Report rno:289757 UniProtKB/TrEMBL
MGC_CLONE MGC:93702 IMAGE-MGC_LOAD
NCBI Gene 289757 ENTREZGENE
Pfam DNA_pol_B_palm UniProtKB/TrEMBL
  DNA_pol_B_thumb UniProtKB/TrEMBL
  DNA_pol_lambd_f UniProtKB/TrEMBL
  HHH_8 UniProtKB/TrEMBL
PhenoGen Polm PhenoGen
PIRSF DNA_NT UniProtKB/TrEMBL
  DNApol_mu UniProtKB/TrEMBL
PRINTS DNAPOLX UniProtKB/TrEMBL
  DNAPOLXTDT UniProtKB/TrEMBL
PROSITE BRCT UniProtKB/TrEMBL
  DNA_POLYMERASE_X UniProtKB/TrEMBL
SMART POLXc UniProtKB/TrEMBL
Superfamily-SCOP BRCT UniProtKB/TrEMBL
  DNApol_B_N_like UniProtKB/TrEMBL
  SSF81301 UniProtKB/TrEMBL
UniGene Rn.16022 ENTREZGENE
UniProt Q66HH0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polm  DNA polymerase mu  Polm  polymerase (DNA) mu  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-09 Polm  polymerase (DNA) mu  Polm  polymerase (DNA directed), mu  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Polm  polymerase (DNA directed), mu  Polm_predicted  polymerase (DNA directed), mu (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Polm_predicted  polymerase (DNA directed), mu (predicted)      Symbol and Name status set to approved 70820 APPROVED