Poln (DNA polymerase nu) - Rat Genome Database
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Gene: Poln (DNA polymerase nu) Rattus norvegicus
Analyze
Symbol: Poln
Name: DNA polymerase nu
RGD ID: 7675413
Description: Predicted to have DNA-directed DNA polymerase activity and cyclin binding activity. Predicted to be involved in DNA repair and DNA-dependent DNA replication. Predicted to localize to cytoplasm and nucleoplasm. Orthologous to human POLN (DNA polymerase nu); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: DNA polymerase N; DNA polymerase nu-like; LOC102555079; polymerase (DNA directed) nu; polymerase (DNA) nu
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
Rnor_6.01481,837,764 - 82,037,999 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1481,858,737 - 82,037,747 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01482,523,719 - 82,722,239 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1475,524,689 - 75,676,034 (+)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
nucleolus  (ISO)
nucleoplasm  (IEA,ISO)
nucleus  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:12794064   PMID:17118716   PMID:19908865   PMID:19995904   PMID:20102227  


Genomics

Comparative Map Data
Poln
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01481,837,764 - 82,037,999 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1481,858,737 - 82,037,747 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01482,523,719 - 82,722,239 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1475,524,689 - 75,676,034 (+)NCBICelera
Cytogenetic Map14q21NCBI
POLN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl42,071,918 - 2,242,121 (-)EnsemblGRCh38hg38GRCh38
GRCh3842,071,918 - 2,242,121 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3742,073,645 - 2,243,848 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3642,043,443 - 2,200,756 (-)NCBINCBI36hg18NCBI36
Build 3442,040,875 - 2,198,189NCBI
Celera41,985,702 - 2,143,306 (-)NCBI
Cytogenetic Map4p16.3NCBI
HuRef42,014,374 - 2,171,947 (-)NCBIHuRef
CHM1_142,072,253 - 2,242,382 (-)NCBICHM1_1
Poln
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39534,164,523 - 34,326,870 (-)NCBIGRCm39mm39
GRCm38534,007,179 - 34,169,526 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl534,007,179 - 34,169,448 (-)EnsemblGRCm38mm10GRCm38
MGSCv37534,349,847 - 34,512,097 (-)NCBIGRCm37mm9NCBIm37
MGSCv36534,324,055 - 34,486,305 (-)NCBImm8
Celera531,476,932 - 31,640,050 (-)NCBICelera
Cytogenetic Map5B2NCBI
Poln
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555141,215,131 - 1,329,024 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555141,214,867 - 1,342,172 (-)NCBIChiLan1.0ChiLan1.0
POLN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.142,122,309 - 2,292,795 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl42,122,309 - 2,292,431 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v042,214,154 - 2,385,094 (-)NCBIMhudiblu_PPA_v0panPan3
POLN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl361,962,193 - 62,102,264 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1361,946,295 - 62,104,112 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Poln
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647721,268,236 - 21,396,526 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl81,069,054 - 1,198,445 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.181,073,337 - 1,198,538 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28526,974 - 609,939 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POLN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12746,523,052 - 46,694,474 (+)NCBI
Poln
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475525,316,590 - 25,464,048 (+)NCBI


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
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:283
Count of miRNA genes:107
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000029784, ENSRNOT00000058067, ENSRNOT00000058068
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 10
Low 16 18 6 17 6 74 21 31 8
Below cutoff 3 25 36 32 2 32 8 10 14 3 8

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006221810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07015859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07072416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000029784   ⟹   ENSRNOP00000034638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1481,858,737 - 82,037,747 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000058067   ⟹   ENSRNOP00000054875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1481,858,743 - 82,037,747 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000058068   ⟹   ENSRNOP00000054876
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1481,858,737 - 82,037,747 (+)Ensembl
RefSeq Acc Id: XM_006221810   ⟹   XP_006221872
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1475,524,689 - 75,676,034 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251412   ⟹   XP_006251474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01481,858,285 - 82,037,999 (+)NCBI
Rnor_5.01482,523,719 - 82,722,239 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251414   ⟹   XP_006251476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01481,858,285 - 82,035,571 (+)NCBI
Rnor_5.01482,523,719 - 82,722,239 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770383   ⟹   XP_008768605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01481,837,764 - 82,036,322 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770384   ⟹   XP_008768606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01481,858,285 - 82,036,322 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599500   ⟹   XP_017454989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01481,858,285 - 82,037,999 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604820   ⟹   XP_017460309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1475,524,689 - 75,676,034 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604821   ⟹   XP_017460310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1475,524,689 - 75,673,606 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_006221872   ⟸   XM_006221810
- Peptide Label: isoform X3
- UniProtKB: F1LWX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251474   ⟸   XM_006251412
- Peptide Label: isoform X3
- UniProtKB: F1LWX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251476   ⟸   XM_006251414
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008768605   ⟸   XM_008770383
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768606   ⟸   XM_008770384
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017460309   ⟸   XM_017604820
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017460310   ⟸   XM_017604821
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017454989   ⟸   XM_017599500
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000054876   ⟸   ENSRNOT00000058068
RefSeq Acc Id: ENSRNOP00000054875   ⟸   ENSRNOT00000058067
RefSeq Acc Id: ENSRNOP00000034638   ⟸   ENSRNOT00000029784
Protein Domains
POLAc

Transcriptome

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


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)
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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)
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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
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)
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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 82524234 82524235 A T snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)
14 82524322 82524323 G A snv DOB/Oda (KyushuU)
14 82524542 82524543 C T snv SR/JrHsd (MCW)
14 82529057 82529058 A G snv SR/JrHsd (MCW)
14 82564080 82564081 C A snv DOB/Oda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 81839220 81839221 C T snv SR/JrHsd (MCW)
14 81843735 81843736 A G snv SR/JrHsd (MCW)
14 81878223 81878224 A G snv CDS, WKY/NHsd (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), MHS/Gib (RGD), WKY/N (MCW), MR/N (MCW)
14 81878568 81878569 G A snv WKY/Gcrc (RGD), SHR/NHsd (RGD), WKY/NCrl (RGD), MHS/Gib (RGD), WKY/N (MCW), WKY/NHsd (RGD), SHRSP/Gcrc (RGD), CDS


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:7675413 AgrOrtholog
Ensembl Genes ENSRNOG00000027929 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034638 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000054875 UniProtKB/TrEMBL
  ENSRNOP00000054876 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029784 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000058067 UniProtKB/TrEMBL
  ENSRNOT00000058068 UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.10 UniProtKB/TrEMBL
InterPro DNA-dir_DNA_pol_A_palm_dom UniProtKB/TrEMBL
  DNA/RNA_pol_sf UniProtKB/TrEMBL
  DNA_pol_P_Exo UniProtKB/TrEMBL
  DNA_polymerase_A UniProtKB/TrEMBL
  RNaseH_sf UniProtKB/TrEMBL
KEGG Report rno:102555079 UniProtKB/TrEMBL
NCBI Gene LOC102555079 ENTREZGENE
PANTHER PTHR10133 UniProtKB/TrEMBL
Pfam DNA_pol_A UniProtKB/TrEMBL
  DNA_pol_P_Exo UniProtKB/TrEMBL
PhenoGen Poln PhenoGen
PRINTS DNAPOLI UniProtKB/TrEMBL
SMART POLAc UniProtKB/TrEMBL
Superfamily-SCOP SSF56672 UniProtKB/TrEMBL
UniProt F1LWX6 ENTREZGENE, UniProtKB/TrEMBL
  F1M178_RAT UniProtKB/TrEMBL
  F1M179_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Poln  DNA polymerase nu  Poln  polymerase (DNA) nu  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-09 Poln  polymerase (DNA) nu  Poln  polymerase (DNA directed) nu  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-01-02 Poln  polymerase (DNA directed) nu  LOC102555079  DNA polymerase nu-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102555079  DNA polymerase nu-like      Symbol and Name status set to provisional 70820 PROVISIONAL