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 enable DNA-directed DNA polymerase activity and cyclin binding activity. Predicted to be involved in double-strand break repair via homologous recombination; interstrand cross-link repair; and translesion synthesis. Predicted to be located in nucleoplasm. Orthologous to human POLN (DNA polymerase nu); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21476,579,983 - 76,752,460 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1476,580,546 - 76,752,463 (+)EnsemblmRatBN7.2 Ensembl
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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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
mRatBN7.21476,579,983 - 76,752,460 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1476,580,546 - 76,752,463 (+)EnsemblmRatBN7.2 Ensembl
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
GRCh3842,071,918 - 2,242,121 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl42,071,918 - 2,242,121 (-)EnsemblGRCh38hg38GRCh38
GRCh3742,073,645 - 2,243,848 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3642,043,443 - 2,200,756 (-)NCBINCBI36Build 36hg18NCBI36
Build 3442,040,875 - 2,198,189NCBI
Celera41,985,702 - 2,143,306 (-)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef42,014,374 - 2,171,947 (-)NCBIHuRef
CHM1_142,072,213 - 2,229,450 (-)NCBICHM1_1
T2T-CHM13v2.042,070,398 - 2,240,896 (-)NCBIT2T-CHM13v2.0
Poln
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39534,164,523 - 34,326,870 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl534,164,523 - 34,326,792 (-)EnsemblGRCm39 Ensembl
GRCm38534,007,179 - 34,169,526 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl534,007,179 - 34,169,448 (-)EnsemblGRCm38mm10GRCm38
MGSCv37534,349,847 - 34,512,097 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36534,324,055 - 34,486,305 (-)NCBIMGSCv36mm8
Celera531,476,932 - 31,640,050 (-)NCBICelera
Cytogenetic Map5B2NCBI
cM Map517.83NCBI
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
NHGRI_mPanPan1-v232,404,778 - 2,575,828 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan142,341,304 - 2,512,246 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v042,214,154 - 2,385,094 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.142,122,309 - 2,292,795 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl42,122,309 - 2,292,431 (-)Ensemblpanpan1.1panPan2
POLN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1361,946,295 - 62,104,112 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl361,962,193 - 62,102,264 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha364,465,228 - 64,620,444 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0362,421,614 - 62,578,083 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl362,421,579 - 62,577,883 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1361,915,440 - 62,070,656 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0362,118,175 - 62,274,316 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0362,478,086 - 62,634,319 (+)NCBIUU_Cfam_GSD_1.0
Poln
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528567,597,931 - 67,668,267 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647721,268,244 - 21,396,256 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647721,268,236 - 21,396,526 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl81,073,889 - 1,197,086 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12746,523,052 - 46,694,474 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660512,893,413 - 3,061,528 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Poln
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475525,330,001 - 25,464,389 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475525,316,590 - 25,464,048 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Poln
1042 total Variants
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.


QTLs in Region (mRatBN7.2)
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)141103062295876975Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat


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


RefSeq Acc Id: ENSRNOT00000029784   ⟹   ENSRNOP00000034638
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1481,858,737 - 82,037,747 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000058067   ⟹   ENSRNOP00000054875
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1481,858,743 - 82,037,747 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000058068   ⟹   ENSRNOP00000054876
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1481,858,737 - 82,037,747 (+)Ensembl
RefSeq Acc Id: XM_039092835   ⟹   XP_038948763
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,599,421 - 76,752,460 (+)NCBI
RefSeq Acc Id: XM_039092836   ⟹   XP_038948764
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,579,983 - 76,752,460 (+)NCBI
RefSeq Acc Id: XM_039092837   ⟹   XP_038948765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,579,983 - 76,752,460 (+)NCBI
RefSeq Acc Id: XM_039092838   ⟹   XP_038948766
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,627,739 - 76,752,460 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001415859 (Get FASTA)   NCBI Sequence Viewer  
  NP_001415860 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034638.6
  ENSRNOP00000054875.4
  ENSRNOP00000054876.3
RefSeq Acc Id: ENSRNOP00000054876   ⟸   ENSRNOT00000058068
RefSeq Acc Id: ENSRNOP00000054875   ⟸   ENSRNOT00000058067
RefSeq Acc Id: ENSRNOP00000034638   ⟸   ENSRNOT00000029784
RefSeq Acc Id: XP_038948764   ⟸   XM_039092836
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948765   ⟸   XM_039092837
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948763   ⟸   XM_039092835
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948766   ⟸   XM_039092838
- Peptide Label: isoform X2
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LWX6-F1-model_v2 AlphaFold F1LWX6 1-862 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:7675413 AgrOrtholog
BioCyc Gene G2FUF-15280 BioCyc
Ensembl Genes ENSRNOG00000027929 Ensembl
  ENSRNOG00000069005 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029784.8 UniProtKB/TrEMBL
  ENSRNOT00000058067.4 UniProtKB/TrEMBL
  ENSRNOT00000058068.6 UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.10 UniProtKB/TrEMBL
  3.30.70.370 UniProtKB/TrEMBL
  5' to 3' exonuclease, C-terminal subdomain 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
  HAUS3 UniProtKB/TrEMBL
  HAUS3_N UniProtKB/TrEMBL
  RNaseH_sf UniProtKB/TrEMBL
NCBI Gene LOC102555079 ENTREZGENE
PANTHER DNA POLYMERASE NU UniProtKB/TrEMBL
  PTHR10133 UniProtKB/TrEMBL
Pfam DNA_pol_A UniProtKB/TrEMBL
  DNA_pol_P_Exo UniProtKB/TrEMBL
  HAUS-augmin3 UniProtKB/TrEMBL
PhenoGen Poln PhenoGen
PRINTS DNAPOLI UniProtKB/TrEMBL
  HAUSAUGMINL3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027929 RatGTEx
  ENSRNOG00000069005 RatGTEx
SMART POLAc UniProtKB/TrEMBL
Superfamily-SCOP SSF56672 UniProtKB/TrEMBL
UniProt F1LWX6_RAT 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