Primpol (primase and DNA directed polymerase) - Rat Genome Database

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Gene: Primpol (primase and DNA directed polymerase) Rattus norvegicus
Analyze
Symbol: Primpol
Name: primase and DNA directed polymerase
RGD ID: 1562119
Description: Predicted to enable chromatin binding activity; nucleotidyltransferase activity; and transition metal ion binding activity. Predicted to be involved in DNA metabolic process; R-loop processing; and response to UV. Predicted to be located in replication fork. Predicted to be active in mitochondrial matrix and nucleus. Human ortholog(s) of this gene implicated in myopia. Orthologous to human PRIMPOL (primase and DNA directed polymerase); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Ccdc111; coiled-coil domain containing 111; LOC361147; primase and polymerase (DNA-directed); RGD1562119; similar to Hypothetical MGC86034
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
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81652,413,894 - 52,450,975 (+)NCBIGRCr8
mRatBN7.21645,681,252 - 45,715,758 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1645,681,326 - 45,715,565 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01648,863,385 - 48,900,409 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1648,863,418 - 48,897,795 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01648,578,483 - 48,615,806 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41648,968,598 - 48,997,032 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1643,684,349 - 43,721,241 (+)NCBICelera
Cytogenetic Map16q11NCBI
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

Biological Process

Cellular Component
mitochondrial matrix  (IBA,ISO)
nucleus  (IBA,ISO)
replication fork  (ISO)

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:24207056   PMID:24240614   PMID:24267451   PMID:24682820   PMID:25746449   PMID:28534480   PMID:29073063   PMID:29608762   PMID:30478192  


Genomics

Comparative Map Data
Primpol
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81652,413,894 - 52,450,975 (+)NCBIGRCr8
mRatBN7.21645,681,252 - 45,715,758 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1645,681,326 - 45,715,565 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01648,863,385 - 48,900,409 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1648,863,418 - 48,897,795 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01648,578,483 - 48,615,806 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41648,968,598 - 48,997,032 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1643,684,349 - 43,721,241 (+)NCBICelera
Cytogenetic Map16q11NCBI
PRIMPOL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384184,649,738 - 184,694,952 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4184,649,667 - 184,694,963 (+)EnsemblGRCh38hg38GRCh38
GRCh374185,570,892 - 185,616,106 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364185,807,896 - 185,853,106 (+)NCBINCBI36Build 36hg18NCBI36
Celera4182,899,431 - 182,944,944 (+)NCBICelera
Cytogenetic Map4q35.1NCBI
HuRef4181,325,094 - 181,369,754 (+)NCBIHuRef
CHM1_14185,547,294 - 185,592,636 (+)NCBICHM1_1
T2T-CHM13v2.04187,993,422 - 188,038,703 (+)NCBIT2T-CHM13v2.0
Primpol
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39847,028,614 - 47,070,282 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl847,028,629 - 47,070,247 (-)EnsemblGRCm39 Ensembl
GRCm38846,575,579 - 46,617,227 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl846,575,594 - 46,617,212 (-)EnsemblGRCm38mm10GRCm38
MGSCv37847,660,948 - 47,702,554 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36848,074,411 - 48,116,017 (-)NCBIMGSCv36mm8
Celera849,258,170 - 49,299,782 (-)NCBICelera
Cytogenetic Map8B1.1NCBI
cM Map826.39NCBI
Primpol
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540324,279,122 - 24,303,682 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540324,278,727 - 24,307,312 (-)NCBIChiLan1.0ChiLan1.0
PRIMPOL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23182,373,488 - 182,419,142 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14182,735,279 - 182,780,912 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04176,815,122 - 176,860,682 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14189,040,324 - 189,085,335 (+)NCBIpanpan1.1PanPan1.1panPan2
PRIMPOL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11645,861,244 - 45,920,183 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1645,856,042 - 45,918,761 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1646,354,134 - 46,412,999 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01648,076,787 - 48,135,773 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1648,070,581 - 48,135,753 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11646,042,091 - 46,100,919 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01646,656,725 - 46,715,297 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01646,789,466 - 46,848,402 (-)NCBIUU_Cfam_GSD_1.0
Primpol
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494333,412,746 - 33,573,466 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365544,534,970 - 4,569,549 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365544,536,246 - 4,571,000 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRIMPOL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1545,709,710 - 45,819,919 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11545,764,261 - 45,851,052 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21552,463,747 - 52,518,946 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRIMPOL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17130,611,105 - 130,653,614 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl7130,611,133 - 130,657,450 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037110,862,699 - 110,906,635 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Primpol
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476915,425,234 - 15,453,613 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476915,414,510 - 15,451,711 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Primpol
182 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:100
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000029868
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
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163195152060148445Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
631833Sach2Saccharin preference QTL 240.01consumption behavior trait (VT:0002069)calculated saccharin drink intake rate (CMO:0001613)164302484250166018Rat

Markers in Region
RH143013  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21645,705,556 - 45,705,688 (+)MAPPERmRatBN7.2
Rnor_6.01648,887,770 - 48,887,901NCBIRnor6.0
Rnor_5.01648,603,168 - 48,603,299UniSTSRnor5.0
RGSC_v3.41648,987,198 - 48,987,329UniSTSRGSC3.4
Celera1643,708,602 - 43,708,733UniSTS
RH 3.4 Map16446.8UniSTS
Cytogenetic Map16q11UniSTS


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 2 16 2 10 23
Low 3 42 47 39 3 39 8 8 74 25 18 11 8
Below cutoff 1 3

Sequence


RefSeq Acc Id: ENSRNOT00000029868   ⟹   ENSRNOP00000030019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1645,681,326 - 45,715,565 (+)Ensembl
Rnor_6.0 Ensembl1648,863,418 - 48,897,795 (+)Ensembl
RefSeq Acc Id: XM_006253167   ⟹   XP_006253229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81652,413,903 - 52,450,975 (+)NCBI
mRatBN7.21645,681,254 - 45,715,758 (+)NCBI
Rnor_6.01648,863,385 - 48,900,409 (+)NCBI
Rnor_5.01648,578,483 - 48,615,806 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094879   ⟹   XP_038950807
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81652,413,942 - 52,450,975 (+)NCBI
mRatBN7.21645,681,316 - 45,715,758 (+)NCBI
RefSeq Acc Id: XM_039094880   ⟹   XP_038950808
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81652,413,942 - 52,450,975 (+)NCBI
mRatBN7.21645,681,316 - 45,715,758 (+)NCBI
RefSeq Acc Id: XM_063275860   ⟹   XP_063131930
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81652,418,058 - 52,450,975 (+)NCBI
RefSeq Acc Id: XM_341433   ⟹   XP_341434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81652,413,904 - 52,450,975 (+)NCBI
mRatBN7.21645,681,254 - 45,715,758 (+)NCBI
Rnor_6.01648,863,385 - 48,900,409 (+)NCBI
Rnor_5.01648,578,483 - 48,615,806 (+)NCBI
RGSC_v3.41648,968,598 - 48,997,032 (+)RGD
Sequence:
RefSeq Acc Id: XR_005494696
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81652,413,894 - 52,442,696 (+)NCBI
mRatBN7.21645,681,252 - 45,710,069 (+)NCBI
RefSeq Acc Id: XP_341434   ⟸   XM_341433
- UniProtKB: D4A8C0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253229   ⟸   XM_006253167
- UniProtKB: D4A8C0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030019   ⟸   ENSRNOT00000029868
RefSeq Acc Id: XP_038950808   ⟸   XM_039094880
- UniProtKB: D4A8C0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038950807   ⟸   XM_039094879
- UniProtKB: D4A8C0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063131930   ⟸   XM_063275860

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8C0-F1-model_v2 AlphaFold D4A8C0 1-534 view protein structure

Transcriptome

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

Promoters
RGD ID:13700102
Promoter ID:EPDNEW_R10620
Type:multiple initiation site
Name:Primpol_1
Description:primase and DNA directed polymerase
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_6.01648,863,425 - 48,863,485EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562119 AgrOrtholog
BioCyc Gene G2FUF-11359 BioCyc
Ensembl Genes ENSRNOG00000022320 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029868.7 UniProtKB/TrEMBL
InterPro DNA_primase_S UniProtKB/TrEMBL
  PRIMPOL UniProtKB/TrEMBL
KEGG Report rno:361147 UniProtKB/TrEMBL
NCBI Gene 361147 ENTREZGENE
PANTHER DNA-DIRECTED PRIMASE/POLYMERASE PROTEIN UniProtKB/TrEMBL
  PTHR31399 UniProtKB/TrEMBL
Pfam DNA_primase_S UniProtKB/TrEMBL
  Herpes_UL52 UniProtKB/TrEMBL
PhenoGen Primpol PhenoGen
RatGTEx ENSRNOG00000022320 RatGTEx
UniProt D4A8C0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-13 Primpol  primase and DNA directed polymerase  Primpol  primase and polymerase (DNA-directed)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-11-13 Primpol  primase and polymerase (DNA-directed)  Ccdc111  coiled-coil domain containing 111  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Ccdc111  coiled-coil domain containing 111  RGD1562119_predicted  similar to Hypothetical MGC86034 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562119_predicted  similar to Hypothetical MGC86034 (predicted)  LOC361147  similar to Hypothetical MGC86034  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC361147  similar to Hypothetical MGC86034      Symbol and Name status set to provisional 70820 PROVISIONAL