Polq (DNA polymerase theta) - Rat Genome Database

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Gene: Polq (DNA polymerase theta) Rattus norvegicus
Analyze
Symbol: Polq
Name: DNA polymerase theta
RGD ID: 1309795
Description: Predicted to enable catalytic activity, acting on DNA; chromatin binding activity; and identical protein binding activity. Predicted to be involved in several processes, including DNA repair; negative regulation of double-strand break repair via homologous recombination; and somatic hypermutation of immunoglobulin genes. Predicted to act upstream of or within DNA repair. Predicted to be located in Golgi apparatus; cytosol; and nucleoplasm. Orthologous to human POLQ (DNA polymerase theta); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC288079; polymerase (DNA directed), theta; polymerase (DNA) theta
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
mRatBN7.21163,673,796 - 63,775,905 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1163,673,816 - 63,775,878 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1172,486,222 - 72,588,279 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01165,148,446 - 65,250,504 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01164,183,460 - 64,286,292 (-)NCBIRnor_WKY
Rnor_6.01166,585,860 - 66,695,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1166,585,881 - 66,695,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01169,680,992 - 69,786,646 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41165,474,661 - 65,577,382 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11165,533,019 - 65,634,858 (-)NCBI
Celera1163,151,051 - 63,249,442 (-)NCBICelera
Cytogenetic Map11q21NCBI
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

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12663541   PMID:14576298   PMID:15542845   PMID:16172387   PMID:16222339   PMID:16890500   PMID:19188258   PMID:22135286   PMID:25642960   PMID:25642963   PMID:25643323   PMID:26636256  


Genomics

Comparative Map Data
Polq
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21163,673,796 - 63,775,905 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1163,673,816 - 63,775,878 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1172,486,222 - 72,588,279 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01165,148,446 - 65,250,504 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01164,183,460 - 64,286,292 (-)NCBIRnor_WKY
Rnor_6.01166,585,860 - 66,695,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1166,585,881 - 66,695,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01169,680,992 - 69,786,646 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41165,474,661 - 65,577,382 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11165,533,019 - 65,634,858 (-)NCBI
Celera1163,151,051 - 63,249,442 (-)NCBICelera
Cytogenetic Map11q21NCBI
POLQ
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383121,431,431 - 121,545,988 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3121,431,431 - 121,545,988 (-)EnsemblGRCh38hg38GRCh38
GRCh373121,150,278 - 121,264,835 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363122,632,963 - 122,747,543 (-)NCBINCBI36Build 36hg18NCBI36
Build 343122,632,970 - 122,747,543NCBI
Celera3119,560,070 - 119,674,301 (-)NCBICelera
Cytogenetic Map3q13.33NCBI
HuRef3118,524,685 - 118,638,983 (-)NCBIHuRef
CHM1_13121,113,983 - 121,228,541 (-)NCBICHM1_1
T2T-CHM13v2.03124,151,355 - 124,265,920 (-)NCBIT2T-CHM13v2.0
Polq
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391636,832,104 - 36,922,321 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1636,832,148 - 36,915,779 (+)EnsemblGRCm39 Ensembl
GRCm381637,011,741 - 37,095,419 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1637,011,786 - 37,095,417 (+)EnsemblGRCm38mm10GRCm38
MGSCv371637,011,872 - 37,095,503 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361636,931,025 - 37,014,636 (+)NCBIMGSCv36mm8
Celera1637,420,971 - 37,504,641 (+)NCBICelera
Cytogenetic Map16B3NCBI
cM Map1626.32NCBI
Polq
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542720,778,952 - 20,894,989 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542720,779,332 - 20,895,094 (-)NCBIChiLan1.0ChiLan1.0
POLQ
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13125,446,829 - 125,558,642 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3125,446,829 - 125,559,283 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03118,535,968 - 118,648,275 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
POLQ
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13324,713,174 - 24,837,113 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3324,714,086 - 24,837,402 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3324,740,603 - 24,864,403 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03324,955,417 - 25,079,364 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3324,955,413 - 25,079,355 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13324,753,758 - 24,877,644 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03324,789,905 - 24,920,067 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03325,352,722 - 25,476,912 (-)NCBIUU_Cfam_GSD_1.0
Polq
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602129,517,678 - 129,617,872 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365367,904,981 - 8,004,199 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365367,904,166 - 8,004,305 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLQ
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13138,978,609 - 139,108,500 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113138,962,634 - 139,108,499 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
POLQ
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12259,336,506 - 59,448,609 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2259,336,842 - 59,448,604 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041106,844,576 - 106,989,077 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Polq
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473126,649,727 - 26,807,222 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473126,649,606 - 26,808,098 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Polq
798 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:92
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000063995
Prediction methods: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
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat

Markers in Region
RH137198  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.039,492,778 - 9,493,079NCBIRnor5.0
RGSC_v3.434,859,269 - 4,859,569UniSTSRGSC3.4
Celera1163,200,736 - 63,200,942UniSTS
Celera34,325,822 - 4,326,122UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map18p12UniSTS


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 8 2 9 2 4 4
Low 3 36 35 28 10 28 3 3 59 24 37 9 3
Below cutoff 7 11 8 8 5 7 11 11 2 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000063995   ⟹   ENSRNOP00000061230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1163,673,816 - 63,775,878 (-)Ensembl
Rnor_6.0 Ensembl1166,585,881 - 66,695,353 (-)Ensembl
RefSeq Acc Id: NM_001105878   ⟹   NP_001099348
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,673,816 - 63,775,878 (-)NCBI
Rnor_6.01166,585,881 - 66,695,353 (-)NCBI
Rnor_5.01169,680,992 - 69,786,646 (-)NCBI
RGSC_v3.41165,474,661 - 65,577,382 (-)RGD
Celera1163,151,051 - 63,249,442 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088124   ⟹   XP_038944052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,673,796 - 63,772,776 (-)NCBI
RefSeq Acc Id: XM_039088125   ⟹   XP_038944053
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,692,446 - 63,775,905 (-)NCBI
RefSeq Acc Id: XM_039088126   ⟹   XP_038944054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,673,796 - 63,720,880 (-)NCBI
RefSeq Acc Id: XM_039088127   ⟹   XP_038944055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,673,796 - 63,720,375 (-)NCBI
RefSeq Acc Id: XR_005491001
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,673,796 - 63,775,905 (-)NCBI
RefSeq Acc Id: XR_005491002
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21163,678,674 - 63,775,905 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099348   ⟸   NM_001105878
- UniProtKB: D4A628 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061230   ⟸   ENSRNOT00000063995
RefSeq Acc Id: XP_038944052   ⟸   XM_039088124
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944054   ⟸   XM_039088126
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944055   ⟸   XM_039088127
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944053   ⟸   XM_039088125
- Peptide Label: isoform X2
Protein Domains
Helicase ATP-binding   Helicase C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A628-F1-model_v2 AlphaFold D4A628 1-2547 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:1309795 AgrOrtholog
BioCyc Gene G2FUF-21250 BioCyc
Ensembl Genes ENSRNOG00000002471 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061230 ENTREZGENE
  ENSRNOP00000061230.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000063995 ENTREZGENE
  ENSRNOT00000063995.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.3380.20 UniProtKB/TrEMBL
  3.30.420.10 UniProtKB/TrEMBL
  3.30.70.370 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
  5' to 3' exonuclease, C-terminal subdomain UniProtKB/TrEMBL
InterPro DNA-dir_DNA_pol_A_CS UniProtKB/TrEMBL
  DNA-dir_DNA_pol_A_palm_dom UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAD/DEAH_N UniProtKB/TrEMBL
  DNA/RNA_pol_sf UniProtKB/TrEMBL
  DNA_polymerase_A UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  HTH_61 UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  RNaseH-like_dom UniProtKB/TrEMBL
  RNaseH_sf UniProtKB/TrEMBL
KEGG Report rno:288079 UniProtKB/TrEMBL
NCBI Gene 288079 ENTREZGENE
PANTHER DNA POLYMERASE THETA UniProtKB/TrEMBL
  PTHR10133 UniProtKB/TrEMBL
Pfam DEAD UniProtKB/TrEMBL
  DNA_pol_A UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  HTH_61 UniProtKB/TrEMBL
PhenoGen Polq PhenoGen
PRINTS DNAPOLI UniProtKB/TrEMBL
PROSITE DNA_POLYMERASE_A UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
  POLAc UniProtKB/TrEMBL
Superfamily-SCOP RNaseH_fold UniProtKB/TrEMBL
  Sec63 N-terminal domain-like UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
  SSF56672 UniProtKB/TrEMBL
UniProt D4A628 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polq  DNA polymerase theta  Polq  polymerase (DNA) theta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-09 Polq  polymerase (DNA) theta  Polq  polymerase (DNA directed), theta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Polq  polymerase (DNA directed), theta   Polq_predicted  polymerase (DNA directed), theta (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Polq_predicted  polymerase (DNA directed), theta (predicted)      Symbol and Name status set to approved 70820 APPROVED