Polr2a (RNA polymerase II subunit A) - Rat Genome Database

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Gene: Polr2a (RNA polymerase II subunit A) Rattus norvegicus
Analyze
Symbol: Polr2a
Name: RNA polymerase II subunit A
RGD ID: 1587326
Description: Predicted to enable several functions, including 5'-3' RNA polymerase activity; enzyme binding activity; and metal ion binding activity. Predicted to contribute to RNA polymerase II activity. Involved in cellular response to oxygen levels and response to organic cyclic compound. Predicted to be located in nucleoplasm. Predicted to be part of Prp19 complex; RNA polymerase II, core complex; and euchromatin. Orthologous to human POLR2A (RNA polymerase II subunit A); PARTICIPATES IN RNA polymerase II transcription pathway; Huntington's disease pathway; purine metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA-directed RNA polymerase II subunit RPB1; Polr2a_mapped; Polymerase (RNA II (DNA directed), large polypeptide; polymerase (RNA) II (DNA directed) polypeptide A; polymerase (RNA) II (DNA directed) polypeptide A (mapped); polymerase (RNA) II (DNA directed) polypeptide A, 220kDa; polymerase (RNA) II subunit A; Rpo2-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81054,951,162 - 54,977,179 (-)NCBIGRCr8
mRatBN7.21054,452,438 - 54,478,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01056,339,277 - 56,364,888 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1056,339,284 - 56,365,084 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01056,084,677 - 56,110,778 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41056,552,872 - 56,579,172 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1053,606,814 - 53,632,373 (-)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,2-naphthoquinone  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-phenylbutyric acid  (ISO)
7,12-dimethyltetraphene  (ISO)
acetylsalicylic acid  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
alpha-amanitin  (ISO)
alvocidib  (ISO)
aristolochic acid A  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
Benzo[ghi]perylene  (ISO)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
Brodifacoum  (EXP)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
choline  (ISO)
clobetasol  (ISO)
coumarin  (ISO)
decabromodiphenyl ether  (ISO)
deferasirox  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
disodium selenite  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
fenthion  (ISO)
folic acid  (ISO)
formaldehyde  (EXP,ISO)
FR900359  (ISO)
gentamycin  (EXP)
ivermectin  (ISO)
L-methionine  (ISO)
leflunomide  (ISO)
methidathion  (ISO)
methotrexate  (ISO)
miconazole  (ISO)
N(4)-hydroxycytidine  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-[2-(methylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel sulfate  (ISO)
okadaic acid  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
tetracycline  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
tungsten  (ISO)
urethane  (ISO)
versicolorin A  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis. Becanovic K, etal., Hum Mol Genet. 2010 Apr 15;19(8):1438-52. doi: 10.1093/hmg/ddq018. Epub 2010 Jan 20.
2. The effect of aryl hydrocarbon receptor ligands on the expression of polymerase (DNA directed) kappa (Polkappa), polymerase RNA II (DNA directed) polypeptide A (PolR2a), CYP1B1 and CYP1A1 genes in rat liver. Brauze D and Rawluszko AA, Environ Toxicol Pharmacol. 2012 Nov;34(3):819-25. doi: 10.1016/j.etap.2012.09.004. Epub 2012 Sep 16.
3. Per-unit-living tissue normalization of real-time RT-PCR data in ischemic rat hearts. Ellefsen S, etal., Physiol Genomics. 2012 Jun 15;44(12):651-6. doi: 10.1152/physiolgenomics.00004.2012. Epub 2012 Apr 24.
4. 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.
5. Intermittent hypoxia regulates RNA polymerase II in hippocampus and prefrontal cortex. Ignacak ML, etal., Neuroscience. 2009 Feb 18;158(4):1436-45. doi: 10.1016/j.neuroscience.2008.11.025. Epub 2008 Nov 21.
6. TFIIB-related factors in RNA polymerase I transcription. Knutson BA and Hahn S, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):265-73. doi: 10.1016/j.bbagrm.2012.08.003. Epub 2012 Aug 30.
7. von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a proline hydroxylation motif and targets it for ubiquitination. Kuznetsova AV, etal., Proc Natl Acad Sci U S A 2003 Mar 4;100(5):2706-11. Epub 2003 Feb 25.
8. RNA polymerase II large subunit is cleaved by caspases during DNA damage-induced apoptosis. Lu Y, etal., Biochem Biophys Res Commun 2002 Aug 30;296(4):954-61.
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:9268387   PMID:9852112   PMID:14580349   PMID:15601870   PMID:15607978   PMID:15992770   PMID:16109376   PMID:17996703   PMID:21536736   PMID:22658674   PMID:22681889   PMID:22723415  
PMID:24441171   PMID:26346254   PMID:26700805   PMID:28076779  


Genomics

Comparative Map Data
Polr2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81054,951,162 - 54,977,179 (-)NCBIGRCr8
mRatBN7.21054,452,438 - 54,478,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01056,339,277 - 56,364,888 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1056,339,284 - 56,365,084 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01056,084,677 - 56,110,778 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41056,552,872 - 56,579,172 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1053,606,814 - 53,632,373 (-)NCBICelera
Cytogenetic Map10q24NCBI
POLR2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38177,484,366 - 7,514,616 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl177,484,366 - 7,514,616 (+)EnsemblGRCh38hg38GRCh38
GRCh37177,387,685 - 7,417,933 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36177,328,422 - 7,358,653 (+)NCBINCBI36Build 36hg18NCBI36
Build 34177,328,421 - 7,358,653NCBI
Celera177,414,117 - 7,444,201 (+)NCBICelera
Cytogenetic Map17p13.1NCBI
HuRef177,281,725 - 7,311,963 (+)NCBIHuRef
CHM1_1177,396,777 - 7,426,944 (+)NCBICHM1_1
T2T-CHM13v2.0177,388,413 - 7,418,678 (+)NCBIT2T-CHM13v2.0
Polr2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391169,624,823 - 69,649,459 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1169,624,823 - 69,649,463 (-)EnsemblGRCm39 Ensembl
GRCm381169,733,997 - 69,758,633 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1169,733,997 - 69,758,637 (-)EnsemblGRCm38mm10GRCm38
MGSCv371169,547,912 - 69,571,725 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361169,550,605 - 69,574,418 (-)NCBIMGSCv36mm8
MGSCv361170,318,517 - 70,342,330 (-)NCBIMGSCv36mm8
Cytogenetic Map11B3NCBI
cM Map1142.86NCBI
Polr2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554679,421,256 - 9,447,530 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554679,423,540 - 9,447,530 (-)NCBIChiLan1.0ChiLan1.0
POLR2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21915,079,746 - 15,109,789 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11717,045,567 - 17,075,869 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0177,516,940 - 7,546,989 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1177,502,807 - 7,532,761 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl177,502,807 - 7,532,521 (+)Ensemblpanpan1.1panPan2
POLR2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1532,403,814 - 32,429,717 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl532,403,829 - 32,429,681 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha532,541,944 - 32,567,696 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0532,509,534 - 32,535,275 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl532,509,552 - 32,535,260 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1532,474,744 - 32,500,516 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0532,433,445 - 32,459,212 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0532,610,752 - 32,636,501 (+)NCBIUU_Cfam_GSD_1.0
Polr2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560247,281,387 - 47,307,489 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936595755,535 - 781,783 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936595755,585 - 781,692 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLR2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1252,779,828 - 52,807,598 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11252,779,833 - 52,806,210 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21254,952,789 - 54,972,415 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POLR2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1166,860,487 - 6,889,054 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl166,860,677 - 6,888,618 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605914,516,279 - 14,548,527 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Polr2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478610,097,294 - 10,122,893 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478610,098,133 - 10,122,783 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Polr2a
58 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:150
Count of miRNA genes:89
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000048518, ENSRNOT00000068013
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
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
1578762Toxo1Toxoplasma gondii resistance QTL 1brain integrity trait (VT:0010579)percentage of study population displaying Toxoplasma gondii brain cysts at a point in time (CMO:0002028)105220003059378278Rat
1354585Eae18aExperimental allergic encephalomyelitis QTL 18a7.50.0004nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)105379738558445852Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat

Markers in Region
PMC56944P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21054,467,901 - 54,468,568 (+)MAPPERmRatBN7.2
Rnor_6.01056,354,742 - 56,355,408NCBIRnor6.0
Rnor_5.01056,100,142 - 56,100,808UniSTSRnor5.0
RGSC_v3.41056,568,619 - 56,569,285UniSTSRGSC3.4
Celera1053,622,197 - 53,622,863UniSTS
Cytogenetic Map10q24UniSTS


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 3 33 54 38 19 38 1 4 68 35 41 11 1
Low 10 3 3 3 7 7 6 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068013   ⟹   ENSRNOP00000061492
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)Ensembl
Rnor_6.0 Ensembl1056,339,284 - 56,365,084 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105702   ⟹   ENSRNOP00000097288
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)Ensembl
RefSeq Acc Id: NM_001427041   ⟹   NP_001413970
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,951,162 - 54,977,179 (-)NCBI
RefSeq Acc Id: XM_039087312   ⟹   XP_038943240
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,951,168 - 54,976,471 (-)NCBI
mRatBN7.21054,452,438 - 54,477,945 (-)NCBI
RefSeq Acc Id: XM_063269519   ⟹   XP_063125589
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81054,951,168 - 54,976,816 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001413970 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943240 (Get FASTA)   NCBI Sequence Viewer  
  XP_063125589 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000061492.1
  ENSRNOP00000097288.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000061492   ⟸   ENSRNOT00000068013
RefSeq Acc Id: XP_038943240   ⟸   XM_039087312
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000097288   ⟸   ENSRNOT00000105702
RefSeq Acc Id: NP_001413970   ⟸   NM_001427041
- UniProtKB: D4A5A6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125589   ⟸   XM_063269519
- Peptide Label: isoform X2
Protein Domains
RNA polymerase N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A5A6-F1-model_v2 AlphaFold D4A5A6 1-1970 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:1587326 AgrOrtholog
BioCyc Gene G2FUF-24520 BioCyc
Ensembl Genes ENSRNOG00000028834 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068013.4 UniProtKB/TrEMBL
  ENSRNOT00000105702.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.132.30 UniProtKB/TrEMBL
  1.10.150.390 UniProtKB/TrEMBL
  1.10.274.100 UniProtKB/TrEMBL
  2.40.40.20 UniProtKB/TrEMBL
  3.30.1360.140 UniProtKB/TrEMBL
  4.10.860.120 UniProtKB/TrEMBL
  6.10.250.2940 UniProtKB/TrEMBL
  6.20.50.80 UniProtKB/TrEMBL
  RNA polymerase ii UniProtKB/TrEMBL
InterPro DNA-dir_RpoC_beta_prime UniProtKB/TrEMBL
  RNA_pol_asu UniProtKB/TrEMBL
  RNA_pol_II_repeat_euk UniProtKB/TrEMBL
  RNA_pol_N UniProtKB/TrEMBL
  RNA_pol_Rpb1_1 UniProtKB/TrEMBL
  RNA_pol_Rpb1_3 UniProtKB/TrEMBL
  RNA_pol_Rpb1_3_sf UniProtKB/TrEMBL
  RNA_pol_Rpb1_4 UniProtKB/TrEMBL
  RNA_pol_Rpb1_5 UniProtKB/TrEMBL
  RNA_pol_Rpb1_6 UniProtKB/TrEMBL
  RNA_pol_Rpb1_7 UniProtKB/TrEMBL
  RNA_pol_Rpb1_7_sf UniProtKB/TrEMBL
  RNA_pol_Rpb1_clamp_domain UniProtKB/TrEMBL
  Rpb1_funnel_sf UniProtKB/TrEMBL
KEGG Report rno:363633 UniProtKB/TrEMBL
NCBI Gene 363633 ENTREZGENE
PANTHER DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 UniProtKB/TrEMBL
  PTHR19376 UniProtKB/TrEMBL
Pfam RNA_pol_Rpb1_1 UniProtKB/TrEMBL
  RNA_pol_Rpb1_2 UniProtKB/TrEMBL
  RNA_pol_Rpb1_3 UniProtKB/TrEMBL
  RNA_pol_Rpb1_4 UniProtKB/TrEMBL
  RNA_pol_Rpb1_5 UniProtKB/TrEMBL
  RNA_pol_Rpb1_6 UniProtKB/TrEMBL
  RNA_pol_Rpb1_7 UniProtKB/TrEMBL
  RNA_pol_Rpb1_R UniProtKB/TrEMBL
PhenoGen Polr2a PhenoGen
PRINTS PRICHEXTENSN UniProtKB/TrEMBL
PROSITE RNA_POL_II_REPEAT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028834 RatGTEx
SMART RPOLA_N UniProtKB/TrEMBL
Superfamily-SCOP beta and beta-prime subunits of DNA dependent RNA-polymerase UniProtKB/TrEMBL
UniProt A0A8I6ASE2_RAT UniProtKB/TrEMBL
  D4A5A6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polr2a  RNA polymerase II subunit A  Polr2a  polymerase (RNA) II subunit A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-16 Polr2a  polymerase (RNA) II subunit A  Polr2a  polymerase (RNA) II (DNA directed) polypeptide A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Polr2a  polymerase (RNA) II (DNA directed) polypeptide A  Polr2a  polymerase (RNA) II (DNA directed) polypeptide A, 220kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Polr2a  polymerase (RNA) II (DNA directed) polypeptide A, 220kDa  Polr2a  polymerase (RNA) II (DNA directed) polypeptide A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-13   polymerase (RNA) II (DNA directed) polypeptide A  Polr2a  polymerase (RNA) II (DNA directed) polypeptide A (mapped)  Name updated 737654 APPROVED
2007-04-11 Polr2a  polymerase (RNA) II (DNA directed) polypeptide A (mapped)  Polr2a_mapped  polymerase (RNA) II (DNA directed) polypeptide A (mapped)  Data merged from RGD:3365 737654 APPROVED
2006-11-19 Polr2a  polymerase (RNA) II (DNA directed) polypeptide A (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Polr2a_mapped  polymerase (RNA) II (DNA directed) polypeptide A (mapped)  Polr2a  polymerase (RNA) II (DNA directed) polypeptide A  Symbol and Name updated 1556543 APPROVED
2003-04-09 Polr2a  polymerase (RNA) II (DNA directed) polypeptide A    Polymerase (RNA II (DNA directed), large polypeptide  Symbol and Name updated 629477 APPROVED
2002-06-10 Polr2a  Polymerase (RNA II (DNA directed), large polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease binding to von Hippel_Lindau protein via UV radiation can lead to von Hippel-Lindau disease, a tumor-associated condition that can lead to cardiovascular pathologies 1299102
gene_function large subunit of RNA pol II that catalyzes the transition from transcription initiation to elongation 1299102
gene_homology human homologue POLR2A is cleaved by caspases during DNA damage-induced apoptosis 1303938
gene_physical_interaction binds von Hippel-Lindau tumor suppressor protein for ubiquitination targeting, a process that is regulated by UV radiation 1299102
gene_process this subunit is hyperphosphorylated during transcription elongation, which makes it a target for ubiquitination, particularly in response to UV radiation 1299102