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 RNA-directed RNA polymerase activity; enzyme binding activity; and metal ion binding activity. Predicted to contribute to DNA-directed RNA polymerase activity. Involved in cellular response to oxygen levels. Predicted to be located in euchromatin and nucleus. Predicted to be part of Prp19 complex and RNA polymerase II, core complex. Predicted to be active in chromosome. 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81054,951,162 - 54,977,179 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1054,951,162 - 54,977,179 (-)EnsemblGRCr8
mRatBN7.21054,452,438 - 54,478,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)EnsemblmRatBN7.2
Rnor_6.01056,339,277 - 56,364,888 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1056,339,284 - 56,365,084 (-)Ensemblrn6Rnor6.0
Rnor_5.01056,084,677 - 56,110,778 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41056,552,872 - 56,579,172 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1053,606,814 - 53,632,373 (-)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse:




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)
4,4'-sulfonyldiphenol  (ISO)
4-phenylbutyric acid  (ISO)
5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole  (ISO)
7,12-dimethyltetraphene  (ISO)
acetylsalicylic acid  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
alpha-amanitin  (ISO)
alvocidib  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
Benzo[ghi]perylene  (ISO)
beta-naphthoflavone  (EXP)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
Brodifacoum  (EXP)
Butylbenzyl phthalate  (ISO)
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)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (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)
nitrates  (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)
thiram  (ISO)
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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1054,951,162 - 54,977,179 (-)EnsemblGRCr8
mRatBN7.21054,452,438 - 54,478,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)EnsemblmRatBN7.2
Rnor_6.01056,339,277 - 56,364,888 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1056,339,284 - 56,365,084 (-)Ensemblrn6Rnor6.0
Rnor_5.01056,084,677 - 56,110,778 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41056,552,872 - 56,579,172 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
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 (+)Ensemblhg38GRCh38
GRCh37177,387,685 - 7,417,933 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36177,328,422 - 7,358,653 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381169,733,997 - 69,758,633 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1169,733,997 - 69,758,637 (-)Ensemblmm10GRCm38
MGSCv371169,547,912 - 69,571,725 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha532,541,944 - 32,567,696 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0532,509,534 - 32,535,275 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462478610,098,133 - 10,122,783 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Polr2a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1949,337,950 - 49,363,776 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Polr2a
103 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103589345164140567Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105107189796071897Rat
152025229Scl83Serum cholesterol level QTL 834.33blood cholesterol amount (VT:0000180)103621155669161158Rat
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)103179628176796281Rat
152025227Bw195Body weight QTL 1955.73body mass (VT:0001259)104748901769161158Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)102744378772443787Rat
152025224Bw193Body weight QTL 1936.47body mass (VT:0001259)105216243375582749Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
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)105269900459876693Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)101993920764939207Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105429633699451733Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104183127886831278Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105046480295464802Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104493935989939359Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104552916496099749Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101866841963668419Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102183375861843633Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105086028895860288Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102895035373950353Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103589326364653589Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102980091064653589Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102744378772443787Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14282327487823274Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104493935989939359Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104282327487823274Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105429622767476781Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
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)10666092373950353Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)104949549294495492Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
1354585Eae18aExperimental allergic encephalomyelitis QTL 18a7.50.0004nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)105429622758944345Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102466212373695339Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102702353561843633Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103550938380509383Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)102011061465110614Rat
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)102758722696099902Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102907697874076978Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104360879388608793Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)102744378772443787Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
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)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104994371094943710Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103112911376129113Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104493935989939359Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104786912992869129Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)103950348784503487Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105060467795604677Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)102011061465110614Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000068013   ⟹   ENSRNOP00000061492
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1054,951,162 - 54,977,179 (-)Ensembl
mRatBN7.2 Ensembl1054,452,441 - 54,478,455 (-)Ensembl
Rnor_6.0 Ensembl1056,339,284 - 56,365,084 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105702   ⟹   ENSRNOP00000097288
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1054,951,167 - 54,977,179 (-)Ensembl
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
  ENSRNOP00000061492.1
  ENSRNOP00000097288.1
Ensembl Acc Id: ENSRNOP00000061492   ⟸   ENSRNOT00000068013
RefSeq Acc Id: XP_038943240   ⟸   XM_039087312
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000097288   ⟸   ENSRNOT00000105702
RefSeq Acc Id: NP_001413970   ⟸   NM_001427041
- UniProtKB: D4A5A6 (UniProtKB/TrEMBL),   A0A8I6ASE2 (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 ENTREZGENE
  ENSRNOT00000068013.5 UniProtKB/TrEMBL
  ENSRNOT00000105702.2 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
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 ENTREZGENE, 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