Polr2b (RNA polymerase II subunit B) - Rat Genome Database

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Gene: Polr2b (RNA polymerase II subunit B) Rattus norvegicus
Analyze
Symbol: Polr2b
Name: RNA polymerase II subunit B
RGD ID: 1309477
Description: Predicted to enable chromatin binding activity. Predicted to contribute to RNA polymerase II activity. Predicted to be involved in transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase II, core complex. Predicted to colocalize with chromosome, telomeric region. Orthologous to human POLR2B (RNA polymerase II subunit B); PARTICIPATES IN RNA polymerase II transcription pathway; Huntington's disease pathway; purine metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA directed RNA polymerase II polypeptide B; DNA-directed RNA polymerase II subunit RPB2; LOC289561; polymerase (RNA) II (DNA directed) polypeptide B; polymerase (RNA) II (DNA directed) polypeptide B, 140kDa; polymerase (RNA) II subunit B; RpB2
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
GRCr81431,151,534 - 31,189,222 (-)NCBIGRCr8
mRatBN7.21430,797,228 - 30,834,916 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1430,797,228 - 30,834,916 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1431,178,151 - 31,215,766 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01432,486,476 - 32,524,093 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01430,971,132 - 31,008,749 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01433,070,104 - 33,107,792 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1433,070,078 - 33,107,776 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01432,863,627 - 32,901,277 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41433,069,966 - 33,107,615 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11433,069,967 - 33,107,600 (-)NCBI
Celera1430,116,602 - 30,154,129 (-)NCBICelera
Cytogenetic Map14p11NCBI
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

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. 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.
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:9268387   PMID:9852112   PMID:19946888   PMID:22287103   PMID:22658674   PMID:22681889   PMID:24270157   PMID:25568312  


Genomics

Comparative Map Data
Polr2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81431,151,534 - 31,189,222 (-)NCBIGRCr8
mRatBN7.21430,797,228 - 30,834,916 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1430,797,228 - 30,834,916 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1431,178,151 - 31,215,766 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01432,486,476 - 32,524,093 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01430,971,132 - 31,008,749 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01433,070,104 - 33,107,792 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1433,070,078 - 33,107,776 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01432,863,627 - 32,901,277 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41433,069,966 - 33,107,615 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11433,069,967 - 33,107,600 (-)NCBI
Celera1430,116,602 - 30,154,129 (-)NCBICelera
Cytogenetic Map14p11NCBI
POLR2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38456,978,896 - 57,031,158 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl456,977,722 - 57,031,158 (+)EnsemblGRCh38hg38GRCh38
GRCh37457,845,062 - 57,897,324 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36457,539,866 - 57,592,091 (+)NCBINCBI36Build 36hg18NCBI36
Build 34457,686,036 - 57,738,262NCBI
Celera455,351,060 - 55,402,358 (+)NCBICelera
Cytogenetic Map4q12NCBI
HuRef453,798,541 - 53,850,908 (+)NCBIHuRef
CHM1_1457,880,501 - 57,933,190 (+)NCBICHM1_1
T2T-CHM13v2.0460,470,344 - 60,522,595 (+)NCBIT2T-CHM13v2.0
Polr2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39577,458,331 - 77,497,175 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl577,457,994 - 77,497,171 (+)EnsemblGRCm39 Ensembl
GRCm38577,310,484 - 77,349,328 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl577,310,147 - 77,349,324 (+)EnsemblGRCm38mm10GRCm38
MGSCv37577,739,509 - 77,778,353 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36578,385,273 - 78,424,099 (+)NCBIMGSCv36mm8
Celera574,577,709 - 74,617,045 (+)NCBICelera
Cytogenetic Map5C3.3NCBI
cM Map541.66NCBI
Polr2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544714,110,182 - 14,150,556 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544714,110,182 - 14,150,556 (-)NCBIChiLan1.0ChiLan1.0
POLR2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2372,744,237 - 72,798,118 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1472,949,670 - 73,003,185 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0466,888,215 - 66,940,702 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1473,462,000 - 73,514,985 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl473,462,000 - 73,514,985 (-)Ensemblpanpan1.1panPan2
POLR2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11349,091,458 - 49,138,413 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1349,090,863 - 49,138,487 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1348,982,054 - 49,028,661 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01349,705,912 - 49,752,974 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1349,705,467 - 49,752,975 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11349,378,679 - 49,425,490 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01348,907,935 - 48,954,761 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01349,852,758 - 49,900,240 (+)NCBIUU_Cfam_GSD_1.0
Polr2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528527,179,024 - 27,225,143 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648219,073,124 - 19,119,421 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648219,073,125 - 19,119,424 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLR2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl856,231,789 - 56,285,011 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1856,232,730 - 56,283,367 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2859,014,262 - 59,064,755 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POLR2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1711,694,446 - 11,736,215 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl711,694,619 - 11,736,611 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606612,273,518 - 12,305,507 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Polr2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476112,387,553 - 12,430,871 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476112,387,553 - 12,430,211 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Polr2b
154 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:10
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000039252
Prediction methods:Miranda, 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
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat

Markers in Region
RH139215  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21430,802,323 - 30,803,044 (+)MAPPERmRatBN7.2
Rnor_6.01433,075,200 - 33,075,920NCBIRnor6.0
Rnor_5.01432,868,685 - 32,869,405UniSTSRnor5.0
RGSC_v3.41433,075,023 - 33,075,743UniSTSRGSC3.4
Celera1430,121,639 - 30,122,359UniSTS
RH 3.4 Map14397.4UniSTS
Cytogenetic Map14p11UniSTS


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039252   ⟹   ENSRNOP00000030781
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1430,797,228 - 30,834,916 (-)Ensembl
Rnor_6.0 Ensembl1433,070,078 - 33,107,776 (-)Ensembl
RefSeq Acc Id: NM_001106002   ⟹   NP_001099472
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81431,151,534 - 31,189,222 (-)NCBI
mRatBN7.21430,797,228 - 30,834,916 (-)NCBI
Rnor_6.01433,070,104 - 33,107,792 (-)NCBI
Rnor_5.01432,863,627 - 32,901,277 (-)NCBI
RGSC_v3.41433,069,966 - 33,107,615 (-)RGD
Celera1430,116,602 - 30,154,129 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099472 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABX80211 (Get FASTA)   NCBI Sequence Viewer  
  EDL89872 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030781
  ENSRNOP00000030781.4
Reference Protein Sequences
RefSeq Acc Id: NP_001099472   ⟸   NM_001106002
- UniProtKB: G3V8Y5 (UniProtKB/TrEMBL),   A6JCV0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030781   ⟸   ENSRNOT00000039252
Protein Domains
DNA-directed RNA polymerase subunit 2 hybrid-   RNA polymerase beta subunit protrusion   RNA polymerase Rpb2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V8Y5-F1-model_v2 AlphaFold G3V8Y5 1-1174 view protein structure

Transcriptome

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

Promoters
RGD ID:13699266
Promoter ID:EPDNEW_R9790
Type:multiple initiation site
Name:Polr2b_1
Description:RNA polymerase II subunit B
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_6.01433,107,750 - 33,107,810EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309477 AgrOrtholog
BioCyc Gene G2FUF-15992 BioCyc
Ensembl Genes ENSRNOG00000024779 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039252 ENTREZGENE
  ENSRNOT00000039252.6 UniProtKB/TrEMBL
Gene3D-CATH 2.40.270.10 UniProtKB/TrEMBL
  2.40.50.150 UniProtKB/TrEMBL
  3.90.1070.20 UniProtKB/TrEMBL
  3.90.1100.10 UniProtKB/TrEMBL
  3.90.1110.10 UniProtKB/TrEMBL
  RNA polymerase alpha subunit dimerisation domain UniProtKB/TrEMBL
InterPro DNA-dir_RNA_pol_su2 UniProtKB/TrEMBL
  DNA-dir_RNA_pol_su2_6 UniProtKB/TrEMBL
  DNA-dir_RNAP_su2_hyb_sf UniProtKB/TrEMBL
  RNA_pol_bsu_CS UniProtKB/TrEMBL
  RNA_pol_bsu_protrusion UniProtKB/TrEMBL
  RNA_pol_Rpb2_2 UniProtKB/TrEMBL
  RNA_pol_Rpb2_2_sf UniProtKB/TrEMBL
  RNA_pol_Rpb2_3 UniProtKB/TrEMBL
  RNA_pol_Rpb2_4 UniProtKB/TrEMBL
  RNA_pol_Rpb2_5 UniProtKB/TrEMBL
  RNA_pol_Rpb2_7 UniProtKB/TrEMBL
  RNA_pol_RPB2_OB-fold UniProtKB/TrEMBL
KEGG Report rno:289561 UniProtKB/TrEMBL
NCBI Gene 289561 ENTREZGENE
PANTHER DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 UniProtKB/TrEMBL
  RNA_pol_I_sub2 UniProtKB/TrEMBL
Pfam RNA_pol_Rpb2_1 UniProtKB/TrEMBL
  RNA_pol_Rpb2_2 UniProtKB/TrEMBL
  RNA_pol_Rpb2_3 UniProtKB/TrEMBL
  RNA_pol_Rpb2_4 UniProtKB/TrEMBL
  RNA_pol_Rpb2_5 UniProtKB/TrEMBL
  RNA_pol_Rpb2_6 UniProtKB/TrEMBL
  RNA_pol_Rpb2_7 UniProtKB/TrEMBL
PhenoGen Polr2b PhenoGen
PROSITE RNA_POL_BETA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024779 RatGTEx
Superfamily-SCOP beta and beta-prime subunits of DNA dependent RNA-polymerase UniProtKB/TrEMBL
UniProt A6JCV0 ENTREZGENE, UniProtKB/TrEMBL
  G3V8Y5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polr2b  RNA polymerase II subunit B  Polr2b  polymerase (RNA) II subunit B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-16 Polr2b  polymerase (RNA) II subunit B  Polr2b  polymerase (RNA) II (DNA directed) polypeptide B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Polr2b  polymerase (RNA) II (DNA directed) polypeptide B  Polr2b  polymerase (RNA) II (DNA directed) polypeptide B, 140kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Polr2b  polymerase (RNA) II (DNA directed) polypeptide B, 140kDa  Polr2b  polymerase (RNA) II (DNA directed) polypeptide B   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Polr2b  polymerase (RNA) II (DNA directed) polypeptide B   Polr2b_predicted  polymerase (RNA) II (DNA directed) polypeptide B (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Polr2b_predicted  polymerase (RNA) II (DNA directed) polypeptide B (predicted)      Symbol and Name status set to approved 70820 APPROVED