Polr3a (RNA polymerase III subunit A) - Rat Genome Database

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Gene: Polr3a (RNA polymerase III subunit A) Rattus norvegicus
Analyze
Symbol: Polr3a
Name: RNA polymerase III subunit A
RGD ID: 1305574
Description: Predicted to enable chromatin binding activity. Predicted to contribute to DNA-directed 5'-3' RNA polymerase activity. Predicted to be involved in innate immune response and positive regulation of interferon-beta production. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase III complex. Human ortholog(s) of this gene implicated in hypomyelinating leukodystrophy 7 with or without oligodontia and-or hypogonadotropic hypogonadism and progeria. Orthologous to human POLR3A (RNA polymerase III subunit A); PARTICIPATES IN RNA polymerase III transcription pathway; purine metabolic pathway; pyrimidine metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: DNA-directed RNA polymerase III subunit RPC1; LOC361102; polymerase (RNA) III (DNA directed) polypeptide A; polymerase (RNA) III (DNA directed) polypeptide A, 155kDa; polymerase (RNA) III subunit A; RGD1305574; similar to polymerase (RNA) III (DNA directed) (155kD)
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
mRatBN7.21649,178 - 88,178 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1649,521 - 88,172 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.016717,821 - 756,002 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl16716,683 - 755,990 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.016712,735 - 750,910 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4164,090 - 42,301 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1164,027 - 40,227 (-)NCBI
Celera1636,720 - 74,901 (-)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Cell growth- and differentiation-dependent regulation of RNA polymerase III transcription. Dumay-Odelot H, etal., Cell Cycle. 2010 Sep 15;9(18):3687-99. Epub 2010 Sep 1.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits. Hu P, etal., Mol Cell Biol. 2002 Nov;22(22):8044-55.
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:19609254   PMID:19946888   PMID:22287103   PMID:24107381   PMID:24912190  


Genomics

Comparative Map Data
Polr3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21649,178 - 88,178 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1649,521 - 88,172 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.016717,821 - 756,002 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl16716,683 - 755,990 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.016712,735 - 750,910 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4164,090 - 42,301 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1164,027 - 40,227 (-)NCBI
Celera1636,720 - 74,901 (-)NCBICelera
Cytogenetic Map16p16NCBI
POLR3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381077,975,149 - 78,029,515 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1077,953,148 - 78,029,522 (-)EnsemblGRCh38hg38GRCh38
GRCh371079,734,907 - 79,789,273 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361079,405,900 - 79,459,265 (-)NCBINCBI36Build 36hg18NCBI36
Build 341079,405,911 - 79,459,265NCBI
Celera1073,021,499 - 73,075,893 (-)NCBICelera
Cytogenetic Map10q22.3NCBI
HuRef1073,729,855 - 73,784,226 (-)NCBIHuRef
CHM1_11080,017,697 - 80,072,040 (-)NCBICHM1_1
T2T-CHM13v2.01078,844,187 - 78,898,555 (-)NCBIT2T-CHM13v2.0
Polr3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391424,498,762 - 24,537,126 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1424,498,764 - 24,537,126 (-)EnsemblGRCm39 Ensembl
GRCm381424,448,694 - 24,487,070 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1424,448,696 - 24,487,058 (-)EnsemblGRCm38mm10GRCm38
MGSCv371425,267,916 - 25,306,268 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361423,281,159 - 23,319,511 (-)NCBIMGSCv36mm8
Celera1420,823,678 - 20,861,770 (-)NCBICelera
Cytogenetic Map14A3NCBI
Polr3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543714,446,024 - 14,483,336 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543714,446,059 - 14,483,336 (+)NCBIChiLan1.0ChiLan1.0
POLR3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11077,157,976 - 77,213,019 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01074,496,121 - 74,550,054 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
POLR3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1427,834,197 - 27,883,065 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl427,835,612 - 27,883,436 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha427,959,412 - 28,008,179 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0428,135,868 - 28,184,686 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl428,135,868 - 28,184,984 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1428,010,348 - 28,059,559 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0428,209,234 - 28,258,410 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0428,562,062 - 28,611,378 (-)NCBIUU_Cfam_GSD_1.0
Polr3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721353,078,129 - 53,121,757 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365211,570,857 - 1,614,409 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365211,570,863 - 1,613,410 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLR3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1480,413,099 - 80,471,697 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11480,410,143 - 80,471,740 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21486,944,625 - 87,003,270 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POLR3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1953,411,869 - 53,462,773 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl953,411,889 - 53,464,668 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604813,832,883 - 13,883,800 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Polr3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475411,173,601 - 11,215,258 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475411,166,126 - 11,215,205 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Polr3a
224 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:32
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000013501
Prediction methods:Miranda, Rnahybrid
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
631524Bp75Blood pressure QTL 750.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)161110831Rat
2325838Bp347Blood pressure QTL 3470.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1613080679Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat

Markers in Region
D16Chm23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21688,524 - 88,716 (+)MAPPERmRatBN7.2
Rnor_6.016756,352 - 756,541NCBIRnor6.0
Rnor_5.016751,266 - 751,455UniSTSRnor5.0
RGSC_v3.41642,656 - 42,845UniSTSRGSC3.4
Celera1675,251 - 75,440UniSTS
Cytogenetic Map16p16UniSTS
RH140575  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21650,055 - 50,271 (+)MAPPERmRatBN7.2
Rnor_6.016717,889 - 718,104NCBIRnor6.0
Rnor_5.016712,803 - 713,018UniSTSRnor5.0
Celera1636,788 - 37,003UniSTS
Cytogenetic Map16p16UniSTS


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 1 29 26 10 19 10 1 1 74 27 35 10 1
Low 2 14 31 31 31 7 10 8 6 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013501   ⟹   ENSRNOP00000013501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1649,521 - 88,172 (-)Ensembl
Rnor_6.0 Ensembl16716,683 - 755,990 (-)Ensembl
RefSeq Acc Id: XM_341388   ⟹   XP_341389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21649,178 - 88,178 (-)NCBI
Rnor_6.016717,821 - 756,002 (-)NCBI
Rnor_5.016712,735 - 750,910 (-)NCBI
RGSC_v3.4164,090 - 42,301 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_341389 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH86344 (Get FASTA)   NCBI Sequence Viewer  
  EDL75115 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_341389   ⟸   XM_341388
- UniProtKB: E9PTB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013501   ⟸   ENSRNOT00000013501
Protein Domains
RNA_pol_Rpb1_5   RPOLA_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PTB6-F1-model_v2 AlphaFold E9PTB6 1-1390 view protein structure

Transcriptome

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

Promoters
RGD ID:13699896
Promoter ID:EPDNEW_R10412
Type:initiation region
Name:Polr3a_1
Description:RNA polymerase III subunit A
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_6.016755,976 - 756,036EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305574 AgrOrtholog
BioCyc Gene G2FUF-12315 BioCyc
Ensembl Genes ENSRNOG00000010008 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013501 ENTREZGENE
  ENSRNOP00000013501.7 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013501 ENTREZGENE
  ENSRNOT00000013501.8 UniProtKB/TrEMBL
Gene3D-CATH 1.10.132.30 UniProtKB/TrEMBL
  1.10.274.100 UniProtKB/TrEMBL
  4.10.860.120 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7301934 IMAGE-MGC_LOAD
InterPro DNA-dir_RpoC_beta_prime UniProtKB/TrEMBL
  RNA_pol_asu 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_clamp_domain UniProtKB/TrEMBL
  RNAP_III_Rpc1_C UniProtKB/TrEMBL
  RNAP_III_RPC1_N UniProtKB/TrEMBL
  Rpb1_funnel_sf UniProtKB/TrEMBL
KEGG Report rno:361102 UniProtKB/TrEMBL
MGC_CLONE MGC:105949 IMAGE-MGC_LOAD
NCBI Gene 361102 ENTREZGENE
PANTHER 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
PhenoGen Polr3a PhenoGen
SMART RPOLA_N UniProtKB/TrEMBL
UniProt E9PTB6 ENTREZGENE, UniProtKB/TrEMBL
  Q5RK26_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polr3a  RNA polymerase III subunit A  Polr3a  polymerase (RNA) III subunit A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-16 Polr3a  polymerase (RNA) III subunit A  Polr3a  polymerase (RNA) III (DNA directed) polypeptide A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Polr3a  polymerase (RNA) III (DNA directed) polypeptide A  Polr3a  polymerase (RNA) III (DNA directed) polypeptide A, 155kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Polr3a  polymerase (RNA) III (DNA directed) polypeptide A, 155kDa  Polr3a  polymerase (RNA) III (DNA directed) polypeptide A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Polr3a  polymerase (RNA) III (DNA directed) polypeptide A  RGD1305574  similar to polymerase (RNA) III (DNA directed) (155kD)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1305574  similar to polymerase (RNA) III (DNA directed) (155kD)  RGD1305574_predicted  similar to polymerase (RNA) III (DNA directed) (155kD) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305574_predicted  similar to polymerase (RNA) III (DNA directed) (155kD) (predicted)  LOC361102_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361102_predicted  similar to polymerase (RNA) III (DNA directed) (155kD) (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL