Polr1c (RNA polymerase I and III subunit C) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Polr1c (RNA polymerase I and III subunit C) Rattus norvegicus
Analyze
Symbol: Polr1c
Name: RNA polymerase I and III subunit C
RGD ID: 1309689
Description: Is predicted to contribute to RNA polymerase I activity and RNA polymerase III activity. Predicted to be involved in transcription by RNA polymerase I and transcription by RNA polymerase III. Predicted to localize to RNA polymerase I complex; RNA polymerase III complex; and nucleoplasm. Human ortholog(s) of this gene implicated in Treacher Collins syndrome 3 and hypomyelinating leukodystrophy 11. Orthologous to human POLR1C (RNA polymerase I and III subunit C); PARTICIPATES IN RNA polymerase I transcription pathway; RNA polymerase III transcription pathway; purine metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ac2-127; DNA-directed RNA polymerases I and III subunit RPAC1; LOC301246; MGC105583; polymerase (RNA) I polypeptide C; polymerase (RNA) I subunit C; RNA polymerase 1-1; RNA polymerase I subunit; RNA polymerase I subunit C; Rpo1-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,735,740 - 14,739,852 (+)NCBI
Rnor_6.0 Ensembl917,120,759 - 17,124,871 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0917,120,759 - 17,124,871 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0916,017,436 - 16,021,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,298,309 - 10,302,421 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1910,295,630 - 10,299,743 (+)NCBI
Celera912,483,058 - 12,487,170 (+)NCBICelera
Cytogenetic Map9q12NCBI
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

Additional References at PubMed
PMID:7929437   PMID:12477932   PMID:24107381  


Genomics

Comparative Map Data
Polr1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,735,740 - 14,739,852 (+)NCBI
Rnor_6.0 Ensembl917,120,759 - 17,124,871 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0917,120,759 - 17,124,871 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0916,017,436 - 16,021,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,298,309 - 10,302,421 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1910,295,630 - 10,299,743 (+)NCBI
Celera912,483,058 - 12,487,170 (+)NCBICelera
Cytogenetic Map9q12NCBI
POLR1C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl643,509,702 - 43,562,419 (+)EnsemblGRCh38hg38GRCh38
GRCh38643,517,089 - 44,461,400 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37643,484,827 - 43,530,144 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,592,769 - 43,605,092 (+)NCBINCBI36hg18NCBI36
Celera645,036,412 - 45,048,735 (+)NCBI
Cytogenetic Map6p21.1NCBI
HuRef643,202,730 - 43,208,225 (+)NCBIHuRef
CHM1_1643,487,894 - 43,500,246 (+)NCBICHM1_1
Polr1c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391746,554,846 - 46,558,971 (-)NCBIGRCm39mm39
GRCm39 Ensembl1746,554,846 - 46,558,980 (-)Ensembl
GRCm381746,243,920 - 46,248,045 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,243,920 - 46,248,054 (-)EnsemblGRCm38mm10GRCm38
MGSCv371746,380,869 - 46,384,994 (-)NCBIGRCm37mm9NCBIm37
MGSCv361745,707,509 - 45,711,545 (-)NCBImm8
Celera1749,677,058 - 49,681,183 (-)NCBICelera
Cytogenetic Map17CNCBI
Polr1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554379,346,397 - 9,350,591 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554379,346,397 - 9,350,591 (+)NCBIChiLan1.0ChiLan1.0
POLR1C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1644,399,936 - 44,404,420 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl644,395,787 - 44,412,257 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0643,101,771 - 43,121,460 (+)NCBIMhudiblu_PPA_v0panPan3
POLR1C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,978,337 - 11,982,265 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,978,422 - 12,008,579 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1212,004,514 - 12,008,441 (+)NCBI
ROS_Cfam_1.01212,461,954 - 12,465,881 (+)NCBI
UMICH_Zoey_3.11211,987,354 - 11,991,281 (+)NCBI
UNSW_CanFamBas_1.01212,074,263 - 12,078,191 (+)NCBI
UU_Cfam_GSD_1.01212,167,748 - 12,171,676 (+)NCBI
Polr1c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494647,472,764 - 47,476,677 (+)NCBI
SpeTri2.0NW_00493647616,483,203 - 16,487,360 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLR1C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,507,073 - 38,537,943 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1738,511,521 - 38,531,938 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2744,092,595 - 44,111,879 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POLR1C
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11728,637,868 - 28,649,898 (-)NCBI
Polr1c
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475416,125,322 - 16,129,339 (-)NCBI

Position Markers
RH127411  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0917,124,384 - 17,124,692NCBIRnor6.0
Rnor_5.0916,021,061 - 16,021,369UniSTSRnor5.0
RGSC_v3.4910,301,934 - 10,302,242UniSTSRGSC3.4
Celera912,486,683 - 12,486,991UniSTS
RH 3.4 Map963.8UniSTS
Cytogenetic Map9q12UniSTS
BF386341  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0917,121,584 - 17,121,733NCBIRnor6.0
Rnor_5.0916,018,261 - 16,018,410UniSTSRnor5.0
RGSC_v3.4910,299,134 - 10,299,283UniSTSRGSC3.4
Celera912,483,883 - 12,484,032UniSTS
RH 3.4 Map963.5UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000025787
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.


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 3 5 74 35 41 11 3
Low 5 6 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025787   ⟹   ENSRNOP00000025787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl917,120,759 - 17,124,871 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077749   ⟹   ENSRNOP00000073552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl917,122,284 - 17,124,675 (+)Ensembl
RefSeq Acc Id: NM_001008330   ⟹   NP_001008331
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2914,735,740 - 14,739,852 (+)NCBI
Rnor_6.0917,120,759 - 17,124,871 (+)NCBI
Rnor_5.0916,017,436 - 16,021,548 (+)NCBI
RGSC_v3.4910,298,309 - 10,302,421 (+)RGD
Celera912,483,058 - 12,487,170 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008331 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH86597 (Get FASTA)   NCBI Sequence Viewer  
  AAP92620 (Get FASTA)   NCBI Sequence Viewer  
  EDM18804 (Get FASTA)   NCBI Sequence Viewer  
  EDM18805 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001008331   ⟸   NM_001008330
- UniProtKB: Q5RJK9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073552   ⟸   ENSRNOT00000077749
RefSeq Acc Id: ENSRNOP00000025787   ⟸   ENSRNOT00000025787
Protein Domains
RPOLD

Transcriptome

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

Promoters
RGD ID:13696530
Promoter ID:EPDNEW_R7053
Type:multiple initiation site
Name:Polr1c_1
Description:RNA polymerase I subunit C
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_6.0917,120,793 - 17,120,853EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 17123110 17123111 T G snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 10300660 10300661 T G snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309689 AgrOrtholog
Ensembl Genes ENSRNOG00000019079 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025787 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073552 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025787 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077749 UniProtKB/TrEMBL
Gene3D-CATH 2.170.120.12 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7312277 IMAGE-MGC_LOAD
InterPro DNA-dir_RNA_pol_30-40kDasu_CS UniProtKB/TrEMBL
  DNA-dir_RNA_pol_insert UniProtKB/TrEMBL
  DNA-dir_RNA_pol_RpoA/D/Rpb3 UniProtKB/TrEMBL
  RBP11-like UniProtKB/TrEMBL
  RNAPI/II_AC40 UniProtKB/TrEMBL
  RNApol_insert_sf UniProtKB/TrEMBL
KEGG Report rno:301246 UniProtKB/TrEMBL
MGC_CLONE MGC:105583 IMAGE-MGC_LOAD
NCBI Gene 301246 ENTREZGENE
PANTHER PTHR11800:SF13 UniProtKB/TrEMBL
Pfam RNA_pol_A_bac UniProtKB/TrEMBL
  RNA_pol_L UniProtKB/TrEMBL
PhenoGen Polr1c PhenoGen
PROSITE RNA_POL_D_30KD UniProtKB/TrEMBL
SMART RPOLD UniProtKB/TrEMBL
Superfamily-SCOP RNAP_insert UniProtKB/TrEMBL
  RNAP_RBP11-like UniProtKB/TrEMBL
UniProt A0A0G2K5T6_RAT UniProtKB/TrEMBL
  Q5RJK9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-16 Polr1c  RNA polymerase I and III subunit C  Polr1c  RNA polymerase I subunit C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-07-21 Polr1c  RNA polymerase I subunit C  Polr1c  polymerase (RNA) I subunit C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-09 Polr1c  polymerase (RNA) I subunit C  Polr1c  polymerase (RNA) I polypeptide C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-06 Polr1c  polymerase (RNA) I polypeptide C  Rpo1-1  RNA polymerase 1-1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Rpo1-1  RNA polymerase 1-1  Rpo1-1_predicted  RNA polymerase 1-1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Rpo1-1_predicted  RNA polymerase 1-1 (predicted)      Symbol and Name status set to approved 70820 APPROVED