Rrn3 (RRN3 RNA polymerase I transcription factor homolog (yeast)) - Rat Genome Database

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Gene: Rrn3 (RRN3 RNA polymerase I transcription factor homolog (yeast)) Mus musculus
Analyze
Symbol: Rrn3
Name: RRN3 RNA polymerase I transcription factor homolog (yeast)
RGD ID: 1553236
MGI Page MGI
Description: Enables RNA polymerase binding activity. Acts upstream of or within several processes, including negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator; regulation of DNA-templated transcription; and transcription initiation at RNA polymerase I promoter. Predicted to be located in nucleolus. Predicted to be active in nucleus. Used to study Parkinson's disease. Orthologous to several human genes including RRN3 (RRN3 homolog, RNA polymerase I transcription factor).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AL023001; E130302O19Rik; R75565; RNA polymerase I-specific transcription initiation factor RRN3; TIF-; TIF-1A; Tif1a; transcription initiation factor TIF-IA
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391613,598,563 - 13,632,705 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1613,598,572 - 13,632,703 (+)EnsemblGRCm39 Ensembl
GRCm381613,780,699 - 13,814,841 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1613,780,708 - 13,814,839 (+)EnsemblGRCm38mm10GRCm38
MGSCv371613,780,792 - 13,814,934 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361613,694,277 - 13,728,419 (+)NCBIMGSCv36mm8
Celera1614,384,965 - 14,419,116 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map169.59NCBI
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

Cellular Component
nucleolus  (IEA,ISO)
nucleus  (IBA)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. 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.
3. MGD IEA MGD IEA
4. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
5. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
Additional References at PubMed
PMID:7671812   PMID:8413268   PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:12015311   PMID:12477932   PMID:12520002   PMID:12620228   PMID:12904583   PMID:14610273  
PMID:15558034   PMID:15782199   PMID:15805466   PMID:15989966   PMID:16141072   PMID:16141073   PMID:17967808   PMID:18559419   PMID:18799693   PMID:19036968   PMID:19217408   PMID:21228155  
PMID:21267068   PMID:21873635   PMID:23393135   PMID:23764776   PMID:24273493   PMID:24297901   PMID:25737280   PMID:27257073   PMID:28360124   PMID:28715449   PMID:30918302   PMID:31110473  
PMID:34880223   PMID:38745938  


Genomics

Comparative Map Data
Rrn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391613,598,563 - 13,632,705 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1613,598,572 - 13,632,703 (+)EnsemblGRCm39 Ensembl
GRCm381613,780,699 - 13,814,841 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1613,780,708 - 13,814,839 (+)EnsemblGRCm38mm10GRCm38
MGSCv371613,780,792 - 13,814,934 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361613,694,277 - 13,728,419 (+)NCBIMGSCv36mm8
Celera1614,384,965 - 14,419,116 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map169.59NCBI
RRN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381615,060,022 - 15,094,335 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1615,060,033 - 15,094,311 (-)EnsemblGRCh38hg38GRCh38
GRCh371615,153,879 - 15,188,192 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361615,061,380 - 15,095,659 (-)NCBINCBI36Build 36hg18NCBI36
Build 341615,061,379 - 15,095,613NCBI
Celera1616,150,521 - 16,184,795 (+)NCBICelera
Cytogenetic Map16p13.11NCBI
HuRef1614,799,197 - 14,833,480 (-)NCBIHuRef
CHM1_11615,095,601 - 15,129,884 (+)NCBICHM1_1
T2T-CHM13v2.01615,061,074 - 15,095,386 (-)NCBIT2T-CHM13v2.0
Rrn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8102,637,016 - 2,672,338 (-)NCBIGRCr8
mRatBN7.2102,129,949 - 2,165,381 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl102,129,978 - 2,165,663 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx106,826,708 - 6,861,997 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01033,703,845 - 33,739,134 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0102,033,162 - 2,067,849 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0103,170,387 - 3,214,648 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl103,170,742 - 3,214,655 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0102,057,042 - 2,092,164 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4101,492,181 - 1,527,197 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1101,492,186 - 1,543,048 (+)NCBI
Celera101,160,178 - 1,195,455 (-)NCBICelera
Cytogenetic Map10q11NCBI
Rrn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955442129,106 - 166,258 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955442129,106 - 166,258 (+)NCBIChiLan1.0ChiLan1.0
RRN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21815,272,893 - 15,309,408 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11619,055,740 - 19,092,270 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01613,664,478 - 13,700,942 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RRN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1628,478,770 - 28,507,722 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl628,478,829 - 28,507,696 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha629,841,964 - 29,870,919 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0628,641,773 - 28,670,927 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl628,641,780 - 28,670,894 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1628,444,804 - 28,473,963 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0628,334,911 - 28,364,048 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0628,740,669 - 28,769,347 (-)NCBIUU_Cfam_GSD_1.0
Rrn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344114,795,421 - 114,828,934 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365012,893,298 - 2,926,804 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365012,893,304 - 2,926,795 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RRN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl37,537,133 - 7,571,992 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.137,537,131 - 7,571,990 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RRN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1514,235,368 - 14,271,790 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl514,235,414 - 14,272,020 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606815,775,231 - 15,812,052 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rrn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248248,582,803 - 8,614,313 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248248,582,754 - 8,615,073 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rrn3
1161 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:452
Count of miRNA genes:355
Interacting mature miRNAs:383
Transcripts:ENSMUST00000023363
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301970Heal11_mwound healing/regeneration 11 (mouse)Not determined16124263853Mouse
26884376Skwq4_mskull length QTL 4, 5 week (mouse)16841786490896888Mouse
1301841Lrnx9_mlearning-contextual 9 (mouse)Not determined161222536046225471Mouse
4142460Nilac10_mnicotine induced locomotor activity 10 (mouse)Not determined16713690629225471Mouse
38501069Tip4_mtuberculosis immunophenotype 4, IFN-g level (mouse)16431786444520363Mouse
1302106Rapop1_mradiation-induced apoptosis 1 (mouse)Not determined16378077915731053Mouse
26884432Zlq7_mzygomatic length QTL 7, 10 week (mouse)16381786464620363Mouse
1300632Loca2_mlocomotor activity 2 (mouse)Not determined16122500574Mouse
1301086Lprm5_mlymphoproliferation modifier 5 (mouse)Not determined161184882445848923Mouse
27226768Tibl9_mtibia length 9, 5 week (mouse)16331786451420363Mouse
1301443Mopkd2_mmodifier of polycystic kidney disease progression 2 (mouse)Not determined16464631438646414Mouse
10043978Obq35_mobesity QTL 35 (mouse)Not determined16988163143881631Mouse
1301575Tanidd3_mtally ho associated non-insulin dependednt diabetes mellitus 3 (mouse)Not determined16122897739Mouse
1357763Lp1_mlymphocyte proliferation 1 (mouse)Not determined16654297965466552Mouse
1301384Dice1_mdetermination of interleukin 4 commitment 1 (mouse)Not determined16128434358Mouse
1300943Skts9_mskin tumor susceptibility 9 (mouse)Not determined16577525239775440Mouse
10402497Lmr23_mleishmaniasis resistance 23 (mouse)Not determined16129674200Mouse
10412289Ppsl_mplasma P-selectin levels (mouse)Not determined16130814572Mouse
4141468Nhdlq10_mnon-HDL QTL 10 (mouse)Not determined16124263853Mouse
1300656Bgeq15_mbody growth early QTL 15 (mouse)Not determined16577525239775440Mouse
1301559Bbaa19_mB.burgdorferi-associated arthritis 19 (mouse)Not determined16130066977Mouse
11251724Ewc6_methanol withdrawal and consumption 6 (mouse)16822605242226052Mouse
1300987Skull23_mskull morphology 23 (mouse)Not determined16577525239775440Mouse
1301945Skl7_mskeletal size (tail length) 7 (mouse)Not determined16577525239775440Mouse
4141010Bbq1_mbrain and behavior QTL 1 (mouse)Not determined16647700935021216Mouse
27095908Scvln7_msacral vertebrae length 2, 5 week (mouse)16331786439820362Mouse
4141060Pbwg19_mpostnatal body weight growth 19 (mouse)Not determined16120780888Mouse
10043879Adip25_madiposity 25 (mouse)Not determined16122520318Mouse
27226785Feml12_mfemur length 12, 5 week (mouse)16331786464620363Mouse

Markers in Region
14.MMHAP57FRE8.seq  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381613,810,263 - 13,810,418UniSTSGRCm38
MGSCv371613,810,356 - 13,810,511UniSTSGRCm37
Celera1614,414,538 - 14,414,693UniSTS
Cytogenetic Map16A1UniSTS
Whitehead_YAC16 UniSTS
RH125263  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381613,814,294 - 13,814,461UniSTSGRCm38
MGSCv371613,814,387 - 13,814,554UniSTSGRCm37
Celera1614,418,569 - 14,418,736UniSTS
Cytogenetic Map16A1UniSTS
RH125396  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381613,813,743 - 13,813,896UniSTSGRCm38
MGSCv371613,813,836 - 13,813,989UniSTSGRCm37
Celera1614,418,018 - 14,418,171UniSTS
Cytogenetic Map16A1UniSTS


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001039521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036159727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA437536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC107769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC154607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK021410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK080397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK080680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK165676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK170340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK172693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK180103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK211678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC034110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC055781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC138774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC138776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CJ175904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSMUST00000023363   ⟹   ENSMUSP00000023363
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1613,598,577 - 13,632,703 (+)Ensembl
GRCm38.p6 Ensembl1613,780,713 - 13,814,839 (+)Ensembl
Ensembl Acc Id: ENSMUST00000230102
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1613,598,572 - 13,600,693 (+)Ensembl
GRCm38.p6 Ensembl1613,780,708 - 13,782,829 (+)Ensembl
RefSeq Acc Id: NM_001039521   ⟹   NP_001034610
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391613,598,563 - 13,632,705 (+)NCBI
GRCm381613,780,699 - 13,814,841 (+)ENTREZGENE
MGSCv371613,780,792 - 13,814,934 (+)RGD
Celera1614,384,965 - 14,419,116 (+)RGD
cM Map16 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_036159727   ⟹   XP_036015620
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391613,601,240 - 13,632,705 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001034610   ⟸   NM_001039521
- UniProtKB: Q8K052 (UniProtKB/Swiss-Prot),   Q7TNE7 (UniProtKB/Swiss-Prot),   B2RS91 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000023363   ⟸   ENSMUST00000023363
RefSeq Acc Id: XP_036015620   ⟸   XM_036159727
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2RS91-F1-model_v2 AlphaFold B2RS91 1-656 view protein structure

Promoters
RGD ID:6827477
Promoter ID:MM_KWN:20176
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Kidney,   Lung,   MEF_B4,   Spleen
Transcripts:NM_001039521
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361613,779,826 - 13,780,882 (+)MPROMDB
RGD ID:8685500
Promoter ID:EPDNEW_M20781
Type:initiation region
Name:Rrn3_1
Description:Mus musculus RRN3 RNA polymerase I transcription factor homolog, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381613,780,745 - 13,780,805EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1925255 AgrOrtholog
Ensembl Genes ENSMUSG00000022682 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000023363 ENTREZGENE
  ENSMUST00000023363.8 UniProtKB/Swiss-Prot
InterPro ARM-type_fold UniProtKB/Swiss-Prot
  RNA_pol_I_trans_ini_fac_RRN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:106298 UniProtKB/Swiss-Prot
MGD MGI:1925255 ENTREZGENE
NCBI Gene Rrn3 ENTREZGENE
PANTHER PTHR12790 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RRN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rrn3 PhenoGen
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot
UniProt B2RS91 ENTREZGENE
  Q3TD74_MOUSE UniProtKB/TrEMBL
  Q7TNE7 ENTREZGENE
  Q8K052 ENTREZGENE
  RRN3_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q7TNE7 UniProtKB/Swiss-Prot
  Q8K052 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-08-26 Rrn3  RRN3 RNA polymerase I transcription factor homolog (yeast)  E130302O19Rik  RIKEN cDNA E130302O19 gene  Symbol and/or name updated 27372883 PROVISIONAL
2024-08-21 E130302O19Rik  RIKEN cDNA E130302O19 gene  Rrn3  RRN3 RNA polymerase I transcription factor homolog (yeast)  Symbol and/or name change 5135510 APPROVED