Brf1 (BRF1, RNA polymerase III transcription initiation factor subunit) - Rat Genome Database

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Gene: Brf1 (BRF1, RNA polymerase III transcription initiation factor subunit) Rattus norvegicus
Analyze
Symbol: Brf1
Name: BRF1, RNA polymerase III transcription initiation factor subunit
RGD ID: 1311158
Description: Predicted to have RNA polymerase III general transcription initiation factor activity and RNA polymerase III type 3 promoter sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase III. Predicted to localize to nucleus; transcription factor TFIIIB complex; and transcription preinitiation complex. Used to study fibroma. Orthologous to human BRF1 (BRF1 RNA polymerase III transcription initiation factor subunit); PARTICIPATES IN histone modification pathway; RNA polymerase III transcription pathway; INTERACTS WITH acrylamide; bisphenol A; fenvalerate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB; BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae); BRF1, RNA polymerase III transcription initiation factor 90 subunit; LOC299347; transcription factor IIIB 90 kDa subunit
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
mRatBN7.26132,034,380 - 132,081,296 (-)NCBI
Rnor_6.0 Ensembl6137,765,122 - 137,808,303 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06137,762,230 - 137,808,573 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06146,758,410 - 146,804,495 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46137,962,953 - 138,007,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16137,969,414 - 138,013,785 (-)NCBI
Celera6129,575,149 - 129,619,238 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:14976220   PMID:16407335  


Genomics

Comparative Map Data
Brf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26132,034,380 - 132,081,296 (-)NCBI
Rnor_6.0 Ensembl6137,765,122 - 137,808,303 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06137,762,230 - 137,808,573 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06146,758,410 - 146,804,495 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46137,962,953 - 138,007,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16137,969,414 - 138,013,785 (-)NCBI
Celera6129,575,149 - 129,619,238 (-)NCBICelera
Cytogenetic Map6q32NCBI
BRF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14105,209,286 - 105,315,589 (-)EnsemblGRCh38hg38GRCh38
GRCh3814105,209,286 - 105,315,589 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714105,675,623 - 105,781,926 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3614104,746,668 - 104,838,374 (-)NCBINCBI36hg18NCBI36
Build 3414104,746,669 - 104,785,813NCBI
Celera1485,728,231 - 85,815,347 (-)NCBI
Cytogenetic Map14q32.33NCBI
HuRef1485,867,702 - 85,977,984 (-)NCBIHuRef
CHM1_114105,613,624 - 105,719,675 (-)NCBICHM1_1
Brf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912112,919,251 - 112,964,327 (-)NCBIGRCm39mm39
GRCm39 Ensembl12112,923,705 - 112,964,324 (-)Ensembl
GRCm3812112,955,631 - 113,000,706 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12112,960,085 - 113,000,704 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712114,198,073 - 114,238,832 (-)NCBIGRCm37mm9NCBIm37
MGSCv3612113,407,670 - 113,448,429 (-)NCBImm8
Celera12114,169,891 - 114,214,927 (-)NCBICelera
Cytogenetic Map12F1NCBI
Brf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555383,470,249 - 3,544,704 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555383,469,322 - 3,544,704 (-)NCBIChiLan1.0ChiLan1.0
BRF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.114105,635,757 - 105,714,465 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14105,635,757 - 105,714,465 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01485,851,908 - 85,950,489 (-)NCBIMhudiblu_PPA_v0panPan3
BRF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1872,588,578 - 72,632,259 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl872,588,693 - 72,632,263 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha872,099,839 - 72,151,572 (-)NCBI
ROS_Cfam_1.0872,875,602 - 72,927,645 (-)NCBI
UMICH_Zoey_3.1872,556,286 - 72,608,091 (-)NCBI
UNSW_CanFamBas_1.0872,607,209 - 72,658,851 (-)NCBI
UU_Cfam_GSD_1.0872,997,125 - 73,048,881 (-)NCBI
Brf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086401,436,877 - 1,500,298 (+)NCBI
SpeTri2.0NW_004936621265,834 - 329,255 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BRF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.27131,386,132 - 131,389,518 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BRF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12483,117,823 - 83,192,435 (-)NCBI
ChlSab1.1 Ensembl2483,117,685 - 83,192,431 (-)Ensembl
Vero_WHO_p1.0NW_02366605370,562,181 - 70,642,058 (-)NCBI
Brf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624734213,536 - 280,816 (+)NCBI

Position Markers
RH135284  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06137,765,220 - 137,765,419NCBIRnor6.0
Rnor_5.06146,761,402 - 146,761,601UniSTSRnor5.0
RGSC_v3.46137,963,051 - 137,963,250UniSTSRGSC3.4
Celera6129,575,247 - 129,575,446UniSTS
RH 3.4 Map6782.7UniSTS
Cytogenetic Map6q32UniSTS
AI072236  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06137,787,720 - 137,787,912NCBIRnor6.0
Rnor_5.06146,783,902 - 146,784,094UniSTSRnor5.0
RGSC_v3.46137,985,712 - 137,985,904UniSTSRGSC3.4
Celera6129,597,746 - 129,597,938UniSTS
RH 3.4 Map6783.1UniSTS
Cytogenetic Map6q32UniSTS
RH135404  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06137,790,314 - 137,790,523NCBIRnor6.0
Rnor_5.06146,786,496 - 146,786,705UniSTSRnor5.0
RGSC_v3.46137,988,306 - 137,988,515UniSTSRGSC3.4
Celera6129,600,340 - 129,600,549UniSTS
RH 3.4 Map6783.1UniSTS
Cytogenetic Map6q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6132652096138068606Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6127286494144745573Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6130561943144745573Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6127286494147249902Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6127286494147991367Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:69
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000019689
Prediction methods: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.


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 29 38 22 19 22 2 2 74 35 41 11 2
Low 14 19 19 19 6 9 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019689   ⟹   ENSRNOP00000019689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6137,765,122 - 137,808,303 (-)Ensembl
RefSeq Acc Id: NM_001106761   ⟹   NP_001100231
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,037,272 - 132,081,278 (-)NCBI
Rnor_6.06137,765,122 - 137,808,303 (-)NCBI
Rnor_5.06146,758,410 - 146,804,495 (-)NCBI
RGSC_v3.46137,962,953 - 138,007,641 (-)RGD
Celera6129,575,149 - 129,619,238 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240658   ⟹   XP_006240720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,034,381 - 132,081,296 (-)NCBI
Rnor_6.06137,762,230 - 137,808,573 (-)NCBI
Rnor_5.06146,758,410 - 146,804,495 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764931   ⟹   XP_008763153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,034,380 - 132,070,134 (-)NCBI
Rnor_6.06137,762,230 - 137,797,301 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594111   ⟹   XP_017449600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,034,380 - 132,062,209 (-)NCBI
Rnor_6.06137,762,230 - 137,792,909 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594112   ⟹   XP_017449601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,034,380 - 132,070,132 (-)NCBI
Rnor_6.06137,762,230 - 137,797,301 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112104   ⟹   XP_038968032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,034,381 - 132,081,287 (-)NCBI
RefSeq Acc Id: XM_039112105   ⟹   XP_038968033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26132,046,270 - 132,081,287 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100231   ⟸   NM_001106761
- UniProtKB: D4A8W8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240720   ⟸   XM_006240658
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008763153   ⟸   XM_008764931
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017449601   ⟸   XM_017594112
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017449600   ⟸   XM_017594111
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000019689   ⟸   ENSRNOT00000019689
RefSeq Acc Id: XP_038968032   ⟸   XM_039112104
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968033   ⟸   XM_039112105
- Peptide Label: isoform X5
Protein Domains
TFIIB-type

Transcriptome

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

Promoters
RGD ID:13694860
Promoter ID:EPDNEW_R5383
Type:multiple initiation site
Name:Brf1_1
Description:BRF1, RNA polymerase III transcription initiation factor subunit
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_6.06137,808,356 - 137,808,416EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311158 AgrOrtholog
Ensembl Genes ENSRNOG00000014595 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019689 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019689 ENTREZGENE, UniProtKB/TrEMBL
InterPro Brf1 UniProtKB/TrEMBL
  BRF1_TBP-bd UniProtKB/TrEMBL
  Cyclin-like_sf UniProtKB/TrEMBL
  Cyclin_related UniProtKB/TrEMBL
  TFIIB-related UniProtKB/TrEMBL
  TFIIB_cyclin UniProtKB/TrEMBL
  Znf_TFIIB UniProtKB/TrEMBL
KEGG Report rno:299347 UniProtKB/TrEMBL
NCBI Gene 299347 ENTREZGENE
PANTHER PTHR11618:SF4 UniProtKB/TrEMBL
  TFIIB_euk_relate UniProtKB/TrEMBL
Pfam BRF1 UniProtKB/TrEMBL
  TFIIB UniProtKB/TrEMBL
  TFIIB_Zn_Ribbon UniProtKB/TrEMBL
PhenoGen Brf1 PhenoGen
PRINTS TIFACTORIIB UniProtKB/TrEMBL
PROSITE ZF_TFIIB UniProtKB/TrEMBL
SMART CYCLIN UniProtKB/TrEMBL
Superfamily-SCOP Cyclin_like UniProtKB/TrEMBL
UniProt D4A8W8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-06-12 Brf1  BRF1, RNA polymerase III transcription initiation factor subunit  Brf1  BRF1, RNA polymerase III transcription initiation factor 90 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-06-05 Brf1  BRF1, RNA polymerase III transcription initiation factor 90 subunit  Brf1  BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Brf1  BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)   Brf1_predicted  BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Brf1_predicted  BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED