Gtf2b (general transcription factor IIB) - Rat Genome Database
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Gene: Gtf2b (general transcription factor IIB) Rattus norvegicus
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Symbol: Gtf2b
Name: general transcription factor IIB
RGD ID: 619735
Description: Predicted to have several functions, including RNA polymerase II core promoter sequence-specific DNA binding activity; RNA polymerase II general transcription initiation factor activity; and transcription factor binding activity. Predicted to be involved in several processes, including RNA polymerase II core complex assembly; positive regulation by host of viral transcription; and transcription initiation from RNA polymerase II promoter. Predicted to localize to chromosome; nucleoplasm; and transcription preinitiation complex. Orthologous to human GTF2B (general transcription factor IIB); PARTICIPATES IN RNA polymerase II transcription initiation pathway; INTERACTS WITH 2,4-dinitrotoluene; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: general transcription factor TFIIB; RNA polymerase II alpha initiation factor; transcription initiation factor IIB
Orthologs:
Homo sapiens (human) : GTF2B (general transcription factor IIB)  HGNC  Alliance
Mus musculus (house mouse) : Gtf2b (general transcription factor IIB)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Gtf2b (general transcription factor IIB)
Pan paniscus (bonobo/pygmy chimpanzee) : GTF2B (general transcription factor IIB)
Canis lupus familiaris (dog) : GTF2B (general transcription factor IIB)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Gtf2b (general transcription factor IIB)
Sus scrofa (pig) : GTF2B (general transcription factor IIB)
Chlorocebus sabaeus (African green monkey) : GTF2B (general transcription factor IIB)
Heterocephalus glaber (naked mole-rat) : Gtf2b (general transcription factor IIB)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02248,709,433 - 248,727,741 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2248,715,281 - 248,727,741 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02267,239,559 - 267,257,867 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42240,877,342 - 240,895,650 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12240,864,081 - 240,882,390 (+)NCBI
Celera2223,777,527 - 223,795,808 (+)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model



Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1517211   PMID:1876184   PMID:3029109   PMID:7601352   PMID:7675079   PMID:8413225   PMID:8504927   PMID:8515820   PMID:8516312   PMID:8524305   PMID:8972203   PMID:9420329  
PMID:9722567   PMID:9841876   PMID:10318856   PMID:10619841   PMID:10893273   PMID:11045620   PMID:12477932   PMID:12931194   PMID:14644612   PMID:15489334   PMID:16230532   PMID:17997859  
PMID:18722179   PMID:22227519   PMID:22323595   PMID:22869340   PMID:23264107   PMID:24441171   PMID:27193682   PMID:29158257  


Genomics

Comparative Map Data
Gtf2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02248,709,433 - 248,727,741 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2248,715,281 - 248,727,741 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02267,239,559 - 267,257,867 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42240,877,342 - 240,895,650 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12240,864,081 - 240,882,390 (+)NCBI
Celera2223,777,527 - 223,795,808 (+)NCBICelera
Cytogenetic Map2q44NCBI
GTF2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl188,852,633 - 88,891,944 (-)EnsemblGRCh38hg38GRCh38
GRCh38188,852,633 - 88,891,944 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37189,318,321 - 89,357,301 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36189,090,909 - 89,129,889 (-)NCBINCBI36hg18NCBI36
Build 34189,030,635 - 89,069,275NCBI
Celera187,564,104 - 87,603,098 (-)NCBI
Cytogenetic Map1p22.2NCBI
HuRef187,435,703 - 87,474,719 (-)NCBIHuRef
CHM1_1189,433,373 - 89,472,373 (-)NCBICHM1_1
Gtf2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393142,471,008 - 142,489,367 (+)NCBI
GRCm383142,765,247 - 142,783,606 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3142,765,045 - 142,783,606 (+)EnsemblGRCm38mm10GRCm38
MGSCv373142,428,211 - 142,446,570 (+)NCBIGRCm37mm9NCBIm37
MGSCv363142,702,633 - 142,720,992 (+)NCBImm8
Celera3149,197,374 - 149,215,676 (+)NCBICelera
Cytogenetic Map3H1NCBI
Gtf2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554235,420,584 - 5,447,148 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554235,420,795 - 5,447,148 (+)NCBIChiLan1.0ChiLan1.0
GTF2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1190,319,637 - 90,359,134 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl190,319,637 - 90,359,134 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0191,568,296 - 91,607,467 (-)NCBI
GTF2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl659,492,055 - 59,527,054 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1659,491,986 - 59,527,142 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Gtf2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936732148,702 - 178,992 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4127,522,524 - 127,571,378 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14127,522,802 - 127,559,605 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24139,747,986 - 139,784,762 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GTF2B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2044,527,599 - 44,566,424 (+)Ensembl
ChlSab1.12044,527,150 - 44,566,398 (+)NCBI
Gtf2b
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
BF389714  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02248,722,087 - 248,722,215NCBIRnor6.0
Rnor_5.02267,252,213 - 267,252,341UniSTSRnor5.0
RGSC_v3.42240,889,996 - 240,890,124UniSTSRGSC3.4
Celera2223,790,154 - 223,790,282UniSTS
Cytogenetic Map2q44UniSTS
RH 3.4 Map21581.3UniSTS
RH136605  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02248,727,420 - 248,727,583NCBIRnor6.0
Rnor_5.02267,257,546 - 267,257,709UniSTSRnor5.0
RGSC_v3.42240,895,329 - 240,895,492UniSTSRGSC3.4
Celera2223,795,487 - 223,795,650UniSTS
Cytogenetic Map2q44UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204585642249585642Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2204585642249585642Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2214870793251212353Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2217498545254132424Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2217743855262743855Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2221488355254121739Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2228712271266435125Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2228712271266435125Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2228712271266435125Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2228712271266435125Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2228712271266435125Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2229606682264899009Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2229793522266435125Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2231224020254132424Rat
631514Scl8Serum cholesterol level QTL84.4blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)2231621666266435125Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2233013605253626471Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2235289967257110527Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2237712398257579826Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2240679103266435125Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2240679103266435125Rat
631563Hcuc3Hepatic copper content QTL 33.87hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2245893572266435125Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:185
Count of miRNA genes:141
Interacting mature miRNAs:159
Transcripts:ENSRNOT00000015032
Prediction methods:Microtar, 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.


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 37 57 41 19 41 1 1 74 35 41 11 1
Low 6 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015032   ⟹   ENSRNOP00000015033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2248,723,255 - 248,727,741 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089648   ⟹   ENSRNOP00000070077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2248,715,281 - 248,727,481 (+)Ensembl
RefSeq Acc Id: NM_031041   ⟹   NP_112303
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02248,709,433 - 248,727,741 (+)NCBI
Rnor_5.02267,239,559 - 267,257,867 (+)NCBI
RGSC_v3.42240,877,342 - 240,895,650 (+)RGD
Celera2223,777,527 - 223,795,808 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_112303 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85345 (Get FASTA)   NCBI Sequence Viewer  
  CAA46766 (Get FASTA)   NCBI Sequence Viewer  
  EDL82360 (Get FASTA)   NCBI Sequence Viewer  
  P62916 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_112303   ⟸   NM_031041
- UniProtKB: P62916 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070077   ⟸   ENSRNOT00000089648
RefSeq Acc Id: ENSRNOP00000015033   ⟸   ENSRNOT00000015032
Protein Domains
CYCLIN

Transcriptome

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


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)
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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:619735 AgrOrtholog
Ensembl Genes ENSRNOG00000011135 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015033 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070077 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015032 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089648 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7303747 IMAGE-MGC_LOAD
InterPro Cyclin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIB_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIB_cyclin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_TFIIB UniProtKB/Swiss-Prot
KEGG Report rno:81673 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105412 IMAGE-MGC_LOAD
NCBI Gene 81673 ENTREZGENE
PANTHER PTHR11618 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TF_Zn_Ribbon UniProtKB/Swiss-Prot
  TFIIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gtf2b PhenoGen
PRINTS TIFACTORIIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TFIIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_TFIIB UniProtKB/Swiss-Prot
SMART CYCLIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47954 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.6109 ENTREZGENE
UniProt A0A0A0MXW7_RAT UniProtKB/TrEMBL
  A0A0G2JWZ8_RAT UniProtKB/TrEMBL
  P62916 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P29053 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Gtf2b  general transcription factor IIB      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Gtf2b  general transcription factor IIB      Symbol and Name status set to provisional 70820 PROVISIONAL

 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.