Tbxt (T-box transcription factor T) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Tbxt (T-box transcription factor T) Rattus norvegicus
Analyze
Symbol: Tbxt
Name: T-box transcription factor T
RGD ID: 1310141
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in cellular response to retinoic acid. Predicted to be located in chromatin; cytoplasm; and nucleoplasm. Human ortholog(s) of this gene implicated in neural tube defect. Orthologous to human TBXT (T-box transcription factor T); INTERACTS WITH bisphenol A; Cuprizon; glycidol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: brachyury; brachyury homolog; brachyury homolog (mouse); LOC292301; T; T brachyury transcription factor; T, brachyury homolog; T, brachyury homolog (mouse)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2152,298,099 - 52,309,813 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl152,298,099 - 52,305,864 (-)Ensembl
Rnor_6.0152,887,067 - 52,900,691 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl152,887,067 - 52,894,832 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0154,139,554 - 54,147,385 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4146,937,223 - 46,944,988 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1146,940,188 - 46,947,933 (-)NCBI
Celera148,061,384 - 48,069,149 (-)NCBICelera
Cytogenetic Map1q12NCBI
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
cellular_component  (ND)
chromatin  (ISO)
cytoplasm  (ISO)
nucleoplasm  (IEA,ISO)
nucleus  (ISO)

References

Additional References at PubMed
PMID:924142   PMID:7588606   PMID:7589801   PMID:7720590   PMID:7883069   PMID:8155581   PMID:8293872   PMID:8344258   PMID:9420335   PMID:10349618   PMID:11071760   PMID:15384171  
PMID:16801560   PMID:16835439   PMID:17360443   PMID:18462699   PMID:19796622   PMID:20350929   PMID:20809182   PMID:21632880   PMID:22164283   PMID:22611028   PMID:24253444  


Genomics

Comparative Map Data
Tbxt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2152,298,099 - 52,309,813 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl152,298,099 - 52,305,864 (-)Ensembl
Rnor_6.0152,887,067 - 52,900,691 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl152,887,067 - 52,894,832 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0154,139,554 - 54,147,385 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4146,937,223 - 46,944,988 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1146,940,188 - 46,947,933 (-)NCBI
Celera148,061,384 - 48,069,149 (-)NCBICelera
Cytogenetic Map1q12NCBI
TBXT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386166,157,656 - 166,168,655 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6166,157,656 - 166,168,700 (-)EnsemblGRCh38hg38GRCh38
GRCh376166,571,144 - 166,582,143 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366166,491,076 - 166,502,121 (-)NCBINCBI36hg18NCBI36
Build 346166,541,496 - 166,552,542NCBI
Celera6167,310,712 - 167,321,757 (-)NCBI
Cytogenetic Map6q27NCBI
HuRef6164,037,863 - 164,048,876 (-)NCBIHuRef
CHM1_16166,835,290 - 166,846,303 (-)NCBICHM1_1
T2T-CHM13v2.06167,527,458 - 167,538,457 (-)NCBI
T
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39178,653,255 - 8,661,328 (+)NCBIGRCm39mm39
GRCm39 Ensembl178,653,255 - 8,661,328 (+)Ensembl
GRCm38178,434,423 - 8,442,496 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl178,434,423 - 8,442,496 (+)EnsemblGRCm38mm10GRCm38
MGSCv37178,627,288 - 8,635,361 (+)NCBIGRCm37mm9NCBIm37
MGSCv36178,272,597 - 8,280,670 (+)NCBImm8
Celera178,480,245 - 8,488,318 (+)NCBICelera
Cytogenetic Map17A1NCBI
cM Map174.92NCBI
Tbxt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543915,676,095 - 15,683,554 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543915,675,680 - 15,683,542 (+)NCBIChiLan1.0ChiLan1.0
TBXT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16169,095,723 - 169,106,595 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6169,095,723 - 169,106,595 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06164,112,117 - 164,122,253 (-)NCBIMhudiblu_PPA_v0panPan3
TBXT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1154,183,495 - 54,192,331 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl154,183,153 - 54,192,352 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha154,970,966 - 54,979,790 (-)NCBI
ROS_Cfam_1.0154,360,266 - 54,369,833 (-)NCBI
ROS_Cfam_1.0 Ensembl154,360,928 - 54,369,833 (-)Ensembl
UMICH_Zoey_3.1154,257,349 - 54,266,189 (-)NCBI
UNSW_CanFamBas_1.0154,107,519 - 54,116,264 (-)NCBI
UU_Cfam_GSD_1.0154,733,858 - 54,742,687 (-)NCBI
Tbxt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946148,774,775 - 148,782,886 (-)NCBI
SpeTri2.0NW_00493648916,027,359 - 16,035,041 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBXT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl12,717,165 - 2,724,976 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.112,717,165 - 2,725,561 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213,857,228 - 3,861,219 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TBXT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11393,854,086 - 93,864,910 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604065,656,160 - 65,666,958 (-)NCBIVero_WHO_p1.0
Tbxt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478513,058,444 - 13,066,719 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462478513,058,520 - 13,066,607 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
T  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2152,303,300 - 52,304,181 (+)MAPPERmRatBN7.2
Rnor_6.0152,892,269 - 52,893,149NCBIRnor6.0
Rnor_5.0154,144,756 - 54,145,636UniSTSRnor5.0
RGSC_v3.4146,942,425 - 46,943,305UniSTSRGSC3.4
Celera148,066,586 - 48,067,466UniSTS
Cytogenetic Map1q11UniSTS
T  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2152,304,121 - 52,304,935 (+)MAPPERmRatBN7.2
Rnor_6.0152,893,090 - 52,893,903NCBIRnor6.0
Rnor_5.0154,145,577 - 54,146,390UniSTSRnor5.0
RGSC_v3.4146,943,246 - 46,944,059UniSTSRGSC3.4
Celera148,067,407 - 48,068,220UniSTS
Cytogenetic Map1q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:151
Count of miRNA genes:103
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000016471
Prediction methods:Microtar, 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

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 2 1
Low 4 7 39 27 10
Below cutoff 4 7 2 11 2 1 1 35 16 12 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016471   ⟹   ENSRNOP00000016471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl152,298,099 - 52,305,864 (-)Ensembl
Rnor_6.0 Ensembl152,887,067 - 52,894,832 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110131   ⟹   ENSRNOP00000092633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl152,298,099 - 52,305,864 (-)Ensembl
RefSeq Acc Id: NM_001106209   ⟹   NP_001099679
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2152,298,099 - 52,305,864 (-)NCBI
Rnor_6.0152,887,067 - 52,894,832 (-)NCBI
Rnor_5.0154,139,554 - 54,147,385 (-)NCBI
RGSC_v3.4146,937,223 - 46,944,988 (-)RGD
Celera148,061,384 - 48,069,149 (-)RGD
Sequence:
RefSeq Acc Id: XM_017588873   ⟹   XP_017444362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2152,298,104 - 52,309,813 (-)NCBI
Rnor_6.0152,887,447 - 52,900,691 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039103470   ⟹   XP_038959398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2152,298,104 - 52,309,813 (-)NCBI
RefSeq Acc Id: XM_039103475   ⟹   XP_038959403
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2152,298,104 - 52,309,812 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099679 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444362 (Get FASTA)   NCBI Sequence Viewer  
  XP_038959398 (Get FASTA)   NCBI Sequence Viewer  
  XP_038959403 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83107 (Get FASTA)   NCBI Sequence Viewer  
  EDL83108 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099679   ⟸   NM_001106209
- UniProtKB: D4A4W8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017444362   ⟸   XM_017588873
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000016471   ⟸   ENSRNOT00000016471
RefSeq Acc Id: XP_038959398   ⟸   XM_039103470
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038959403   ⟸   XM_039103475
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000092633   ⟸   ENSRNOT00000110131

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4W8-F1-model_v2 AlphaFold D4A4W8 1-436 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 54145588 54145589 T G snv ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 46943257 46943258 T G snv ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310141 AgrOrtholog
BioCyc Gene G2FUF-61518 BioCyc
Ensembl Genes ENSRNOG00000012229 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016471 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000092633 ENTREZGENE
Ensembl Transcript ENSRNOT00000016471 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000110131 ENTREZGENE
Gene3D-CATH 2.60.40.820 UniProtKB/TrEMBL
InterPro p53-like_TF_DNA-bd UniProtKB/TrEMBL
  T-box_sf UniProtKB/TrEMBL
  TF_Brachyury UniProtKB/TrEMBL
  TF_T-box UniProtKB/TrEMBL
  TF_T-box_CS UniProtKB/TrEMBL
KEGG Report rno:292301 UniProtKB/TrEMBL
NCBI Gene 292301 ENTREZGENE
PANTHER TF_T-box UniProtKB/TrEMBL
Pfam T-box UniProtKB/TrEMBL
PhenoGen Tbxt PhenoGen
PRINTS BRACHYURY UniProtKB/TrEMBL
  TBOX UniProtKB/TrEMBL
PROSITE TBOX_1 UniProtKB/TrEMBL
  TBOX_2 UniProtKB/TrEMBL
  TBOX_3 UniProtKB/TrEMBL
SMART TBOX UniProtKB/TrEMBL
Superfamily-SCOP P53_like_DNA_bnd UniProtKB/TrEMBL
UniProt D4A4W8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-12-22 Tbxt  T-box transcription factor T  T brachyury transcription factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-08-13 T brachyury transcription factor  brachyury  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 brachyury  brachyury homolog (mouse)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-26 brachyury homolog (mouse)  T, brachyury homolog (mouse)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-09 T, brachyury homolog (mouse)  brachyury  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 brachyury  T_predicted  T, brachyury homolog (mouse) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 T_predicted  T, brachyury homolog (mouse) (predicted)    brachyury (predicted)  Name updated 1299863 APPROVED
2005-01-12 T_predicted  brachyury (predicted)      Symbol and Name status set to approved 70820 APPROVED