Tfeb (transcription factor EB) - Rat Genome Database

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Gene: Tfeb (transcription factor EB) Rattus norvegicus
Analyze
Symbol: Tfeb
Name: transcription factor EB
RGD ID: 1309583
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including cellular response to amino acid starvation; defense response to Gram-negative bacterium; and lysosome localization. Predicted to act upstream of or within lysosome organization and positive regulation of transcription, DNA-templated. Predicted to be located in cytosol; lysosomal membrane; and nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human TFEB (transcription factor EB); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC316214; MGC116240; Tcfeb
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
mRatBN7.2913,198,890 - 13,254,726 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl913,198,891 - 13,254,714 (-)Ensembl
Rnor_6.0915,208,141 - 15,264,101 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl915,207,822 - 15,214,596 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0914,132,621 - 14,188,412 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,665,061 - 8,671,743 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.198,664,602 - 8,671,285 (-)NCBI
Celera910,951,098 - 10,957,780 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9806910   PMID:12477932   PMID:15994295   PMID:16936731   PMID:19556463   PMID:21617040   PMID:22343943   PMID:22576015   PMID:22692423   PMID:23434374   PMID:26601776   PMID:27184844  
PMID:27278822   PMID:28002813   PMID:29146937   PMID:32085781   PMID:32306793   PMID:32716134   PMID:34071043   PMID:34482051  


Genomics

Comparative Map Data
Tfeb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2913,198,890 - 13,254,726 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl913,198,891 - 13,254,714 (-)Ensembl
Rnor_6.0915,208,141 - 15,264,101 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl915,207,822 - 15,214,596 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0914,132,621 - 14,188,412 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,665,061 - 8,671,743 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.198,664,602 - 8,671,285 (-)NCBI
Celera910,951,098 - 10,957,780 (-)NCBICelera
Cytogenetic Map9q12NCBI
TFEB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38641,683,978 - 41,736,223 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl641,683,978 - 41,736,259 (-)EnsemblGRCh38hg38GRCh38
GRCh37641,651,716 - 41,703,961 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36641,759,694 - 41,810,776 (-)NCBINCBI36hg18NCBI36
Build 34641,759,694 - 41,810,776NCBI
Celera643,205,150 - 43,257,434 (-)NCBI
Cytogenetic Map6p21.1NCBI
HuRef641,370,592 - 41,422,827 (-)NCBIHuRef
CHM1_1641,655,195 - 41,707,480 (-)NCBICHM1_1
T2T-CHM13v2.0641,512,540 - 41,564,779 (-)NCBI
Tfeb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391748,047,962 - 48,103,341 (+)NCBIGRCm39mm39
GRCm39 Ensembl1748,047,955 - 48,103,344 (+)Ensembl
GRCm381747,737,037 - 47,792,416 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1747,737,030 - 47,792,419 (+)EnsemblGRCm38mm10GRCm38
MGSCv371747,873,986 - 47,929,365 (+)NCBIGRCm37mm9NCBIm37
MGSCv361747,248,935 - 47,255,607 (+)NCBImm8
Celera1751,174,084 - 51,229,512 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1723.99NCBI
Tfeb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,098,976 - 8,141,001 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,102,241 - 8,141,001 (-)NCBIChiLan1.0ChiLan1.0
TFEB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1642,574,416 - 42,596,615 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl642,574,416 - 42,627,031 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0641,268,169 - 41,320,822 (-)NCBIMhudiblu_PPA_v0panPan3
TFEB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11210,367,979 - 10,423,478 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1210,368,599 - 10,452,619 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1210,397,632 - 10,453,009 (-)NCBI
ROS_Cfam_1.01210,848,131 - 10,903,700 (-)NCBI
ROS_Cfam_1.0 Ensembl1210,848,131 - 10,868,839 (-)Ensembl
UMICH_Zoey_3.11210,378,806 - 10,434,436 (-)NCBI
UNSW_CanFamBas_1.01210,462,511 - 10,517,872 (-)NCBI
UU_Cfam_GSD_1.01210,556,169 - 10,611,532 (-)NCBI
Tfeb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494645,726,580 - 45,771,013 (-)NCBI
SpeTri2.0NW_00493647618,189,096 - 18,233,622 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFEB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl736,869,565 - 36,920,875 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1736,870,240 - 36,920,887 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2742,165,273 - 42,189,485 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TFEB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11730,425,893 - 30,478,954 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1730,426,260 - 30,479,124 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604441,678,714 - 41,731,770 (-)NCBIVero_WHO_p1.0
Tfeb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475417,321,162 - 17,358,524 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462475417,321,179 - 17,358,402 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
REN60515  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2913,199,495 - 13,199,742 (+)MAPPERmRatBN7.2
Rnor_6.0915,208,747 - 15,208,993NCBIRnor6.0
Rnor_5.0914,133,227 - 14,133,473UniSTSRnor5.0
RGSC_v3.498,665,667 - 8,665,913UniSTSRGSC3.4
Celera910,951,704 - 10,951,950UniSTS
Cytogenetic Map9q12UniSTS
REN60529  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2913,202,786 - 13,203,036 (+)MAPPERmRatBN7.2
Rnor_6.0915,212,036 - 15,212,285NCBIRnor6.0
Rnor_5.0914,136,516 - 14,136,765UniSTSRnor5.0
RGSC_v3.498,668,956 - 8,669,205UniSTSRGSC3.4
Celera910,954,993 - 10,955,242UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:83
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000039102
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 35 13 6 18 6 7 10 8 23 11 10 7
Low 8 44 35 1 35 1 1 66 12 30 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039102   ⟹   ENSRNOP00000037517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl913,198,891 - 13,206,466 (-)Ensembl
Rnor_6.0 Ensembl915,207,822 - 15,214,596 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112521   ⟹   ENSRNOP00000096641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl913,201,984 - 13,254,714 (-)Ensembl
RefSeq Acc Id: NM_001025707   ⟹   NP_001020878
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,198,890 - 13,205,576 (-)NCBI
Rnor_6.0915,208,141 - 15,214,823 (-)NCBI
Rnor_5.0914,132,621 - 14,188,412 (-)NCBI
RGSC_v3.498,665,061 - 8,671,743 (-)RGD
Celera910,951,098 - 10,957,780 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244442   ⟹   XP_006244504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,198,893 - 13,254,726 (-)NCBI
Rnor_6.0915,208,144 - 15,264,101 (-)NCBI
Rnor_5.0914,132,621 - 14,188,412 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244446   ⟹   XP_006244508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,198,893 - 13,223,161 (-)NCBI
Rnor_6.0915,208,144 - 15,232,418 (-)NCBI
Rnor_5.0914,132,621 - 14,188,412 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083486   ⟹   XP_038939414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,198,893 - 13,254,721 (-)NCBI
RefSeq Acc Id: XM_039083488   ⟹   XP_038939416
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,198,893 - 13,253,166 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020878   ⟸   NM_001025707
- UniProtKB: Q4KLM8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244504   ⟸   XM_006244442
- Peptide Label: isoform X1
- UniProtKB: F7F5J1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244508   ⟸   XM_006244446
- Peptide Label: isoform X1
- UniProtKB: F7F5J1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037517   ⟸   ENSRNOT00000039102
RefSeq Acc Id: XP_038939414   ⟸   XM_039083486
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939416   ⟸   XM_039083488
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000096641   ⟸   ENSRNOT00000112521
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F7F5J1-F1-model_v2 AlphaFold F7F5J1 1-476 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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 15209190 15209191 C T snv MR/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 8666110 8666111 C T snv MR/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309583 AgrOrtholog
BioCyc Gene G2FUF-28283 BioCyc
Ensembl Genes ENSRNOG00000014666 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037517 ENTREZGENE
  ENSRNOP00000037517.6 UniProtKB/TrEMBL
  ENSRNOP00000096641.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039102 ENTREZGENE
  ENSRNOT00000039102.6 UniProtKB/TrEMBL
  ENSRNOT00000112521.1 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7460021 IMAGE-MGC_LOAD
InterPro bHLH_ZIP_TF_MiT/TFE UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  HLH_DNA_bd UniProtKB/TrEMBL
  MiT/TFE_N UniProtKB/TrEMBL
  TFEB UniProtKB/TrEMBL
KEGG Report rno:316214 UniProtKB/TrEMBL
MGC_CLONE MGC:116240 IMAGE-MGC_LOAD
NCBI Gene 316214 ENTREZGENE
PANTHER PTHR45776:SF5 UniProtKB/TrEMBL
Pfam DUF3371 UniProtKB/TrEMBL
  HLH UniProtKB/TrEMBL
  MITF_TFEB_C_3_N UniProtKB/TrEMBL
PhenoGen Tfeb PhenoGen
PROSITE HLH UniProtKB/TrEMBL
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt A0A8I6ATP3_RAT UniProtKB/TrEMBL
  F7F5J1 ENTREZGENE, UniProtKB/TrEMBL
  Q4KLM8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tfeb  transcription factor EB  Tcfeb  transcription factor EB  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tcfeb  transcription factor EB  Tcfeb_predicted  transcription factor EB (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tcfeb_predicted  transcription factor EB (predicted)      Symbol and Name status set to approved 70820 APPROVED