Tcf3 (transcription factor 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Tcf3 (transcription factor 3) Rattus norvegicus
Analyze
Symbol: Tcf3
Name: transcription factor 3
RGD ID: 620914
Description: Enables PDZ domain binding activity and bHLH transcription factor binding activity. Contributes to E-box binding activity. Involved in positive regulation of DNA-templated transcription and positive regulation of gene expression. Part of transcription regulator complex. Human ortholog(s) of this gene implicated in agammaglobulinemia 8A; agammaglobulinemia 8B; and colorectal cancer. Orthologous to human TCF3 (transcription factor 3); PARTICIPATES IN acute myeloid leukemia pathway; arrhythmogenic right ventricular cardiomyopathy pathway; basal cell carcinoma pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: immunoglobulin enhancer-binding factor E12/E47; LOC100364490; LOC688265; Pan2; pancreas specific transcription factor 1c; similar to Transcription factor E2-alpha (Immunoglobulin enhancer-binding factor E12/E47) (Transcription factor 3) (TCF-3) (Transcription regulator Pan); TCF-3; Tcfe2a; transcription factor E2-alpha; transcription factor E2a; transcription factor E2a-like; transcription regulator Pan
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,931,251 - 9,952,994 (+)NCBIGRCr8
mRatBN7.279,280,571 - 9,302,315 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,280,571 - 9,302,314 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,157,100 - 12,178,811 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,032,424 - 14,054,151 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,900,016 - 11,921,838 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,146,642 - 12,168,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,144,162 - 12,168,410 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,316,323 - 12,338,455 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,791,311 - 10,813,613 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1710,791,310 - 10,813,165 (+)NCBI
Celera77,461,200 - 7,481,028 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
caffeine  (ISO)
carbamazepine  (ISO)
CGP 52608  (ISO)
cisplatin  (EXP)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
coumarin  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
Dibutyl phosphate  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Erionite  (ISO)
ethyl methanesulfonate  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
hydrogen cyanide  (ISO)
hydrogen peroxide  (ISO)
isoprenaline  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methyl methanesulfonate  (ISO)
N-Vinyl-2-pyrrolidone  (EXP)
ochratoxin A  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
piroxicam  (ISO)
potassium cyanide  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
thapsigargin  (ISO)
theophylline  (ISO)
topotecan  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA,ISO)
cytoplasm  (IEA,ISO,ISS)
cytosol  (ISO)
euchromatin  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleosome  (ISO)
nucleus  (IEA,ISO,ISS)
protein-containing complex  (ISO,ISS)
RNA polymerase II transcription regulator complex  (IEA,ISO)
transcription regulator complex  (IBA,IDA,ISO,ISS)

References

References - curated
# Reference Title Reference Citation
1. Role of the transcriptional coactivator CBP/p300 in linking basic helix-loop-helix and CREB responses for follicle-stimulating hormone-mediated activation of the transferrin promoter in Sertoli cells. Chaudhary J and Skinner MK, Biol Reprod. 2001 Aug;65(2):568-74.
2. Scleraxis and E47 cooperatively regulate the Sox9-dependent transcription. Furumatsu T, etal., Int J Biochem Cell Biol. 2010 Jan;42(1):148-56. doi: 10.1016/j.biocel.2009.10.003. Epub 2009 Oct 12.
3. 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.
4. E2A predicts prognosis of colorectal cancer patients and regulates cancer cell growth by targeting miR-320a. Huang A, etal., PLoS One. 2014 Jan 13;9(1):e85201. doi: 10.1371/journal.pone.0085201. eCollection 2014.
5. Human IgG antibody profiles differentiate between symptomatic patients with and without colorectal cancer. Kijanka G, etal., Gut. 2010 Jan;59(1):69-78. doi: 10.1136/gut.2009.178574.
6. Hypomethylation-associated up-regulation of TCF3 expression and recurrence in stage II and III colorectal cancer. Li C, etal., PLoS One. 2014 Nov 6;9(11):e112005. doi: 10.1371/journal.pone.0112005. eCollection 2014.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Role of the basic helix-loop-helix transcription factor, scleraxis, in the regulation of Sertoli cell function and differentiation. Muir T, etal., Mol Endocrinol. 2005 Aug;19(8):2164-74. Epub 2005 Apr 14.
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. Pan: a transcriptional regulator that binds chymotrypsin, insulin, and AP-4 enhancer motifs. Nelson C, etal., Genes Dev 1990 Jun;4(6):1035-43.
11. Increased expression of bHLH transcription factor E2A (TCF3) in prostate cancer promotes proliferation and confers resistance to doxorubicin induced apoptosis. Patel D and Chaudhary J, Biochem Biophys Res Commun. 2012 May 25;422(1):146-51. doi: 10.1016/j.bbrc.2012.04.126. Epub 2012 Apr 30.
12. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
13. GOA pipeline RGD automated data pipeline
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Targeted re-sequencing identified rs3106189 at the 5' UTR of TAPBP and rs1052918 at the 3' UTR of TCF3 to be associated with the overall survival of colorectal cancer patients. Shao J, etal., PLoS One. 2013 Aug 5;8(8):e70307. doi: 10.1371/journal.pone.0070307. Print 2013.
16. TCF7 is suppressed by the androgen receptor via microRNA-1-mediated downregulation and is involved in the development of resistance to androgen deprivation in prostate cancer. Siu MK, etal., Prostate Cancer Prostatic Dis. 2017 Jun;20(2):172-178. doi: 10.1038/pcan.2017.2. Epub 2017 Feb 21.
17. Bridge-1, a novel PDZ-domain coactivator of E2A-mediated regulation of insulin gene transcription. Thomas MK, etal., Mol Cell Biol 1999 Dec;19(12):8492-504.
18. Edelfosine Promotes Apoptosis in Androgen-Deprived Prostate Tumors by Increasing ATF3 and Inhibiting Androgen Receptor Activity. Udayakumar TS, etal., Mol Cancer Ther. 2016 Jun;15(6):1353-63. doi: 10.1158/1535-7163.MCT-15-0332. Epub 2016 Mar 4.
19. Loss of ATF3 promotes hormone-induced prostate carcinogenesis and the emergence of CK5(+)CK8(+) epithelial cells. Wang Z, etal., Oncogene. 2016 Jul 7;35(27):3555-64. doi: 10.1038/onc.2015.417. Epub 2015 Nov 2.
20. PAK5-mediated E47 phosphorylation promotes epithelial-mesenchymal transition and metastasis of colon cancer. Zhu G, etal., Oncogene. 2016 Apr 14;35(15):1943-54. doi: 10.1038/onc.2015.259. Epub 2015 Jul 27.
Additional References at PubMed
PMID:1720355   PMID:1766666   PMID:2105528   PMID:2503252   PMID:7933101   PMID:8759016   PMID:8760303   PMID:8889548   PMID:8900141   PMID:9013644   PMID:9545521   PMID:9676199  
PMID:10373552   PMID:10545951   PMID:10749989   PMID:10775504   PMID:10958665   PMID:11439353   PMID:11509675   PMID:11802795   PMID:11812799   PMID:12070084   PMID:12200424   PMID:12435739  
PMID:12446773   PMID:12477932   PMID:12493738   PMID:14573534   PMID:14576336   PMID:14752053   PMID:14757642   PMID:15030778   PMID:15044608   PMID:15121856   PMID:15314159   PMID:15322112  
PMID:15351717   PMID:15509787   PMID:15520228   PMID:16007160   PMID:16043483   PMID:16140986   PMID:16428437   PMID:16648472   PMID:16673016   PMID:17426122   PMID:17430895   PMID:17452521  
PMID:17938243   PMID:18184866   PMID:18214987   PMID:18361414   PMID:18388149   PMID:18550854   PMID:18958875   PMID:19011221   PMID:19323994   PMID:19362560   PMID:19796622   PMID:19799863  
PMID:19801649   PMID:20144608   PMID:21718540   PMID:21828274   PMID:32309849  


Genomics

Comparative Map Data
Tcf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,931,251 - 9,952,994 (+)NCBIGRCr8
mRatBN7.279,280,571 - 9,302,315 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,280,571 - 9,302,314 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,157,100 - 12,178,811 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,032,424 - 14,054,151 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,900,016 - 11,921,838 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,146,642 - 12,168,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,144,162 - 12,168,410 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,316,323 - 12,338,455 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,791,311 - 10,813,613 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1710,791,310 - 10,813,165 (+)NCBI
Celera77,461,200 - 7,481,028 (+)NCBICelera
Cytogenetic Map7q11NCBI
TCF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38191,609,292 - 1,652,615 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl191,609,291 - 1,652,615 (-)EnsemblGRCh38hg38GRCh38
GRCh37191,609,291 - 1,652,614 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36191,560,293 - 1,601,277 (-)NCBINCBI36Build 36hg18NCBI36
Build 34191,560,294 - 1,601,277NCBI
Celera191,544,148 - 1,586,451 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef191,383,232 - 1,423,075 (-)NCBIHuRef
CHM1_1191,609,123 - 1,649,881 (-)NCBICHM1_1
T2T-CHM13v2.0191,580,117 - 1,623,781 (-)NCBIT2T-CHM13v2.0
Tcf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,245,375 - 80,269,814 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1080,245,348 - 80,269,481 (-)EnsemblGRCm39 Ensembl
GRCm381080,409,541 - 80,433,976 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,409,514 - 80,433,647 (-)EnsemblGRCm38mm10GRCm38
MGSCv371079,871,910 - 79,896,398 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361079,812,723 - 79,836,736 (-)NCBIMGSCv36mm8
Celera1081,426,533 - 81,451,021 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Tcf3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,337,870 - 6,367,487 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554956,337,311 - 6,365,193 (+)NCBIChiLan1.0ChiLan1.0
TCF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2205,974,390 - 6,017,153 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1195,205,287 - 5,248,110 (-)NCBINHGRI_mPanPan1
PanPan1.1191,582,297 - 1,622,025 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl191,582,297 - 1,622,025 (-)Ensemblpanpan1.1panPan2
TCF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,255,091 - 57,284,223 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,254,384 - 57,283,981 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,045,568 - 57,076,063 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02057,984,288 - 58,014,495 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2057,985,608 - 58,014,477 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12057,041,346 - 57,071,536 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,520,665 - 57,550,910 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02057,722,526 - 57,752,778 (+)NCBIUU_Cfam_GSD_1.0
Tcf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,921,770 - 216,949,966 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936588884,789 - 912,753 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936588884,817 - 913,052 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TCF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,859,089 - 76,898,351 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,859,079 - 76,906,275 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2278,181,360 - 78,220,554 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TCF3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.161,393,147 - 1,440,515 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl61,393,107 - 1,440,479 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660817,409,480 - 7,459,296 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tcf3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,090,605 - 7,121,428 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248287,090,562 - 7,119,970 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tcf3
81 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:656
Count of miRNA genes:192
Interacting mature miRNAs:229
Transcripts:ENSRNOT00000023473, ENSRNOT00000023597
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat

Markers in Region
AW209082  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,301,989 - 9,302,123 (+)MAPPERmRatBN7.2
Rnor_6.0712,168,075 - 12,168,208NCBIRnor6.0
Rnor_5.0712,338,130 - 12,338,263UniSTSRnor5.0
RGSC_v3.4710,813,288 - 10,813,421UniSTSRGSC3.4
Celera77,480,703 - 7,480,836UniSTS
Cytogenetic Map7q11UniSTS
RH124709  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,302,048 - 9,302,143 (+)MAPPERmRatBN7.2
Rnor_6.0712,168,134 - 12,168,228NCBIRnor6.0
Rnor_5.0712,338,189 - 12,338,283UniSTSRnor5.0
RGSC_v3.4710,813,347 - 10,813,441UniSTSRGSC3.4
Celera77,480,762 - 7,480,856UniSTS
Cytogenetic Map7q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000077122   ⟹   ENSRNOP00000074654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,280,571 - 9,302,314 (+)Ensembl
Rnor_6.0 Ensembl712,144,162 - 12,168,410 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085899   ⟹   ENSRNOP00000071280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,280,571 - 9,302,314 (+)Ensembl
Rnor_6.0 Ensembl712,146,642 - 12,168,399 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118873   ⟹   ENSRNOP00000087531
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,280,571 - 9,302,314 (+)Ensembl
RefSeq Acc Id: NM_001035237   ⟹   NP_001030314
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,931,251 - 9,952,994 (+)NCBI
mRatBN7.279,280,571 - 9,302,315 (+)NCBI
Rnor_6.0712,146,642 - 12,168,400 (+)NCBI
Rnor_5.0712,316,323 - 12,338,455 (+)NCBI
RGSC_v3.4710,791,311 - 10,813,613 (+)RGD
Celera77,461,200 - 7,481,028 (+)NCBI
Sequence:
RefSeq Acc Id: NM_133524   ⟹   NP_598208
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,931,251 - 9,952,994 (+)NCBI
mRatBN7.279,280,571 - 9,302,315 (+)NCBI
Rnor_6.0712,146,642 - 12,168,400 (+)NCBI
Rnor_5.0712,316,323 - 12,338,455 (+)NCBI
RGSC_v3.4710,791,311 - 10,813,613 (+)RGD
Celera77,461,200 - 7,481,028 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001030314   ⟸   NM_001035237
- Peptide Label: isoform b
- UniProtKB: Q68G29 (UniProtKB/TrEMBL),   E9PTG9 (UniProtKB/TrEMBL),   A0A0G2K030 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_598208   ⟸   NM_133524
- Peptide Label: isoform a
- UniProtKB: Q4VY47 (UniProtKB/Swiss-Prot),   Q08440 (UniProtKB/Swiss-Prot),   P21676 (UniProtKB/Swiss-Prot),   P21677 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074654   ⟸   ENSRNOT00000077122
Ensembl Acc Id: ENSRNOP00000071280   ⟸   ENSRNOT00000085899
Ensembl Acc Id: ENSRNOP00000087531   ⟸   ENSRNOT00000118873
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P21677-F1-model_v2 AlphaFold P21677 1-649 view protein structure

Transcriptome

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

Promoters
RGD ID:13695017
Promoter ID:EPDNEW_R5542
Type:initiation region
Name:Tcf3_1
Description:transcription factor 3
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_6.0712,144,093 - 12,144,153EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620914 AgrOrtholog
BioCyc Gene G2FUF-34943 BioCyc
Ensembl Genes ENSRNOG00000051499 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077122.2 UniProtKB/TrEMBL
  ENSRNOT00000085899.2 UniProtKB/TrEMBL
  ENSRNOT00000118873.1 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123064 IMAGE-MGC_LOAD
InterPro bHLH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NeuroDiff_E-box_TFs UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171046 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93222 IMAGE-MGC_LOAD
NCBI Gene 171046 ENTREZGENE
PANTHER BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR E2-ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tcf3 PhenoGen
PROSITE BHLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051499 RatGTEx
SMART HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47459 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K030 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K8L6_RAT UniProtKB/TrEMBL
  A0A8I6A3B8_RAT UniProtKB/TrEMBL
  E9PTG9 ENTREZGENE
  P21676 ENTREZGENE
  P21677 ENTREZGENE
  Q08440 ENTREZGENE
  Q4VY47 ENTREZGENE
  Q68G29 ENTREZGENE, UniProtKB/TrEMBL
  TFE2_RAT UniProtKB/Swiss-Prot
UniProt Secondary E9PTG9 UniProtKB/TrEMBL
  P21676 UniProtKB/Swiss-Prot
  Q08440 UniProtKB/Swiss-Prot
  Q4VY47 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-04-17 Tcf3  transcription factor 3  LOC100364490  transcription factor E2a-like  Data merged from RGD:2320970 737654 PROVISIONAL
2013-04-17 Tcf3  transcription factor 3  LOC688265  similar to Transcription factor E2-alpha (Immunoglobulin enhancer-binding factor E12/E47) (Transcription factor 3) (TCF-3) (Transcription regulator Pan)  Data merged from RGD:1591161 737654 PROVISIONAL
2010-05-05 LOC100364490  transcription factor E2a-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-12-16 Tcf3  transcription factor 3  Tcfe2a  transcription factor E2a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC688265  similar to Transcription factor E2-alpha (Immunoglobulin enhancer-binding factor E12/E47) (Transcription factor 3) (TCF-3) (Transcription regulator Pan)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-08 Tcfe2a  transcription factor E2a      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Tcfe2a  transcription factor E2a      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein 67.7 kDa 634397