Tff3 (trefoil factor 3) - Rat Genome Database

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Gene: Tff3 (trefoil factor 3) Rattus norvegicus
Analyze
Symbol: Tff3
Name: trefoil factor 3
RGD ID: 3847
Description: Involved in response to peptide hormone. Predicted to localize to extracellular space and secretory granule. Biomarker of colon cancer and pre-malignant neoplasm. Orthologous to human TFF3 (trefoil factor 3); PARTICIPATES IN hypoxia inducible factor pathway; interleukin-4 signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: intestinal trefoil factor; ITF; polypeptide P1.B; rITF; rP1.B; TREFOIL; Trefoil factor (intestinal); trefoil factor 3, intestinal
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2209,193,259 - 9,197,969 (-)NCBI
Rnor_6.0 Ensembl209,850,803 - 9,855,481 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0209,850,800 - 9,855,481 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02012,030,957 - 12,035,638 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4209,469,888 - 9,474,604 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1209,470,114 - 9,474,831 (-)NCBI
Celera2010,718,676 - 10,723,298 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-acetamidofluorene  (EXP)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
adenine  (ISO)
aflatoxin B1  (EXP)
amiodarone  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
Benzo[k]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
cholesterol  (ISO)
ciguatoxin CTX1B  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
coumestrol  (ISO)
cytarabine  (ISO)
deoxynivalenol  (ISO)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
doxorubicin  (EXP,ISO)
enilconazole  (ISO)
Enterolactone  (ISO)
etoposide  (ISO)
fulvestrant  (ISO)
furan  (EXP,ISO)
gamma-linolenic acid  (ISO)
genistein  (ISO)
hydrogen peroxide  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indometacin  (ISO)
irinotecan  (EXP)
melamine  (EXP)
menadione  (ISO)
methapyrilene  (ISO)
mitomycin C  (ISO)
mitoxantrone  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
paracetamol  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
prochloraz  (EXP)
progesterone  (ISO)
propanal  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
SB 203580  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sulfasalazine  (EXP)
sulindac sulfide  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Chinery R, etal., Biochem J 1992 Jul 1;285 ( Pt 1):5-8.
2. Esposito R, etal., Front Cell Infect Microbiol. 2017 Oct 9;7:434. doi: 10.3389/fcimb.2017.00434. eCollection 2017.
3. Fanca-Berthon P, etal., Pediatr Res. 2009 Jul;66(1):47-52. doi: 10.1203/PDR.0b013e3181a2047e.
4. Femia AP, etal., Int J Cancer. 2008 Jan 1;122(1):117-23.
5. Fernandez-Estivariz C, etal., Am J Physiol Regul Integr Comp Physiol 2003 Feb;284(2):R564-73.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Jackerott M, etal., Endocrinology. 2006 Dec;147(12):5752-9. Epub 2006 Sep 14.
9. MGD data from the GO Consortium
10. NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
12. Poulsom R, etal., Scand J Gastroenterol Suppl 1992;192:17-28.
13. Probst JC, etal., Brain Res Mol Brain Res 1995 Nov;33(2):269-76.
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Tan XD, etal., Biochem Biophys Res Commun 1997 Aug 28;237(3):673-7.
18. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
19. Van De Bovenkamp JH, etal., Hum Pathol. 2003 Feb;34(2):156-65.
20. Vestergaard EM, etal., Clin Cancer Res. 2006 Feb 1;12(3 Pt 1):807-12.
21. Wu X, etal., Am J Physiol Endocrinol Metab. 2019 Sep 1;317(3):E436-E445. doi: 10.1152/ajpendo.00454.2018. Epub 2019 Jun 18.
22. Yu H, etal., PLoS One. 2011;6(5):e20334. doi: 10.1371/journal.pone.0020334. Epub 2011 May 23.
Additional References at PubMed
PMID:1763017   PMID:7721858   PMID:8454642   PMID:12477932   PMID:15645444   PMID:15680474   PMID:15818741   PMID:16086236   PMID:16865413   PMID:17436098   PMID:17624936   PMID:18258687  
PMID:18813976   PMID:18979216   PMID:23376485   PMID:24086476   PMID:24588600   PMID:25504043   PMID:29453360   PMID:29723130  


Genomics

Comparative Map Data
Tff3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2209,193,259 - 9,197,969 (-)NCBI
Rnor_6.0 Ensembl209,850,803 - 9,855,481 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0209,850,800 - 9,855,481 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02012,030,957 - 12,035,638 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4209,469,888 - 9,474,604 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1209,470,114 - 9,474,831 (-)NCBI
Celera2010,718,676 - 10,723,298 (-)NCBICelera
Cytogenetic Map20p12NCBI
TFF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2142,311,667 - 42,315,651 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2142,311,667 - 42,315,409 (-)EnsemblGRCh38hg38GRCh38
GRCh382142,311,667 - 42,315,409 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372143,731,777 - 43,735,519 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362142,605,232 - 42,608,775 (-)NCBINCBI36hg18NCBI36
Build 342142,605,232 - 42,608,775NCBI
Celera2128,880,742 - 28,884,671 (-)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2129,149,059 - 29,152,988 (-)NCBIHuRef
CHM1_12143,291,988 - 43,295,917 (-)NCBICHM1_1
Tff3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391731,344,280 - 31,348,585 (-)NCBIGRCm39mm39
GRCm39 Ensembl1731,344,280 - 31,348,620 (-)Ensembl
GRCm381731,125,306 - 31,129,611 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1731,125,306 - 31,129,646 (-)EnsemblGRCm38mm10GRCm38
MGSCv371731,262,251 - 31,266,556 (-)NCBIGRCm37mm9NCBIm37
MGSCv361730,852,327 - 30,856,623 (-)NCBImm8
Celera1732,042,584 - 32,046,915 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1715.8NCBI
Tff3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540739,398,074 - 39,401,248 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540739,398,534 - 39,401,085 (+)NCBIChiLan1.0ChiLan1.0
TFF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12141,948,674 - 41,952,207 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2141,948,696 - 41,952,268 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02128,627,191 - 28,631,341 (-)NCBIMhudiblu_PPA_v0panPan3
TFF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13136,638,762 - 36,641,696 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3135,789,681 - 35,792,613 (-)NCBI
ROS_Cfam_1.03136,155,220 - 36,158,156 (-)NCBI
UMICH_Zoey_3.13136,048,305 - 36,051,229 (-)NCBI
UNSW_CanFamBas_1.03136,028,347 - 36,031,279 (-)NCBI
UU_Cfam_GSD_1.03136,523,422 - 36,526,353 (-)NCBI
TFF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13205,642,374 - 205,644,334 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113205,641,038 - 205,644,333 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213216,043,521 - 216,046,817 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
AI411511  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2209,193,278 - 9,193,378 (+)MAPPER
Rnor_6.0209,850,820 - 9,850,919NCBIRnor6.0
Rnor_5.02012,030,977 - 12,031,076UniSTSRnor5.0
RGSC_v3.4209,469,905 - 9,470,004UniSTSRGSC3.4
Celera2010,718,696 - 10,718,795UniSTS
RH 3.4 Map20117.7UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:120
Count of miRNA genes:99
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000066266
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

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 8 7
Medium 1 16 16 16 6 22 7
Low 2 20 18 2 18 1 1 53 6 29 3 1
Below cutoff 26 19 7 12 7 3 4 13 5 8 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066266   ⟹   ENSRNOP00000060620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl209,850,803 - 9,855,481 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090275   ⟹   ENSRNOP00000071550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl209,851,448 - 9,855,443 (-)Ensembl
RefSeq Acc Id: NM_013042   ⟹   NP_037174
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2209,193,259 - 9,197,969 (-)NCBI
Rnor_6.0209,850,800 - 9,855,481 (-)NCBI
Rnor_5.02012,030,957 - 12,035,638 (-)NCBI
RGSC_v3.4209,469,888 - 9,474,604 (-)RGD
Celera2010,718,676 - 10,723,298 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037174   ⟸   NM_013042
- Peptide Label: precursor
- UniProtKB: Q03191 (UniProtKB/Swiss-Prot),   A0A0G2JSY6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071550   ⟸   ENSRNOT00000090275
RefSeq Acc Id: ENSRNOP00000060620   ⟸   ENSRNOT00000066266
Protein Domains
P-type

Transcriptome

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

Promoters
RGD ID:13701482
Promoter ID:EPDNEW_R11994
Type:multiple initiation site
Name:Tff3_1
Description:trefoil 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_6.0209,855,474 - 9,855,534EPDNEW

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)
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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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3847 AgrOrtholog
Ensembl Genes ENSRNOG00000001159 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060620 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071550 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066266 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090275 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127312 IMAGE-MGC_LOAD
InterPro P_trefoil_chordata UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_trefoil_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_trefoil_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25563 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93548 IMAGE-MGC_LOAD
NCBI Gene 25563 ENTREZGENE
PANTHER PTHR13826 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Trefoil UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tff3 PhenoGen
PRINTS PTREFOIL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE P_TREFOIL_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_TREFOIL_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00018 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC208131
UniProt A0A0G2JSY6 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K0R2_RAT UniProtKB/TrEMBL
  Q03191 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q68FZ2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-11-29 Tff3  trefoil factor 3  Tff3  trefoil factor 3, intestinal  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Tff3  trefoil factor 3, intestinal  Tff3  trefoil factor 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Tff3  trefoil factor 3  Tff3  Trefoil factor (intestinal)  Name updated 629478 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization secreted by intestinal goblet cells 730274