Fat1 (FAT atypical cadherin 1) - Rat Genome Database
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Gene: Fat1 (FAT atypical cadherin 1) Rattus norvegicus
Analyze
Symbol: Fat1
Name: FAT atypical cadherin 1
RGD ID: 621254
Description: Predicted to have calcium ion binding activity. Predicted to be involved in several processes, including actin filament organization; camera-type eye development; and epithelial cell morphogenesis. Predicted to localize to several cellular components, including apical plasma membrane; filopodium; and lamellipodium. Orthologous to human FAT1 (FAT atypical cadherin 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cadherin FAT1 isoform +12; Fat; FAT tumor suppressor (Drosophila) homolog; fat tumor suppressor homolog (Drosophila); FAT tumor suppressor homolog 1; FAT tumor suppressor homolog 1 (Drosophila); Fath; protocadherin Fat 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21647,177,253 - 47,296,261 (-)NCBI
Rnor_6.0 Ensembl1650,372,128 - 50,501,921 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01650,372,150 - 50,501,716 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01650,093,077 - 50,220,862 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41650,472,074 - 50,591,399 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11650,472,148 - 50,591,474 (-)NCBI
Celera1645,165,920 - 45,284,243 (-)NCBICelera
Cytogenetic Map16q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
2-nitrotoluene  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (EXP)
buspirone  (EXP)
cadmium dichloride  (ISO)
captan  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichromium trioxide  (ISO)
dicrotophos  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
genistein  (EXP)
indometacin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
mitomycin C  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nicotine  (ISO)
NS-398  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
Ptaquiloside  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
rotenone  (ISO)
Securinine  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
tamibarotene  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
topotecan  (EXP)
valproic acid  (EXP,ISO)

References

Additional References at PubMed
PMID:10650949   PMID:15148305   PMID:15922730   PMID:16014031   PMID:16682528   PMID:17110338   PMID:17500054   PMID:19056867   PMID:19131340   PMID:21423176   PMID:23376485   PMID:26114487  


Genomics

Comparative Map Data
Fat1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21647,177,253 - 47,296,261 (-)NCBI
Rnor_6.0 Ensembl1650,372,128 - 50,501,921 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01650,372,150 - 50,501,716 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01650,093,077 - 50,220,862 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41650,472,074 - 50,591,399 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11650,472,148 - 50,591,474 (-)NCBI
Celera1645,165,920 - 45,284,243 (-)NCBICelera
Cytogenetic Map16q11NCBI
FAT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4186,587,794 - 186,726,722 (-)EnsemblGRCh38hg38GRCh38
GRCh384186,587,789 - 186,726,696 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374187,508,948 - 187,645,010 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh374187,508,937 - 187,647,876 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364187,745,931 - 187,881,981 (-)NCBINCBI36hg18NCBI36
Build 344187,884,097 - 188,020,136NCBI
Celera4184,830,318 - 184,965,946 (-)NCBI
Cytogenetic Map4q35.2NCBI
HuRef4183,256,134 - 183,392,436 (-)NCBIHuRef
CHM1_14187,485,399 - 187,621,051 (-)NCBICHM1_1
Fat1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39845,386,137 - 45,505,294 (+)NCBIGRCm39mm39
GRCm38844,933,100 - 45,052,257 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl844,935,447 - 45,052,257 (+)EnsemblGRCm38mm10GRCm38
MGSCv37846,035,562 - 46,137,611 (+)NCBIGRCm37mm9NCBIm37
MGSCv36846,449,031 - 46,551,074 (+)NCBImm8
Celera847,637,354 - 47,739,945 (+)NCBICelera
Cytogenetic Map8B1.1NCBI
cM Map824.81NCBI
Fat1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540322,502,625 - 22,619,211 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540322,502,625 - 22,618,513 (+)NCBIChiLan1.0ChiLan1.0
FAT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14190,952,728 - 191,093,357 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4190,952,737 - 191,093,357 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04178,752,261 - 178,895,038 (-)NCBIMhudiblu_PPA_v0panPan3
FAT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1644,128,386 - 44,241,192 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11644,113,621 - 44,241,187 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Fat1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365542,872,729 - 2,996,821 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl178,448,760 - 8,580,715 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1178,466,099 - 8,580,715 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2179,339,790 - 9,455,160 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FAT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17132,475,689 - 132,616,151 (-)NCBI
ChlSab1.1 Ensembl7132,483,032 - 132,616,112 (-)Ensembl
Fat1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476917,801,796 - 17,924,685 (+)NCBI

Position Markers
D16Got40  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01650,493,999 - 50,494,218NCBIRnor6.0
Rnor_5.01650,213,067 - 50,213,286UniSTSRnor5.0
RGSC_v3.41650,583,684 - 50,583,901RGDRGSC3.4
RGSC_v3.41650,583,682 - 50,583,901UniSTSRGSC3.4
RGSC_v3.11650,583,759 - 50,583,976RGD
Celera1645,276,598 - 45,276,817UniSTS
RH 3.4 Map16460.7UniSTS
RH 3.4 Map16460.7RGD
RH 2.0 Map16466.8RGD
Cytogenetic Map16q11UniSTS
D8S560  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01339,822,565 - 39,822,615UniSTSRnor5.0
Rnor_5.01650,144,240 - 50,145,628UniSTSRnor5.0
RGSC_v3.41331,417,148 - 31,417,198UniSTSRGSC3.4
Celera1329,718,499 - 29,718,549UniSTS
Cytogenetic Map16q11UniSTS
BF389656  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01650,476,971 - 50,477,109NCBIRnor6.0
Rnor_5.01650,196,039 - 50,196,177UniSTSRnor5.0
RGSC_v3.41650,566,654 - 50,566,792UniSTSRGSC3.4
Celera1645,259,653 - 45,259,791UniSTS
RH 3.4 Map16460.9UniSTS
Cytogenetic Map16q11UniSTS
UniSTS:143077  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01650,392,179 - 50,392,377NCBIRnor6.0
Rnor_5.01650,113,105 - 50,113,303UniSTSRnor5.0
RGSC_v3.41650,492,085 - 50,492,283UniSTSRGSC3.4
Celera1645,185,930 - 45,186,128UniSTS
Cytogenetic Map16q11UniSTS
AU023433  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01650,372,294 - 50,372,435NCBIRnor6.0
Rnor_5.01650,093,220 - 50,093,361UniSTSRnor5.0
RGSC_v3.41650,472,200 - 50,472,341UniSTSRGSC3.4
Celera1645,166,046 - 45,166,187UniSTS
Cytogenetic Map16q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162484654169846541Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162751998072519980Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162834031573340315Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163530711063909364Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
631833Sach2Saccharin preference QTL 240.01consumption behavior trait (VT:0002069)calculated saccharin drink intake rate (CMO:0001613)164590509753253355Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:66
Count of miRNA genes:62
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000067486
Prediction methods:Miranda
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 41 27 12 17 12 3 3 74 35 35 11 3
Low 2 30 29 2 29 5 8 6 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067486   ⟹   ENSRNOP00000061869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1650,372,168 - 50,501,716 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081023   ⟹   ENSRNOP00000073466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1650,372,128 - 50,501,921 (-)Ensembl
RefSeq Acc Id: NM_031819   ⟹   NP_114007
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,270 - 47,296,107 (-)NCBI
Rnor_6.01650,372,168 - 50,501,716 (-)NCBI
Rnor_5.01650,093,077 - 50,220,862 (-)NCBI
RGSC_v3.41650,472,074 - 50,591,399 (-)RGD
Celera1645,165,920 - 45,284,243 (-)RGD
Sequence:
RefSeq Acc Id: XM_017600259   ⟹   XP_017455748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,296,260 (-)NCBI
Rnor_6.01650,372,151 - 50,501,628 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600260   ⟹   XP_017455749
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,293,299 (-)NCBI
Rnor_6.01650,372,150 - 50,498,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600261   ⟹   XP_017455750
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,295,557 (-)NCBI
Rnor_6.01650,372,150 - 50,500,947 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600262   ⟹   XP_017455751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,296,260 (-)NCBI
Rnor_6.01650,372,151 - 50,501,628 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600263   ⟹   XP_017455752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,296,260 (-)NCBI
Rnor_6.01650,372,151 - 50,501,628 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600264   ⟹   XP_017455753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,183,731 - 47,296,261 (-)NCBI
Rnor_6.01650,374,593 - 50,501,628 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600265   ⟹   XP_017455754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01650,374,594 - 50,501,628 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039094865   ⟹   XP_038950793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,293,530 (-)NCBI
RefSeq Acc Id: XM_039094866   ⟹   XP_038950794
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,177,253 - 47,296,260 (-)NCBI
RefSeq Acc Id: XR_005494675
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21647,179,649 - 47,296,261 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_114007   ⟸   NM_031819
- Peptide Label: precursor
- UniProtKB: Q9WU10 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455750   ⟸   XM_017600261
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455749   ⟸   XM_017600260
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455752   ⟸   XM_017600263
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K5L1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455751   ⟸   XM_017600262
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455748   ⟸   XM_017600259
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455753   ⟸   XM_017600264
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017455754   ⟸   XM_017600265
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000061869   ⟸   ENSRNOT00000067486
RefSeq Acc Id: ENSRNOP00000073466   ⟸   ENSRNOT00000081023
RefSeq Acc Id: XP_038950794   ⟸   XM_039094866
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038950793   ⟸   XM_039094865
- Peptide Label: isoform X1
Protein Domains
Cadherin   EGF-like   LAM_G_DOMAIN

Transcriptome

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

Promoters
RGD ID:13700116
Promoter ID:EPDNEW_R10636
Type:multiple initiation site
Name:Fat1_1
Description:FAT atypical cadherin 1
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_6.01650,501,878 - 50,501,938EPDNEW

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)
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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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 50384528 50384529 C A snv BBDP/Wor (RGD)
16 50399227 50399228 T G snv LEW/Crl (RGD)
16 50413695 50413696 G C snv ACI/EurMcwi (RGD)
16 50486999 50487000 G A snv SBN/Ygl (RGD), F344/NCrl (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), WN/N (MCW), MR/N (MCW), F344/NRrrc (MCW), BBDP/Wor (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621254 AgrOrtholog
Ensembl Genes ENSRNOG00000030954 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061869 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073466 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067486 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081023 UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
  EG-like_dom UniProtKB/TrEMBL
  EGF-like_Ca-bd UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
KEGG Report rno:83720 UniProtKB/TrEMBL
NCBI Gene 83720 ENTREZGENE
Pfam Cadherin UniProtKB/TrEMBL
  EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
PhenoGen Fat1 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
  EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
  SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
  ConA_like_lec_gl UniProtKB/TrEMBL
UniProt A0A0G2K5L1 ENTREZGENE, UniProtKB/TrEMBL
  G3V9W9_RAT UniProtKB/TrEMBL
  Q9WU10 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-05 Fat1  FAT atypical cadherin 1  Fat1  FAT tumor suppressor homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-25 Fat1  FAT tumor suppressor homolog 1 (Drosophila)  Fat  FAT tumor suppressor homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Fat  FAT tumor suppressor homolog 1 (Drosophila)  Fat1  FAT tumor suppressor homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-19 Fat1  FAT tumor suppressor homolog 1 (Drosophila)  Fath  fat tumor suppressor homolog (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Fath  fat tumor suppressor homolog (Drosophila)  Fat  FAT tumor suppressor (Drosophila) homolog  Symbol and Name updated 1299863 APPROVED
2002-08-07 Fat  FAT tumor suppressor (Drosophila) homolog      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a large protocadherin with 34 cadherin repeats, five epidermal growth factor (EGF)-like repeats containing a single laminin A-G domain and a putative transmembrane portion followed by a cytoplasmic sequence 632716
gene_expression expressed in fetal epithelial cell layers and in the CNS 632716