Ret (ret proto-oncogene) - Rat Genome Database

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Gene: Ret (ret proto-oncogene) Rattus norvegicus
Analyze
Symbol: Ret
Name: ret proto-oncogene
RGD ID: 3556
Description: Predicted to enable calcium ion binding activity and transmembrane receptor protein tyrosine kinase activity. Involved in several processes, including innervation; positive regulation of neuron maturation; and retina development in camera-type eye. Located in several cellular components, including early endosome; membrane raft; and neuronal cell body. Biomarker of Parkinsonism; brain ischemia; and pheochromocytoma. Human ortholog(s) of this gene implicated in several diseases, including Hirschsprung's disease; congenital central hypoventilation syndrome; familial medullary thyroid carcinoma; multiple endocrine neoplasia type 2A; and multiple endocrine neoplasia type 2B. Orthologous to human RET (ret proto-oncogene); PARTICIPATES IN endocytosis pathway; thyroid cancer pathway; INTERACTS WITH (+)-pilocarpine; (-)-anisomycin; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: proto-oncogene tyrosine-protein kinase receptor Ret; receptor tyrosine kinase; Ret gene for receptor tyrosin; Ret proto-oncogene (multiple endocrine neoplasia MEN2A MEN2B and medullary thyroid carcinoma 1 Hirschsprung disease); Ret proto-oncogene (multiple endocrine neoplasia MEN2A, MEN2B and medullary thyroid carcinoma 1, Hirschsprung disease)
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
mRatBN7.24151,325,969 - 151,368,176 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4151,326,431 - 151,368,176 (-)Ensembl
Rnor_6.04150,202,170 - 150,249,196 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4150,202,058 - 150,244,372 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04216,130,142 - 216,177,139 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44154,448,179 - 154,491,103 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14154,693,019 - 154,735,944 (-)NCBI
Celera4140,198,457 - 140,240,663 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
appendicitis  (ISO)
B-lymphoblastic leukemia/lymphoma with hypodiploidy  (ISO)
Brain Injuries  (IEP)
brain ischemia  (IEP)
breast cancer  (ISO)
Breast Cancer, Familial  (ISO)
Burkitt lymphoma  (ISO)
CAKUT  (ISO)
clubfoot  (ISS)
colorectal cancer  (ISO)
Colorectal Neoplasms  (ISO)
congenital central hypoventilation syndrome  (ISO)
constipation  (ISO)
Deafness  (IEP)
disease of cellular proliferation  (ISO)
Dwarfism  (ISO)
extraosseous Ewing sarcoma  (ISO)
Facial Nerve Injuries  (IEP)
Familial Amyloidosis  (ISO)
familial medullary thyroid carcinoma  (ISO)
genetic disease  (ISO)
Gingival Hyperplasia  (ISO)
gingival overgrowth  (ISO)
hepatocellular carcinoma  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
high grade glioma  (ISO)
Hirschsprung Disease 1  (ISO)
Hirschsprung's disease  (ISO)
Hypertelorism  (ISO)
Hypoglossal Nerve Injuries  (IEP)
hypothyroidism  (ISO)
Islet Cell Tumor Syndrome  (ISO)
Joint Instability  (ISO)
Lymphatic Metastasis  (ISO)
Medullary Carcinomas  (ISO)
medulloblastoma  (ISO)
megacolon  (ISO)
microcephaly  (ISO)
multiple endocrine neoplasia  (ISO)
multiple endocrine neoplasia type 1  (ISO)
multiple endocrine neoplasia type 2A  (ISO)
multiple endocrine neoplasia type 2B  (ISO)
multiple endocrine neoplasia type 4  (ISO)
pancreatic cancer  (ISO)
Parkinsonism  (IEP)
pheochromocytoma  (IEP,ISO)
pilocytic astrocytoma  (ISO)
renal agenesis  (ISO)
Renal Hypodysplasia/Aplasia 1  (ISO)
status epilepticus  (ISO)
tetralogy of Fallot  (ISO)
thyroid gland carcinoma  (ISO)
thyroid gland medullary carcinoma  (ISO)
thyroid gland papillary carcinoma  (ISO)
Thyroid Neoplasms  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-anisomycin  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP)
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-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
camptothecin  (EXP)
chlordecone  (ISO)
chlorpyrifos  (ISO)
cisplatin  (EXP)
clomiphene  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cycloheximide  (EXP)
D-glucose  (EXP)
dabigatran  (EXP)
DDD  (ISO)
DDE  (ISO)
DDT  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP)
diazinon  (EXP)
dichromium trioxide  (ISO)
diclofenac  (ISO)
dieldrin  (EXP,ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
endrin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
estrone  (ISO)
ethanol  (EXP,ISO)
fonofos  (ISO)
fulvestrant  (ISO)
gamma-hexachlorocyclohexane  (ISO)
genistein  (EXP,ISO)
glucose  (EXP)
graphite  (EXP)
Indeno[1,2,3-cd]pyrene  (ISO)
irbesartan  (ISO)
ivermectin  (ISO)
L-cysteine  (ISO)
lead diacetate  (EXP,ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
manganese(II) chloride  (EXP)
Meclizine  (ISO)
medroxyprogesterone acetate  (ISO)
megestrol  (ISO)
mercury dibromide  (ISO)
mestranol  (ISO)
methapyrilene  (ISO)
Methazolamide  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
mifepristone  (EXP)
N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2-ylidene)acetamide  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
oxaliplatin  (EXP)
oxidopamine  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (EXP)
parathion  (ISO)
PCB138  (ISO)
pentanal  (ISO)
phenethyl caffeate  (EXP)
phenylmercury acetate  (ISO)
picene  (ISO)
ponatinib  (ISO)
propanal  (ISO)
Ptaquiloside  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sorafenib  (ISO)
staurosporine  (EXP)
sulindac  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
terbufos  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
vandetanib  (ISO)
verapamil  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
cellular response to retinoic acid  (ISO)
embryonic epithelial tube formation  (ISO)
enteric nervous system development  (ISO)
glial cell-derived neurotrophic factor receptor signaling pathway  (ISO,ISS)
homophilic cell adhesion via plasma membrane adhesion molecules  (IEA)
innervation  (IMP)
MAPK cascade  (ISO)
membrane protein proteolysis  (ISO)
nervous system development  (ISO)
neural crest cell migration  (ISO)
neuron cell-cell adhesion  (ISO)
neuron differentiation  (ISO)
neuron maturation  (ISO)
peptidyl-tyrosine phosphorylation  (IEA)
Peyer's patch morphogenesis  (ISO)
positive regulation of cell adhesion mediated by integrin  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell size  (ISO)
positive regulation of extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of kinase activity  (IBA)
positive regulation of MAPK cascade  (ISO,ISS)
positive regulation of metanephric glomerulus development  (ISO)
positive regulation of neuron maturation  (IMP)
positive regulation of neuron projection development  (ISO)
positive regulation of peptidyl-serine phosphorylation of STAT protein  (ISO)
positive regulation of protein kinase B signaling  (ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO)
regulation of axonogenesis  (ISO)
regulation of cell adhesion  (ISO)
regulation of peptidyl-serine phosphorylation of STAT protein  (ISO)
response to pain  (ISO)
response to xenobiotic stimulus  (IEP)
retina development in camera-type eye  (IEP)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA,ISO)
ureter maturation  (ISO)
ureteric bud development  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Burazin TC and Gundlach AL, Brain Res Mol Brain Res. 1998 Apr;55(2):331-6.
2. Canzian F, etal., Mamm Genome 1995 Jun;6(6):433-5.
3. Cheng Q, etal., Neurosci Lett. 2008 Jul 4;439(1):24-9. Epub 2008 May 1.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Incoronato M, etal., Cell Signal. 2004 Jul;16(7):847-56.
7. Ito Y, etal., Surgery. 2005 Oct;138(4):788-94.
8. Iwashita T, etal., Science 2003 Aug 15;301(5635):972-6.
9. Jiao L, etal., Cell Res. 2011 Feb;21(2):327-37. doi: 10.1038/cr.2010.139. Epub 2010 Sep 28.
10. Kitagawa H, etal., Brain Res. 1999 Jul 10;834(1-2):190-5.
11. Kretz A, etal., Brain Res. 2006 May 23;1090(1):1-14. Epub 2006 May 2.
12. Marco S, etal., J Neurobiol. 2002 Sep 15;52(4):343-51.
13. Matera I, etal., DNA Seq 2000;11(5):405-17.
14. MGD data from the GO Consortium
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. OMIM Disease Annotation Pipeline
17. Pierchala BA, etal., J Neurosci. 2006 Mar 8;26(10):2777-87.
18. Pipeline to import KEGG annotations from KEGG into RGD
19. Powers JF, etal., Endocr Pathol. 2008 Spring;19(1):9-16.
20. Powers JF, etal., Neuroscience. 2005;132(3):605-12.
21. RGD automated data pipeline
22. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. RGD automated import pipeline for gene-chemical interactions
24. RGD comprehensive gene curation
25. Tsui-Pierchala BA, etal., J Biol Chem 2002 Sep 13;277(37):34618-25. Epub 2002 Jun 28.
26. Tsujino H, etal., Brain Res Mol Brain Res. 1999 Jul 5;70(2):298-303.
27. Vaclavikova E, etal., PLoS One. 2014 Jun 4;9(6):e98957. doi: 10.1371/journal.pone.0098957. eCollection 2014.
28. Wissel K, etal., Neuroreport. 2006 Jun 26;17(9):875-8.
29. Zeng Q, etal., J Int Med Res. 2008 Jul-Aug;36(4):656-64.
30. Zhou GW, etal., Chin Med J (Engl). 2009 Jul 5;122(13):1495-500.
Additional References at PubMed
PMID:9576965   PMID:9834195   PMID:10545102   PMID:10921886   PMID:11069590   PMID:11445581   PMID:12195422   PMID:12527893   PMID:14555660   PMID:15233745   PMID:15242795   PMID:15302866  
PMID:15569713   PMID:16569669   PMID:16672314   PMID:16773224   PMID:16818623   PMID:17047028   PMID:17183535   PMID:17322904   PMID:17380130   PMID:17538205   PMID:17553423   PMID:17910947  
PMID:18668157   PMID:18753381   PMID:18845535   PMID:19133164   PMID:19366855   PMID:19551609   PMID:19823924   PMID:20237269   PMID:20392937   PMID:20533997   PMID:20682772   PMID:20702524  
PMID:21134561   PMID:21357690   PMID:21521737   PMID:22128160   PMID:22897442   PMID:23382219   PMID:23413818   PMID:23872421   PMID:27226544   PMID:27994058   PMID:28846097   PMID:28846099  
PMID:28953886   PMID:29018141   PMID:30541958  


Genomics

Candidate Gene Status
Ret is a candidate Gene for QTL Ept5
Comparative Map Data
Ret
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24151,325,969 - 151,368,176 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4151,326,431 - 151,368,176 (-)Ensembl
Rnor_6.04150,202,170 - 150,249,196 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4150,202,058 - 150,244,372 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04216,130,142 - 216,177,139 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44154,448,179 - 154,491,103 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14154,693,019 - 154,735,944 (-)NCBI
Celera4140,198,457 - 140,240,663 (-)NCBICelera
Cytogenetic Map4q42NCBI
RET
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1043,077,064 - 43,130,351 (+)EnsemblGRCh38hg38GRCh38
GRCh381043,077,069 - 43,130,351 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371043,572,517 - 43,625,799 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361042,892,523 - 42,945,805 (+)NCBINCBI36hg18NCBI36
Build 341042,892,532 - 42,944,955NCBI
Celera1039,575,663 - 39,628,954 (+)NCBI
Cytogenetic Map10q11.21NCBI
HuRef1040,098,756 - 40,151,896 (+)NCBIHuRef
CHM1_11043,611,715 - 43,665,000 (+)NCBICHM1_1
Ret
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396118,128,709 - 118,174,705 (-)NCBIGRCm39mm39
GRCm39 Ensembl6118,128,706 - 118,174,679 (-)Ensembl
GRCm386118,151,748 - 118,197,744 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6118,151,745 - 118,197,718 (-)EnsemblGRCm38mm10GRCm38
MGSCv376118,101,766 - 118,147,762 (-)NCBIGRCm37mm9NCBIm37
MGSCv366118,119,472 - 118,162,752 (-)NCBImm8
Celera6119,974,414 - 120,020,450 (-)NCBICelera
Cytogenetic Map6F1NCBI
cM Map655.86NCBI
Ret
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555461,221,995 - 1,253,946 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555461,221,995 - 1,252,147 (+)NCBIChiLan1.0ChiLan1.0
RET
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11043,256,437 - 43,286,340 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1043,249,468 - 43,284,331 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01040,050,396 - 40,103,629 (+)NCBIMhudiblu_PPA_v0panPan3
RET
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1283,946,132 - 3,995,505 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl283,947,232 - 3,994,210 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha284,180,472 - 4,211,554 (-)NCBI
ROS_Cfam_1.0284,124,929 - 4,176,146 (-)NCBI
UMICH_Zoey_3.1283,922,935 - 3,954,018 (-)NCBI
UNSW_CanFamBas_1.0283,965,997 - 3,997,076 (-)NCBI
UU_Cfam_GSD_1.0284,100,288 - 4,131,400 (-)NCBI
Ret
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721383,803,446 - 83,856,824 (-)NCBI
SpeTri2.0NW_0049366172,927,185 - 2,980,594 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RET
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1461,305,841 - 61,361,415 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11461,305,818 - 61,361,416 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21466,136,477 - 66,192,220 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RET
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1938,746,088 - 38,798,773 (+)NCBI
ChlSab1.1 Ensembl938,769,170 - 38,796,712 (+)Ensembl
Vero_WHO_p1.0NW_02366605647,691,006 - 47,743,756 (-)NCBI
Ret
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624922382,462 - 413,227 (+)NCBI

Position Markers
AA859878  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,328,880 - 151,329,062 (+)MAPPERmRatBN7.2
Rnor_6.04150,205,086 - 150,205,267NCBIRnor6.0
Rnor_5.04216,133,054 - 216,133,235UniSTSRnor5.0
RGSC_v3.44154,451,091 - 154,451,272UniSTSRGSC3.4
Celera4140,201,369 - 140,201,550UniSTS
RH 3.4 Map4969.31UniSTS
Cytogenetic Map4q42UniSTS
Ret  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24151,329,531 - 151,329,638 (+)MAPPERmRatBN7.2
Rnor_6.04150,205,737 - 150,205,843NCBIRnor6.0
Rnor_5.04216,133,705 - 216,133,811UniSTSRnor5.0
RGSC_v3.44154,451,742 - 154,451,848UniSTSRGSC3.4
Celera4140,202,020 - 140,202,126UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:445
Count of miRNA genes:245
Interacting mature miRNAs:296
Transcripts:ENSRNOT00000047685
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
Medium 18 14 12 4
Low 3 29 16 4 19 4 8 11 52 2 26 7 8
Below cutoff 14 35 31 31 4 17 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001110099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH006777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ298999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ299017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000047685   ⟹   ENSRNOP00000047793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4151,326,431 - 151,368,176 (-)Ensembl
Rnor_6.0 Ensembl4150,202,058 - 150,244,372 (-)Ensembl
RefSeq Acc Id: NM_001110099   ⟹   NP_001103569
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24151,328,786 - 151,368,176 (-)NCBI
Rnor_6.04150,204,991 - 150,244,380 (-)NCBI
Rnor_5.04216,130,142 - 216,177,139 (-)NCBI
RGSC_v3.44154,448,179 - 154,491,103 (-)RGD
Celera4140,201,274 - 140,240,663 (-)NCBI
Sequence:
RefSeq Acc Id: NM_012643   ⟹   NP_036775
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24151,325,969 - 151,368,176 (-)NCBI
Rnor_6.04150,202,174 - 150,244,380 (-)NCBI
Rnor_5.04216,130,142 - 216,177,139 (-)NCBI
RGSC_v3.44154,448,179 - 154,491,103 (-)RGD
Celera4140,198,457 - 140,240,663 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036775   ⟸   NM_012643
- Peptide Label: isoform a precursor
- UniProtKB: G3V9H8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001103569   ⟸   NM_001110099
- Peptide Label: isoform b precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000047793   ⟸   ENSRNOT00000047685
Protein Domains
Cadherin   Protein kinase   RET_CLD1

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000