Ptch1 (patched 1) - Rat Genome Database

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Gene: Ptch1 (patched 1) Rattus norvegicus
Analyze
Symbol: Ptch1
Name: patched 1
RGD ID: 621425
Description: Predicted to enable several functions, including cholesterol binding activity; cyclin binding activity; and signaling receptor binding activity. Involved in several processes, including commissural neuron axon guidance; gland development; and response to estradiol. Located in growth cone; nucleus; and postsynaptic density. Human ortholog(s) of this gene implicated in carcinoma (multiple); holoprosencephaly (multiple); nevoid basal cell carcinoma syndrome; and stomach cancer. Orthologous to human PTCH1 (patched 1); PARTICIPATES IN altered Hedgehog signaling pathway; glypican signaling pathway; Hedgehog signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC290961; patched (Drosophila) homolog; patched homolog 1; patched homolog 1 (Drosophila); patched homolog 2; Ptch; Ptch2
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
mRatBN7.2171,542,705 - 1,607,730 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl171,542,877 - 1,607,333 (+)Ensembl
Rnor_6.0171,032,242 - 1,085,885 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl171,029,048 - 1,093,873 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0171,025,798 - 1,079,561 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,088,234 - 7,142,459 (+)NCBIRGSC3.4rn4RGSC3.4
Celera17917,710 - 971,638 (-)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Aberrant Crypt Foci  (ISO)
acute myeloid leukemia  (ISO)
Axenfeld-Rieger syndrome  (ISO)
basal cell carcinoma  (ISO)
basaloid squamous cell carcinoma  (ISO)
Brain Neoplasms  (ISO)
breast carcinoma  (ISO)
Chronic Experimental Pancreatitis  (IEP)
cleft lip  (ISO)
cleft palate  (ISO)
colorectal adenoma  (ISO)
congenital heart disease  (ISO)
COVID-19  (ISO)
Craniofacial Abnormalities  (ISO)
craniopharyngioma  (ISO)
Craniosynostosis Syndrome, Autosomal Recessive  (ISO)
demyelinating disease  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Arthritis  (IEP)
Fanconi anemia  (ISO)
focal dermal hypoplasia  (ISO)
Fraser syndrome 3  (ISO)
gallbladder carcinoma  (ISO)
Gastrointestinal Neoplasms  (ISO)
gastrointestinal stromal tumor  (ISO)
genetic disease  (ISO)
germinoma  (ISO)
hepatocellular carcinoma  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
Hirschsprung Disease 1  (ISO)
holoprosencephaly  (ISO)
holoprosencephaly 7  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hydrocephalus  (ISO)
hyperglycemia  (ISO)
Hyperoxic Lung Injury  (IEP)
intellectual disability  (ISO)
lung adenocarcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
medulloblastoma  (ISO)
nasopharyngitis  (ISO)
Neoplasm Metastasis  (ISO)
neuroblastoma  (ISO)
nevoid basal cell carcinoma syndrome  (ISO)
pancreatic cancer  (ISO)
Peters anomaly  (ISO)
Pituitary Stalk Interruption Syndrome  (ISO)
Preaxial Polydactyly II  (ISO)
Precocious Puberty  (ISO)
Primitive Neuroectodermal Tumors  (ISO)
retinoblastoma  (ISO)
rhabdomyosarcoma  (ISO)
Skin Neoplasms  (ISO)
spina bifida  (ISO)
stomach cancer  (ISO)
Subarachnoid Hemorrhage  (IEP)
syndromic microphthalmia 5  (ISO)
uterine fibroid  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butan-2-yl-4-[4-[4-[4-[[2-(2,4-dichlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]-1-piperazinyl]phenyl]-1,2,4-triazol-3-one  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
Ac-Ser-Asp-Lys-Pro-OH  (EXP,ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzoates  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
cannabidiol  (EXP)
captopril  (EXP,ISO)
carbon nanotube  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
colforsin daropate hydrochloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
curcumin  (EXP)
Cyclopamine  (EXP,ISO)
D-glucose  (ISO)
DDE  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP,ISO)
diheptyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (EXP,ISO)
gemcitabine  (ISO)
glucose  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
itraconazole  (EXP)
L-methionine  (ISO)
lipopolysaccharide  (EXP,ISO)
melittin  (ISO)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nitrofen  (EXP)
paracetamol  (EXP)
paraquat  (EXP)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vismodegib  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (ISO,ISS)
brain development  (ISO)
branching involved in ureteric bud morphogenesis  (ISO)
cell differentiation involved in kidney development  (ISO)
cell fate determination  (ISO)
cell proliferation involved in metanephros development  (ISO)
cellular response to cholesterol  (ISO)
commissural neuron axon guidance  (IMP)
dorsal/ventral neural tube patterning  (ISO)
dorsal/ventral pattern formation  (ISO,ISS)
embryonic limb morphogenesis  (ISO,ISS)
embryonic organ development  (ISO)
epidermal cell fate specification  (ISO)
epidermis development  (ISO)
glucose homeostasis  (ISO)
heart morphogenesis  (ISO)
hindlimb morphogenesis  (ISO)
in utero embryonic development  (ISO)
keratinocyte proliferation  (ISO)
limb morphogenesis  (ISO)
liver regeneration  (IEP)
mammary gland development  (ISO)
mammary gland duct morphogenesis  (ISO)
mammary gland epithelial cell differentiation  (ISO)
metanephric collecting duct development  (ISO)
negative regulation of cell division  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of multicellular organism growth  (ISO,ISS)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of smoothened signaling pathway  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
neural plate axis specification  (ISO)
neural tube closure  (ISO)
neural tube formation  (ISO)
neural tube patterning  (ISO)
pattern specification process  (ISO)
pharyngeal system development  (ISO)
positive regulation of cholesterol efflux  (ISO)
positive regulation of epidermal cell differentiation  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
prostate gland development  (IEP)
protein localization to plasma membrane  (ISO)
protein processing  (ISO,ISS)
regulation of cell population proliferation  (ISO)
regulation of growth  (ISO)
regulation of mitotic cell cycle  (ISO)
regulation of protein localization  (ISO)
regulation of smoothened signaling pathway  (ISS)
response to chlorate  (ISO)
response to estradiol  (IEP)
response to mechanical stimulus  (IEP)
response to organic cyclic compound  (IEP)
response to retinoic acid  (IEP)
response to xenobiotic stimulus  (IEP)
signal transduction  (ISO)
smooth muscle tissue development  (ISO)
smoothened signaling pathway  (IBA,ISO,ISS)
smoothened signaling pathway involved in dorsal/ventral neural tube patterning  (ISO)
somite development  (ISO)
spermatid development  (IEP)
spinal cord motor neuron differentiation  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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2. Brokken LJ, etal., Endocrinology. 2009 Jan;150(1):445-51. Epub 2008 Sep 4.
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4. Charytoniuk D, etal., Eur J Neurosci 2002 Dec;16(12):2351-7.
5. Choi JY, etal., Bone. 2021 Mar;144:115829. doi: 10.1016/j.bone.2020.115829. Epub 2020 Dec 29.
6. Cohen MM, Am J Med Genet A. 2010 Aug;152A(8):1875-914. doi: 10.1002/ajmg.a.32909.
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10. Fu X, etal., Exp Mol Pathol. 2008 Jun;84(3):195-9. doi: 10.1016/j.yexmp.2008.04.002. Epub 2008 May 2.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. GOA data from the GO Consortium
13. Ishiyama A, etal., Anticancer Res. 2006 Jan-Feb;26(1A):195-8.
14. Jeng KS, etal., Ann Surg Oncol. 2013 Feb;20(2):464-73. doi: 10.1245/s10434-012-2593-y. Epub 2012 Aug 22.
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17. Lee SJ, etal., Target Oncol. 2013 Dec;8(4):271-80. doi: 10.1007/s11523-013-0253-1. Epub 2013 Feb 1.
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24. MGD data from the GO Consortium
25. Mimeault M and Batra SK, Pharmacol Rev. 2010 Sep;62(3):497-524.
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27. Morimoto T, etal., J Gastroenterol Hepatol. 2014 Jun;29(6):1192-9. doi: 10.1111/jgh.12553.
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29. Mäkelä JA, etal., Reproduction. 2011 Nov;142(5):711-21. doi: 10.1530/REP-11-0110. Epub 2011 Sep 5.
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. Ohki K, etal., Int J Oral Maxillofac Surg. 2004 Sep;33(6):584-92.
32. OMIM Disease Annotation Pipeline
33. Parra LM and Zou Y, Nat Neurosci. 2010 Jan;13(1):29-35. doi: 10.1038/nn.2457. Epub 2009 Nov 29.
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35. Petralia RS, etal., J Comp Neurol. 2011 Dec 15;519(18):3684-99. doi: 10.1002/cne.22681.
36. Pipeline to import KEGG annotations from KEGG into RGD
37. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
38. Pu Y, etal., Dev Biol 2004 Sep 15;273(2):257-75.
39. RGD automated data pipeline
40. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
41. RGD automated import pipeline for gene-chemical interactions
42. RGD comprehensive gene curation
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Additional References at PubMed
PMID:8681379   PMID:8981943   PMID:9006067   PMID:9262482   PMID:9811851   PMID:10500113   PMID:10529434   PMID:11044404   PMID:11278759   PMID:11331587   PMID:11389830   PMID:11476578  
PMID:11493558   PMID:11517919   PMID:11784021   PMID:12635140   PMID:12917290   PMID:15166316   PMID:15576403   PMID:16061793   PMID:16229683   PMID:16489008   PMID:17631878   PMID:17850284  
PMID:19004860   PMID:19654211   PMID:19684112   PMID:19809516   PMID:21110116   PMID:21406566   PMID:21552265   PMID:21931618   PMID:22133807   PMID:22477363   PMID:23333245   PMID:24062445  
PMID:24302887   PMID:24492243   PMID:24548465   PMID:28573530   PMID:29244790   PMID:30114436   PMID:30306574   PMID:30502245   PMID:33506921   PMID:34287088  


Genomics

Comparative Map Data
Ptch1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2171,542,705 - 1,607,730 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl171,542,877 - 1,607,333 (+)Ensembl
Rnor_6.0171,032,242 - 1,085,885 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl171,029,048 - 1,093,873 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0171,025,798 - 1,079,561 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,088,234 - 7,142,459 (+)NCBIRGSC3.4rn4RGSC3.4
Celera17917,710 - 971,638 (-)NCBICelera
Cytogenetic Map17p14NCBI
PTCH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl995,442,980 - 95,517,057 (-)EnsemblGRCh38hg38GRCh38
GRCh38995,442,980 - 95,516,971 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37998,205,262 - 98,279,253 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36997,245,085 - 97,319,068 (-)NCBINCBI36hg18NCBI36
Build 34995,285,954 - 95,350,386NCBI
Celera968,646,306 - 68,719,962 (-)NCBI
Cytogenetic Map9q22.32NCBI
HuRef967,814,741 - 67,888,045 (-)NCBIHuRef
CHM1_1998,351,712 - 98,425,709 (-)NCBICHM1_1
Ptch1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391363,656,142 - 63,721,274 (-)NCBIGRCm39mm39
GRCm39 Ensembl1363,656,142 - 63,721,412 (-)Ensembl
GRCm381363,508,328 - 63,573,460 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1363,508,328 - 63,573,598 (-)EnsemblGRCm38mm10GRCm38
MGSCv371363,612,841 - 63,666,828 (-)NCBIGRCm37mm9NCBIm37
MGSCv361363,520,755 - 63,574,742 (-)NCBImm8
Celera1365,162,237 - 65,216,237 (-)NCBICelera
Cytogenetic Map13B3NCBI
cM Map1332.8NCBI
Ptch1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542222,362,221 - 22,427,622 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542222,362,330 - 22,418,062 (-)NCBIChiLan1.0ChiLan1.0
PTCH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1994,668,792 - 94,741,517 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl994,668,365 - 94,741,453 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0966,542,675 - 66,616,820 (-)NCBIMhudiblu_PPA_v0panPan3
PTCH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1171,246,750 - 71,309,036 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl171,238,195 - 71,305,662 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha172,001,309 - 72,071,860 (+)NCBI
ROS_Cfam_1.0171,542,960 - 71,613,625 (+)NCBI
ROS_Cfam_1.0 Ensembl171,542,581 - 71,613,625 (+)Ensembl
UMICH_Zoey_3.1171,355,076 - 71,425,574 (+)NCBI
UNSW_CanFamBas_1.0171,118,402 - 71,189,186 (+)NCBI
UU_Cfam_GSD_1.0171,824,991 - 71,895,587 (+)NCBI
Ptch1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049445,013,677 - 5,072,720 (-)NCBI
SpeTri2.0NW_0049366264,241,993 - 4,301,919 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTCH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1026,627,325 - 26,703,225 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11026,627,165 - 26,703,225 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21030,839,486 - 30,915,228 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103219825
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112107,580,895 - 107,656,443 (+)NCBIChlSab1.1chlSab2
ChlSab1.112107,580,895 - 107,656,443 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl12107,590,663 - 107,652,985 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366670535 - 26,483 (+)NCBIVero_WHO_p1.0
Ptch1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475316,929,503 - 16,995,255 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
BF387421  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,556,951 - 1,557,102 (-)MAPPERmRatBN7.2
Rnor_6.0171,079,356 - 1,079,506NCBIRnor6.0
Rnor_5.0171,073,032 - 1,073,182UniSTSRnor5.0
RGSC_v3.4177,094,613 - 7,094,763UniSTSRGSC3.4
Celera17965,324 - 965,474UniSTS
RH 3.4 Map1716.0UniSTS
Cytogenetic Map17p14UniSTS
BF404235  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,556,855 - 1,557,071 (-)MAPPERmRatBN7.2
Rnor_6.0171,079,387 - 1,079,602NCBIRnor6.0
Rnor_5.0171,073,063 - 1,073,278UniSTSRnor5.0
RGSC_v3.4177,094,517 - 7,094,732UniSTSRGSC3.4
Celera17965,355 - 965,570UniSTS
RH 3.4 Map175.1UniSTS
Cytogenetic Map17p14UniSTS
UniSTS:465490  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,604,206 - 1,604,507 (-)MAPPERmRatBN7.2
Rnor_6.0171,032,465 - 1,032,765NCBIRnor6.0
Rnor_5.0171,026,021 - 1,026,321UniSTSRnor5.0
RGSC_v3.4177,141,934 - 7,142,234UniSTSRGSC3.4
Celera17917,933 - 918,233UniSTS
Cytogenetic Map17p14UniSTS
Ptch1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,551,597 - 1,552,461 (-)MAPPERmRatBN7.2
Rnor_6.0171,083,996 - 1,084,859NCBIRnor6.0
Rnor_5.0171,077,672 - 1,078,535UniSTSRnor5.0
RGSC_v3.4177,089,260 - 7,090,123UniSTSRGSC3.4
Celera17969,749 - 970,612UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:101
Interacting mature miRNAs:111
Transcripts:ENSRNOT00000026287
Prediction methods:Microtar, Miranda, Rnahybrid
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 1 8 11 6 6 74 29 31 11
Low 2 35 46 35 19 35 8 11 6 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026287   ⟹   ENSRNOP00000026287
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl171,550,385 - 1,607,333 (+)Ensembl
Rnor_6.0 Ensembl171,032,240 - 1,085,885 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086130   ⟹   ENSRNOP00000069422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl171,542,877 - 1,607,333 (+)Ensembl
Rnor_6.0 Ensembl171,029,048 - 1,093,873 (-)Ensembl
RefSeq Acc Id: NM_001389256   ⟹   NP_001376185
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,542,705 - 1,607,730 (+)NCBI
RefSeq Acc Id: NM_053566   ⟹   NP_446018
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,549,824 - 1,607,730 (+)NCBI
Rnor_6.0171,032,242 - 1,085,885 (-)NCBI
Rnor_5.0171,025,798 - 1,079,561 (-)NCBI
RGSC_v3.4177,088,234 - 7,142,459 (+)RGD
Celera17917,710 - 971,638 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039096134   ⟹   XP_038952062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,552,506 - 1,607,730 (+)NCBI
RefSeq Acc Id: XM_039096135   ⟹   XP_038952063
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,552,505 - 1,607,730 (+)NCBI
RefSeq Acc Id: XM_039096136   ⟹   XP_038952064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,550,276 - 1,604,732 (+)NCBI
RefSeq Acc Id: XM_039096137   ⟹   XP_038952065
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,551,312 - 1,604,732 (+)NCBI
RefSeq Acc Id: XM_039096138   ⟹   XP_038952066
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,578,960 - 1,607,730 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_446018   ⟸   NM_053566
- Peptide Label: isoform 1
- UniProtKB: Q6UY90 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026287   ⟸   ENSRNOT00000026287
RefSeq Acc Id: ENSRNOP00000069422   ⟸   ENSRNOT00000086130
RefSeq Acc Id: NP_001376185   ⟸   NM_001389256
- Peptide Label: isoform 2
RefSeq Acc Id: XP_038952064   ⟸   XM_039096136
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038952065   ⟸   XM_039096137
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952063   ⟸   XM_039096135
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952062   ⟸   XM_039096134
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952066   ⟸   XM_039096138
- Peptide Label: isoform X5
Protein Domains
SSD

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
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/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/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
LE/Stm (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
LEW/Crl (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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (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
LEXF11/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
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/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
LEXF4/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
LH/MavRrrc (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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/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/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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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
M520/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
M520/NRrrcMcwi (2019)
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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
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 (2020)
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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
MR/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
MWF/Hsd (2019)
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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
PVG/Seac (2019)
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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
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)
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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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
SHRSP/A3NCrl (2019)
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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
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 (2020)
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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
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 (2019)
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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
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
WAG/RijCrl (2020)
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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
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 (2020)
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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
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 (2019)
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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
WKY/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
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 (2020)
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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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621425 AgrOrtholog
Ensembl Genes ENSRNOG00000019354 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026287 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069422 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026287 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000086130 ENTREZGENE, UniProtKB/TrEMBL
InterPro Patched UniProtKB/TrEMBL
  SSD_5TM UniProtKB/TrEMBL
  TM_rcpt_patched UniProtKB/TrEMBL
NCBI Gene 89830 ENTREZGENE
Pfam Patched UniProtKB/TrEMBL
  Sterol-sensing UniProtKB/TrEMBL
PhenoGen Ptch1 PhenoGen
PROSITE SSD UniProtKB/TrEMBL
TIGRFAMs 2A060602 UniProtKB/TrEMBL
UniProt A0A0G2JVB8_RAT UniProtKB/TrEMBL
  Q6UY90 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Ptch1  patched 1  Ptch1  patched homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-23 Ptch1  patched homolog 1 (Drosophila)  Ptch2_predicted  patched homolog 2 (Drosophila) (predicted)  Data Merged 737654 APPROVED
2005-01-20 Ptch1  patched homolog 1 (Drosophila)  Ptch  patched (Drosophila) homolog  Symbol and Name updated 1299863 APPROVED
2005-01-12 Ptch2_predicted  patched homolog 2 (Drosophila) (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-08-07 Ptch  patched (Drosophila) homolog      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog is mutated in some patients with basal-cell nevus syndrome 704355
gene_other gene may be present in 10-14 copies 704355