Ihh (Indian hedgehog signaling molecule) - Rat Genome Database

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Gene: Ihh (Indian hedgehog signaling molecule) Rattus norvegicus
Analyze
Symbol: Ihh
Name: Indian hedgehog signaling molecule
RGD ID: 620021
Description: Predicted to enable calcium ion binding activity and patched binding activity. Involved in several processes, including liver regeneration; maternal process involved in female pregnancy; and response to estradiol. Predicted to be located in extracellular matrix and plasma membrane. Predicted to be active in extracellular space. Biomarker of osteoarthritis. Human ortholog(s) of this gene implicated in acrocapitofemoral dysplasia; brachydactyly type A1; retinopathy of prematurity; and syndactyly type 1. Orthologous to human IHH (Indian hedgehog signaling molecule); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH (+)-schisandrin B; (S)-nicotine; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Indian hedgehog; indian hedgehog homolog; Indian hedgehog homolog, (Drosophila)
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
mRatBN7.2976,504,315 - 76,510,532 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl976,504,315 - 76,510,532 (-)Ensembl
Rnor_6.0982,208,223 - 82,214,440 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl982,208,223 - 82,214,440 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0981,977,484 - 81,983,701 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4974,287,115 - 74,293,332 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1974,435,304 - 74,439,783 (-)NCBI
Celera974,074,990 - 74,081,207 (-)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(S)-nicotine  (EXP)
1,2-dimethylhydrazine  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
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',4,4',5-pentachlorobiphenyl  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP,ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bromobenzene  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
CHIR 99021  (ISO)
chloroethene  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dichloroacetic acid  (ISO)
diuron  (EXP)
endosulfan  (EXP)
fipronil  (EXP)
folic acid  (ISO)
fulvestrant  (EXP)
genistein  (ISO)
glycidol  (EXP)
itraconazole  (EXP)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
methotrexate  (ISO)
Monobutylphthalate  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
nicotine  (EXP)
ochratoxin A  (EXP)
orphenadrine  (EXP)
paracetamol  (EXP,ISO)
phenobarbital  (ISO)
phenytoin  (ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
Ptaquiloside  (ISO)
quercetin  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
succimer  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
theophylline  (ISO)
titanium dioxide  (EXP,ISO)
tributylstannane  (ISO)
trichloroethene  (EXP,ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bone resorption  (ISO)
branching involved in blood vessel morphogenesis  (ISO)
camera-type eye development  (ISO)
camera-type eye photoreceptor cell fate commitment  (ISO)
cartilage development  (ISO)
cell differentiation  (ISO)
cell fate specification  (IBA,ISO)
cell maturation  (ISO)
cell-cell signaling  (IEA)
chondrocyte differentiation involved in endochondral bone morphogenesis  (ISO)
chondrocyte proliferation  (ISO)
embryonic camera-type eye morphogenesis  (ISO)
embryonic digestive tract morphogenesis  (ISO)
embryonic digit morphogenesis  (ISO)
embryonic pattern specification  (ISO)
embryonic skeletal joint development  (ISO)
epithelial cell morphogenesis  (ISO)
epithelial cell-cell adhesion  (ISO)
head morphogenesis  (ISO)
heart looping  (ISO)
in utero embryonic development  (ISO)
intein-mediated protein splicing  (IEA)
liver regeneration  (IEP)
maternal process involved in female pregnancy  (IEP)
morphogenesis of a branching structure  (ISO)
multicellular organism growth  (ISO)
negative regulation of alpha-beta T cell differentiation  (ISO)
negative regulation of apoptotic process  (IMP)
negative regulation of cell differentiation  (ISO)
negative regulation of eye pigmentation  (ISO)
negative regulation of immature T cell proliferation in thymus  (ISO)
negative regulation of T cell differentiation in thymus  (ISO)
neuron development  (ISO)
ossification  (ISO)
osteoblast differentiation  (ISO)
pancreas development  (ISO)
pattern specification process  (ISO)
positive regulation of alpha-beta T cell differentiation  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of collagen biosynthetic process  (ISO)
positive regulation of epithelial cell proliferation  (IMP)
positive regulation of mesenchymal cell proliferation  (ISO)
positive regulation of smoothened signaling pathway  (ISO)
positive regulation of T cell differentiation in thymus  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
protein autoprocessing  (IEA)
proteoglycan metabolic process  (ISO)
regulation of gene expression  (IBA)
regulation of growth  (ISO)
response to estradiol  (IEP)
response to mechanical stimulus  (IEP)
retinal pigment epithelium development  (ISO)
skeletal system development  (ISO)
smooth muscle tissue development  (ISO)
smoothened signaling pathway  (IBA,ISO)
somite development  (ISO)
vasculature development  (ISO)
vitelline membrane formation  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Beachy PA, etal., Genes Dev. 2010 Sep 15;24(18):2001-12.
2. Buller NV, etal., Gastroenterology. 2015 Jan;148(1):170-180.e6. doi: 10.1053/j.gastro.2014.10.006. Epub 2014 Oct 13.
3. Byrnes AM, etal., Eur J Hum Genet. 2009 Sep;17(9):1112-20. doi: 10.1038/ejhg.2009.18. Epub 2009 Mar 11.
4. Cai Y, etal., Hepatogastroenterology. 2011 Nov-Dec;58(112):2071-6. doi: 10.5754/hge11155.
5. Deckelbaum RA, etal., J Cell Sci 2002 Jul 15;115(Pt 14):3015-25.
6. Dong S, etal., Ann Clin Lab Sci. 2015 Winter;45(1):94-9.
7. Gao B, etal., Nat Genet. 2001 Aug;28(4):386-8.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Halepoto DM, etal., J Coll Physicians Surg Pak. 2015 Dec;25(12):882-5. doi: 12.2015/JCPSP.882885.
11. Hellemans J, etal., Am J Hum Genet. 2003 Apr;72(4):1040-6. Epub 2003 Mar 11.
12. Katayama S, etal., Toxicol Appl Pharmacol. 2006 Dec 15;217(3):375-83. Epub 2006 Oct 6.
13. Kirkpatrick TJ, etal., J Med Genet. 2003 Jan;40(1):42-4.
14. Klopocki E, etal., Am J Hum Genet. 2011 Jan 7;88(1):70-5. doi: 10.1016/j.ajhg.2010.11.006. Epub 2010 Dec 17.
15. Kubota K, etal., J Reprod Dev. 2008 Oct;54(5):340-5. Epub 2008 Jul 8.
16. Liu M, etal., J Hum Genet. 2006;51(8):727-31. Epub 2006 Jul 27.
17. Lodder EM, etal., Am J Med Genet A. 2008 Aug 15;146A(16):2152-4. doi: 10.1002/ajmg.a.32441.
18. McCready ME, etal., Hum Genet. 2002 Oct;111(4-5):368-75. Epub 2002 Sep 7.
19. MGD data from the GO Consortium
20. Mimeault M and Batra SK, Pharmacol Rev. 2010 Sep;62(3):497-524.
21. Mohamed S, etal., Pediatr Res. 2009 Feb;65(2):193-7. doi: 10.1203/PDR.0b013e31818d1dbd.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. OMIM Disease Annotation Pipeline
24. Pereira TA, etal., Liver Int. 2013 Jan;33(1):149-61. doi: 10.1111/liv.12016. Epub 2012 Nov 1.
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. RGD comprehensive gene curation
31. Stattin EL, etal., Eur J Med Genet. 2009 Sep-Oct;52(5):297-302. doi: 10.1016/j.ejmg.2009.05.008. Epub 2009 May 21.
32. Sui G, etal., J Surg Res. 2006 Jul;134(1):1-9. Epub 2006 Feb 20.
33. Tang GH, etal., J Dent Res. 2004 May;83(5):434-8.
34. Tatsumi H, etal., Int J Oral Maxillofac Surg. 2014 Feb;43(2):185-93. doi: 10.1016/j.ijom.2013.07.742. Epub 2013 Aug 28.
35. Zhang C, etal., Int J Mol Sci. 2014 Apr 28;15(5):7250-65. doi: 10.3390/ijms15057250.
36. Zhou S, etal., PLoS Genet. 2015 Jun 19;11(6):e1005214. doi: 10.1371/journal.pgen.1005214. eCollection 2015 Jun.
Additional References at PubMed
PMID:9671585   PMID:9811851   PMID:10208865   PMID:10821773   PMID:11044404   PMID:11476578   PMID:11517919   PMID:11748145   PMID:14973297   PMID:15389630   PMID:15576404   PMID:15645142  
PMID:15689378   PMID:15951842   PMID:16146784   PMID:16278811   PMID:16284117   PMID:16935278   PMID:17191253   PMID:17464332   PMID:17881493   PMID:17889828   PMID:18582859   PMID:19109233  
PMID:19224160   PMID:19264869   PMID:19590577   PMID:20232216   PMID:20533175   PMID:20660756   PMID:21073445   PMID:21537345   PMID:25639508   PMID:26447744   PMID:31302828   PMID:33637095  
PMID:33850470  


Genomics

Comparative Map Data
Ihh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2976,504,315 - 76,510,532 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl976,504,315 - 76,510,532 (-)Ensembl
Rnor_6.0982,208,223 - 82,214,440 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl982,208,223 - 82,214,440 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0981,977,484 - 81,983,701 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4974,287,115 - 74,293,332 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1974,435,304 - 74,439,783 (-)NCBI
Celera974,074,990 - 74,081,207 (-)NCBICelera
Cytogenetic Map9q33NCBI
IHH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2219,054,424 - 219,060,921 (-)EnsemblGRCh38hg38GRCh38
GRCh382219,054,424 - 219,060,921 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372219,919,146 - 219,925,643 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362219,627,390 - 219,633,433 (-)NCBINCBI36hg18NCBI36
Celera2213,688,833 - 213,694,930 (-)NCBI
Cytogenetic Map2q35NCBI
HuRef2211,773,140 - 211,779,240 (-)NCBIHuRef
CHM1_12219,926,506 - 219,932,606 (-)NCBICHM1_1
Ihh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39174,984,474 - 74,990,831 (-)NCBIGRCm39mm39
GRCm39 Ensembl174,984,474 - 74,990,831 (-)Ensembl
GRCm38174,945,315 - 74,951,672 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl174,945,315 - 74,951,672 (-)EnsemblGRCm38mm10GRCm38
MGSCv37174,991,892 - 74,998,225 (-)NCBIGRCm37mm9NCBIm37
MGSCv36174,878,525 - 74,884,858 (-)NCBImm8
Celera175,500,289 - 75,506,631 (-)NCBICelera
Cytogenetic Map1C4NCBI
cM Map138.55NCBI
Ihh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545314,376,718 - 14,381,747 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545314,376,665 - 14,382,536 (+)NCBIChiLan1.0ChiLan1.0
IHH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B224,905,488 - 224,917,887 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B224,906,271 - 224,911,506 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B106,312,472 - 106,319,124 (-)NCBIMhudiblu_PPA_v0panPan3
IHH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13725,616,942 - 25,622,989 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3726,443,433 - 26,449,482 (-)NCBI
ROS_Cfam_1.03725,632,373 - 25,638,422 (-)NCBI
ROS_Cfam_1.0 Ensembl3725,633,157 - 25,638,407 (-)Ensembl
UMICH_Zoey_3.13725,536,946 - 25,542,995 (-)NCBI
UNSW_CanFamBas_1.03725,472,029 - 25,478,078 (-)NCBI
UU_Cfam_GSD_1.03725,492,880 - 25,498,929 (-)NCBI
Ihh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303175,131,886 - 175,137,781 (-)NCBI
SpeTri2.0NW_0049365691,474,693 - 1,480,562 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IHH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15121,083,753 - 121,090,121 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115121,083,750 - 121,090,548 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215134,122,714 - 134,129,084 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IHH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110104,960,296 - 104,966,596 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl10104,960,120 - 104,966,585 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604094,431,690 - 94,438,180 (+)NCBIVero_WHO_p1.0
Ihh
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248235,959,329 - 5,965,584 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH140517  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,504,598 - 76,504,690 (+)MAPPERmRatBN7.2
Rnor_6.0982,208,507 - 82,208,598NCBIRnor6.0
Rnor_5.0981,977,768 - 81,977,859UniSTSRnor5.0
RGSC_v3.4974,287,399 - 74,287,490UniSTSRGSC3.4
Celera974,075,274 - 74,075,365UniSTS
RH 3.4 Map9768.39UniSTS
Cytogenetic Map9q33UniSTS
BI275434  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,506,783 - 76,506,932 (+)MAPPERmRatBN7.2
Rnor_6.0982,210,692 - 82,210,840NCBIRnor6.0
Rnor_5.0981,979,953 - 81,980,101UniSTSRnor5.0
RGSC_v3.4974,289,584 - 74,289,732UniSTSRGSC3.4
Celera974,077,459 - 74,077,607UniSTS
RH 3.4 Map9743.29UniSTS
Cytogenetic Map9q33UniSTS
Ihh  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,505,209 - 76,505,321 (+)MAPPERmRatBN7.2
Rnor_6.0982,209,118 - 82,209,229NCBIRnor6.0
Rnor_5.0981,978,379 - 81,978,490UniSTSRnor5.0
RGSC_v3.4974,288,010 - 74,288,121UniSTSRGSC3.4
Celera974,075,885 - 74,075,996UniSTS
Cytogenetic Map9q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95584784177026453Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95662771378595166Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:110
Interacting mature miRNAs:129
Transcripts:ENSRNOT00000024419
Prediction methods: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 3 4 4 4 7 3
Low 37 37 37 24 12 3
Below cutoff 16 11 15 1 2 62 4 26 8 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024419   ⟹   ENSRNOP00000024419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl976,504,315 - 76,510,532 (-)Ensembl
Rnor_6.0 Ensembl982,208,223 - 82,214,440 (-)Ensembl
RefSeq Acc Id: NM_053384   ⟹   NP_445836
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2976,504,315 - 76,510,532 (-)NCBI
Rnor_6.0982,208,223 - 82,214,440 (-)NCBI
Rnor_5.0981,977,484 - 81,983,701 (-)NCBI
RGSC_v3.4974,287,115 - 74,293,332 (-)RGD
Celera974,074,990 - 74,081,207 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445836 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD45372 (Get FASTA)   NCBI Sequence Viewer  
  AAG09197 (Get FASTA)   NCBI Sequence Viewer  
  EDL75378 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445836   ⟸   NM_053384
- Peptide Label: precursor
- UniProtKB: F1LP42 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024419   ⟸   ENSRNOT00000024419
Protein Domains
HintC   HintN

Transcriptome

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

Promoters
RGD ID:13696764
Promoter ID:EPDNEW_R7288
Type:multiple initiation site
Name:Ihh_1
Description:Indian hedgehog
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_6.0982,214,440 - 82,214,500EPDNEW

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)
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
LN/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
LN/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
M520/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
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)
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
MHS/Gib (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
MNS/Gib (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
MR/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
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)
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
PVG/Seac (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
SBH/Ygl (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: 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)
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: 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
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)
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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 (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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620021 AgrOrtholog
Ensembl Genes ENSRNOG00000018059 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024419 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024419 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.1380.10 UniProtKB/TrEMBL
InterPro Hedgehog UniProtKB/TrEMBL
  Hedgehog_hint_N UniProtKB/TrEMBL
  Hedgehog_sig/DD-Pept_Zn-bd_dom UniProtKB/TrEMBL
  Hedgehog_signaling_dom UniProtKB/TrEMBL
  Hint_dom_C UniProtKB/TrEMBL
  Hint_dom_sf UniProtKB/TrEMBL
  IHH UniProtKB/TrEMBL
  Intein_splice_site UniProtKB/TrEMBL
  Peptidase_C46_hint UniProtKB/TrEMBL
KEGG Report rno:84399 UniProtKB/TrEMBL
NCBI Gene 84399 ENTREZGENE
PANTHER PTHR11889:SF39 UniProtKB/TrEMBL
Pfam HH_signal UniProtKB/TrEMBL
  Hint UniProtKB/TrEMBL
PhenoGen Ihh PhenoGen
PIRSF Peptidase_C46 UniProtKB/TrEMBL
PRINTS SONICHHOG UniProtKB/TrEMBL
PROSITE INTEIN_N_TER UniProtKB/TrEMBL
SMART HintC UniProtKB/TrEMBL
  HintN UniProtKB/TrEMBL
Superfamily-SCOP Hedgehog_sig_N UniProtKB/TrEMBL
  SSF51294 UniProtKB/TrEMBL
UniProt F1LP42 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-12-04 Ihh  Indian hedgehog signaling molecule  Ihh  Indian hedgehog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Ihh  Indian hedgehog  Ihh  Indian hedgehog homolog, (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Ihh  Indian hedgehog homolog, (Drosophila)    indian hedgehog homolog, (Drosophila)  Name updated 1299863 APPROVED
2002-08-07 Ihh  indian hedgehog homolog, (Drosophila)      Symbol and Name status set to provisional 70820 PROVISIONAL