Shh (sonic hedgehog signaling molecule) - Rat Genome Database
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Gene: Shh (sonic hedgehog signaling molecule) Rattus norvegicus
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Symbol: Shh
Name: sonic hedgehog signaling molecule
RGD ID: 3673
Description: Predicted to have several functions, including laminin-1 binding activity; metal ion binding activity; and patched binding activity. Involved in several processes, including animal organ development; negative regulation of cell death; and nervous system development. Localizes to several cellular components, including membrane raft; neuronal cell body; and synaptic vesicle. Used to study myocardial infarction. Biomarker of several diseases, including VACTERL association; chronic kidney disease; esophageal atresia/tracheoesophageal fistula; ocular hypertension; and temporal lobe epilepsy. Human ortholog(s) of this gene implicated in several diseases, including Hirschsprung's disease; holoprosencephaly (multiple); hypoplastic or aplastic tibia with polydactyly; middle cerebral artery infarction; and polydactyly. Orthologous to human SHH (sonic hedgehog signaling molecule); PARTICIPATES IN altered Hedgehog signaling pathway; forkhead class A signaling pathway; glypican signaling pathway; INTERACTS WITH (S)-amphetamine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: shh unprocessed N-terminal signaling and C-terminal autoprocessing domains; ShhNC; sonic hedgehog; sonic hedgehog homolog; sonic hedgehog homolog (Drosophila); sonic hedgehog homolog, (Drosophila); sonic hedgehog protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.246,954,017 - 6,963,170 (+)NCBI
Rnor_6.0 Ensembl4718,538 - 727,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04718,538 - 727,691 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04711,420 - 720,573 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.442,200,504 - 2,209,657 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.142,200,503 - 2,209,657 (+)NCBI
Celera43,316,537 - 3,325,690 (-)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acrocallosal syndrome  (ISO)
Anorectal Malformations  (IEP,ISO)
atrioventricular septal defect  (ISO)
autism spectrum disorder  (ISO)
autistic disorder  (ISO)
basal cell carcinoma  (ISO)
biliary atresia  (ISO)
brachydactyly type A1  (ISO,ISS)
chronic kidney disease  (IEP,ISO)
cleft palate  (ISO)
Congenital Limb Deformities  (ISO)
demyelinating disease  (ISO)
esophageal atresia/tracheoesophageal fistula  (IEP)
Experimental Arthritis  (IEP)
Experimental Autoimmune Encephalomyelitis  (IEP,ISO)
Eye Abnormalities  (ISO)
Facial Dysmorphism with Multiple Malformations  (ISO)
Fluoride Poisoning  (IEP)
focal segmental glomerulosclerosis  (ISO)
genetic disease  (ISO)
hepatocellular carcinoma  (ISO)
Hirschsprung's disease  (ISO)
holoprosencephaly  (ISO)
holoprosencephaly 3  (ISO)
Hyperoxic Lung Injury  (IEP)
hypoplastic or aplastic tibia with polydactyly  (ISO)
hypothyroidism  (IEP)
IgA glomerulonephritis  (ISO)
Isolated Microphthalmia with Coloboma 5  (ISO)
Kidney Reperfusion Injury  (ISO)
membranous glomerulonephritis  (ISO)
microphthalmia  (ISO)
middle cerebral artery infarction  (ISO)
multiple sclerosis  (ISO)
myocardial infarction  (IMP)
Myocardial Reperfusion Injury  (IEP)
nevoid basal cell carcinoma syndrome  (ISO)
ocular hypertension  (IEP)
pancreatic cancer  (ISO)
Parkinsonism  (IMP)
Patterson Stevenson Syndrome  (ISO)
Peripheral Nerve Injuries  (IEP)
Persistent Cloaca  (ISO)
polydactyly  (ISO)
Preaxial Polydactyly II  (ISO)
primary progressive multiple sclerosis  (ISO)
Schizencephaly  (ISO)
secondary Parkinson disease  (ISO)
solitary median maxillary central incisor  (ISO)
Spinal Cord Injuries  (IMP)
Subarachnoid Hemorrhage  (IEP)
syndactyly type 4  (ISO)
temporal lobe epilepsy  (IEP,ISO)
ureteral obstruction  (ISO)
VACTERL association  (IEP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-amphetamine  (EXP)
1,1-dichloroethene  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
actinomycin D  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
ammonium chloride  (EXP)
apomorphine  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzylpenicillin  (ISO)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP,ISO)
captopril  (EXP,ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
Cyclopamine  (EXP,ISO)
D-glucose  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
ethanol  (ISO)
Ethylenethiourea  (EXP)
flavonoids  (EXP)
folic acid  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
glucose  (ISO)
hydrogen peroxide  (EXP)
ipriflavone  (ISO)
isotretinoin  (ISO)
lansoprazole  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (ISO)
melittin  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nitrofen  (EXP)
ochratoxin A  (EXP)
oxidopamine  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctanoic acid  (ISO)
phenytoin  (ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin 3-O-beta-D-galactopyranoside  (EXP)
resveratrol  (ISO)
saccharin  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
testosterone  (EXP)
tetrachloromethane  (ISO)
tetramethylpyrazine  (ISO)
titanium dioxide  (ISO)
tofacitinib  (ISO)
tolnaftate  (ISO)
trans-piceid  (ISO)
triadimefon  (EXP)
triptonide  (ISO)
udenafil  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vismodegib  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (ISO)
anatomical structure formation involved in morphogenesis  (ISO)
androgen metabolic process  (IEA,ISO,ISS)
angiogenesis  (ISO)
animal organ formation  (IEA,ISO)
anterior/posterior pattern specification  (ISO)
apoptotic signaling pathway  (IEA,ISO,ISS)
artery development  (IEA,ISO)
axon guidance  (IEA,ISO,ISS)
Bergmann glial cell differentiation  (IEA,ISO)
blood coagulation  (IEA,ISO)
branching involved in blood vessel morphogenesis  (IEA,ISO,ISS)
branching involved in prostate gland morphogenesis  (ISO)
branching involved in salivary gland morphogenesis  (IEA,ISO)
branching involved in ureteric bud morphogenesis  (IEA,ISO,ISS)
branching morphogenesis of an epithelial tube  (ISO,ISS)
bud outgrowth involved in lung branching  (IEA,ISO)
camera-type eye development  (IEA,ISO)
canonical Wnt signaling pathway  (IEA,ISO)
CD4-positive or CD8-positive, alpha-beta T cell lineage commitment  (IEA,ISO,ISS)
cell development  (ISO,ISS)
cell fate commitment  (ISO)
cell fate specification  (IBA,IEA,ISO,ISS)
cell population proliferation  (ISO)
cell proliferation in external granule layer  (ISO)
cell-cell signaling  (ISO,ISS)
cellular response to lithium ion  (IEA,ISO)
central nervous system development  (ISO,ISS)
cerebellar granule cell precursor proliferation  (IEA,ISO,ISS)
commissural neuron axon guidance  (IMP)
determination of left/right asymmetry in lateral mesoderm  (IEA,ISO)
determination of left/right symmetry  (ISO)
developmental growth  (ISO)
digestive tract mesoderm development  (IDA)
digestive tract morphogenesis  (ISO)
dorsal/ventral neural tube patterning  (IEA,ISO)
dorsal/ventral pattern formation  (ISO,ISS)
ectoderm development  (IEA,ISO)
embryonic digestive tract morphogenesis  (IEA,ISO)
embryonic digit morphogenesis  (IEA,ISO,ISS)
embryonic foregut morphogenesis  (IEA,ISO)
embryonic forelimb morphogenesis  (IEA,ISO)
embryonic hindlimb morphogenesis  (IEA,ISO)
embryonic limb morphogenesis  (ISO,ISS)
embryonic morphogenesis  (ISO)
embryonic organ development  (ISO)
embryonic skeletal system development  (IEA,ISO)
endocytosis  (IEA,ISO)
epithelial cell proliferation involved in salivary gland morphogenesis  (IEA,ISO)
epithelial tube branching involved in lung morphogenesis  (IEP,ISO)
epithelial-mesenchymal cell signaling  (ISO)
epithelial-mesenchymal signaling involved in prostate gland development  (ISO)
establishment of cell polarity  (IEA,ISO)
forebrain development  (ISO,ISS)
forebrain regionalization  (ISO)
formation of anatomical boundary  (IEA,ISO)
fungiform papilla development  (IMP)
fungiform papilla formation  (IMP)
fungiform papilla morphogenesis  (IMP)
hair follicle development  (ISO)
hair follicle morphogenesis  (IEA,ISO)
heart development  (ISO,ISS)
heart looping  (IEA,ISO)
hindbrain development  (ISO,ISS)
hindgut morphogenesis  (IEA,ISO)
inner ear development  (IEA,ISO)
intein-mediated protein splicing  (IEA)
intermediate filament organization  (IEA,ISO)
kidney development  (ISO)
left lung development  (IEA,ISO)
limb bud formation  (IEA,ISO)
limb development  (ISO)
liver regeneration  (IEP)
lung development  (ISO,ISS)
lung epithelium development  (IEA,ISO)
lung lobe morphogenesis  (IEA,ISO)
lung morphogenesis  (ISO)
lung-associated mesenchyme development  (IEA,ISO)
lymphoid progenitor cell differentiation  (IEA,ISO,ISS)
male genitalia development  (IEA,ISO,ISS)
male genitalia morphogenesis  (IMP)
mesenchymal cell proliferation  (ISO)
mesenchymal cell proliferation involved in lung development  (IEA,ISO)
mesenchymal smoothened signaling pathway involved in prostate gland development  (IEA,ISO)
metanephric collecting duct development  (IEA,ISO)
metanephric mesenchymal cell proliferation involved in metanephros development  (IEA,ISO,ISS)
metanephros development  (ISO,ISS)
midbrain development  (IEA,ISO,ISS)
myoblast differentiation  (IEA,ISO)
myotube differentiation  (IEA,ISO)
negative regulation of alpha-beta T cell differentiation  (IEA,ISO)
negative regulation of apoptotic process  (IMP,ISO)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO)
negative regulation of cell differentiation  (ISO,ISS)
negative regulation of cell migration  (IEA,ISO,ISS)
negative regulation of cholesterol efflux  (IEA,ISO)
negative regulation of dopaminergic neuron differentiation  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of kidney smooth muscle cell differentiation  (IEA,ISO,ISS)
negative regulation of mesenchymal cell apoptotic process  (IEA,ISO)
negative regulation of neuron death  (IMP)
negative regulation of proteasomal ubiquitin-dependent protein catabolic process  (IEA,ISO)
negative regulation of protein catabolic process  (ISO)
negative regulation of T cell proliferation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription elongation from RNA polymerase II promoter  (IEA,ISO)
negative regulation of ureter smooth muscle cell differentiation  (IEA,ISO,ISS)
negative regulation of Wnt signaling pathway  (ISO)
negative thymic T cell selection  (IEA,ISO,ISS)
neural crest cell migration  (IEA,ISO,ISS)
neural tube formation  (IMP)
neuroblast proliferation  (IEA,ISO,ISS)
neuron fate commitment  (IEA,ISO,ISS)
odontogenesis  (ISO)
odontogenesis of dentin-containing tooth  (IEA,ISO)
oligodendrocyte development  (IEA,ISO)
oligodendrocyte differentiation  (IBA,ISO)
osteoblast development  (IEA,ISO)
pancreas development  (IEA,ISO)
pattern specification process  (ISO,ISS)
polarity specification of anterior/posterior axis  (IEA,ISO,ISS)
positive regulation of alpha-beta T cell differentiation  (IEA,ISO,ISS)
positive regulation of cell differentiation  (ISO)
positive regulation of cell division  (IEA,ISO)
positive regulation of cell population proliferation  (IDA,ISO,ISS)
positive regulation of cerebellar granule cell precursor proliferation  (ISO)
positive regulation of endothelial cell chemotaxis  (IDA)
positive regulation of epithelial cell proliferation involved in prostate gland development  (IEA,ISO)
positive regulation of gene expression  (IEA,ISO)
positive regulation of hh target transcription factor activity  (IEA,ISO)
positive regulation of immature T cell proliferation in thymus  (IEA,ISO,ISS)
positive regulation of kidney smooth muscle cell differentiation  (IEA,ISO,ISS)
positive regulation of mesenchymal cell proliferation  (ISO)
positive regulation of mesenchymal cell proliferation involved in ureter development  (IEA,ISO,ISS)
positive regulation of neuroblast proliferation  (IEA,IMP,ISO)
positive regulation of neuron differentiation  (IMP)
positive regulation of neurotrophin production  (IMP)
positive regulation of oligodendrocyte differentiation  (IEA,ISO)
positive regulation of oligodendrocyte progenitor proliferation  (IDA)
positive regulation of penile erection  (IMP)
positive regulation of photoreceptor cell differentiation  (IDA)
positive regulation of protein import into nucleus  (IEA,ISO)
positive regulation of sclerotome development  (IEA,ISO)
positive regulation of skeletal muscle cell proliferation  (IEA,ISO)
positive regulation of skeletal muscle tissue development  (IEA,ISO)
positive regulation of smoothened signaling pathway  (IEA,ISO,ISS)
positive regulation of sprouting angiogenesis  (IDA)
positive regulation of striated muscle cell differentiation  (IEA,ISO)
positive regulation of T cell differentiation in thymus  (IEA,ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of ureter smooth muscle cell differentiation  (IEA,ISO,ISS)
positive regulation of Wnt signaling pathway  (IEA,ISO)
positive thymic T cell selection  (IEA,ISO,ISS)
primary prostatic bud elongation  (IEA,ISO)
prostate epithelial cord elongation  (IEA,ISO)
prostate gland development  (IEP,ISO,ISS)
prostatic bud formation  (ISO)
protein autoprocessing  (IEA)
protein localization to nucleus  (IEA,ISO)
regulation of cell population proliferation  (IDA,ISO,ISS)
regulation of epithelial cell differentiation  (IEP)
regulation of epithelial cell proliferation involved in prostate gland development  (ISO)
regulation of gene expression  (IBA,ISO)
regulation of mesenchymal cell proliferation involved in prostate gland development  (IEA,ISO)
regulation of odontogenesis  (IEA,ISO)
regulation of prostatic bud formation  (IEA,ISO)
regulation of protein localization to nucleus  (ISO)
regulation of proteolysis  (ISO,ISS)
regulation of transcription, DNA-templated  (ISO)
respiratory tube development  (ISO)
response to axon injury  (IMP)
response to estradiol  (IEP)
response to ethanol  (IDA)
response to hypoxia  (IEP)
response to organonitrogen compound  (IEP)
response to retinoic acid  (IEP)
right lung development  (IEA,ISO)
roof of mouth development  (IEA,ISO)
salivary gland cavitation  (IEA,ISO)
skin development  (ISO)
smooth muscle tissue development  (IEA,ISO)
smoothened signaling pathway  (IBA,ISO,ISS)
smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation  (IEA,ISO)
somite development  (IEA,ISO)
spinal cord dorsal/ventral patterning  (IDA,IEA,ISO)
spinal cord motor neuron differentiation  (IEA,ISO)
stem cell development  (ISO,ISS)
striated muscle cell differentiation  (ISO)
striated muscle tissue development  (IEA,ISO)
T cell differentiation in thymus  (ISO,ISS)
telencephalon regionalization  (IEA,IMP,ISO)
thalamus development  (IEA,ISO)
thymus development  (IEA,ISO,ISS)
thyroid gland development  (IEA,ISO)
tongue development  (IMP)
tongue morphogenesis  (IMP)
trachea development  (ISO)
trachea morphogenesis  (IEA,ISO)
tracheoesophageal septum formation  (IEA,ISO)
vasculature development  (ISO)
vasculogenesis  (IEA,ISO,ISS)
ventral spinal cord interneuron specification  (IDA)
zona limitans intrathalamica formation  (IDA)

Cellular Component
axon  (IDA)
cell surface  (IEA,ISO,ISS)
dendrite  (IDA)
endoplasmic reticulum  (IDA)
extracellular matrix  (IEA,ISO)
extracellular space  (IBA,IDA,IEA,ISO,ISS)
Golgi apparatus  (IDA)
membrane  (ISO)
membrane raft  (IDA,IEA,ISO,ISS)
neuronal cell body  (IDA)
nucleus  (IDA)
plasma membrane  (IEA)
synaptic vesicle  (IDA)
transport vesicle  (IDA)

Molecular Function
calcium ion binding  (IBA,IEA,ISO,ISS)
glycosaminoglycan binding  (IEA,ISO)
hydrolase activity  (ISO)
laminin-1 binding  (IEA,ISO,ISS)
patched binding  (IBA,IEA,ISO)
peptidase activity  (IEA)
protein binding  (IPI,ISO)
zinc ion binding  (IEA,ISO,ISS)

References

References - curated
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68. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:7891723   PMID:8660874   PMID:8835524   PMID:8906787   PMID:9006067   PMID:9356179   PMID:9585504   PMID:9731532   PMID:9768360   PMID:9768363   PMID:9769173   PMID:9811851  
PMID:10027293   PMID:10208740   PMID:10331973   PMID:10340755   PMID:10357934   PMID:10375501   PMID:10385121   PMID:10411502   PMID:10500113   PMID:10500184   PMID:10654605   PMID:10781055  
PMID:10821773   PMID:10970885   PMID:10981962   PMID:11044393   PMID:11044396   PMID:11044404   PMID:11060228   PMID:11118883   PMID:11171336   PMID:11171399   PMID:11172440   PMID:11331587  
PMID:11389830   PMID:11395778   PMID:11412027   PMID:11476578   PMID:11476582   PMID:11485934   PMID:11493558   PMID:11493571   PMID:11517919   PMID:11520664   PMID:11684660   PMID:11748151  
PMID:11748155   PMID:11906206   PMID:12195432   PMID:12221011   PMID:12231626   PMID:12399320   PMID:12435628   PMID:12547712   PMID:12679031   PMID:12748119   PMID:12756179   PMID:12843296  
PMID:12947339   PMID:14602680   PMID:14623238   PMID:14660548   PMID:14687547   PMID:14764698   PMID:15009684   PMID:15013801   PMID:15042696   PMID:15056720   PMID:15065125   PMID:15075292  
PMID:15136151   PMID:15183722   PMID:15193287   PMID:15199404   PMID:15238161   PMID:15294868   PMID:15305287   PMID:15315763   PMID:15337776   PMID:15496441   PMID:15576403   PMID:15680353  
PMID:15880651   PMID:15930098   PMID:15936751   PMID:15987773   PMID:16020517   PMID:16054035   PMID:16221724   PMID:16236765   PMID:16332353   PMID:16396903   PMID:16492970   PMID:16611981  
PMID:16630542   PMID:16647304   PMID:16778080   PMID:16880529   PMID:16940239   PMID:16968815   PMID:17043310   PMID:17187775   PMID:17227833   PMID:17284610   PMID:17395647   PMID:17442700  
PMID:17504940   PMID:17504941   PMID:17519786   PMID:17657839   PMID:17850284   PMID:17880919   PMID:17881493   PMID:18022723   PMID:18076286   PMID:18256331   PMID:18330924   PMID:18393306  
PMID:18477453   PMID:18582859   PMID:18590716   PMID:18612197   PMID:18786173   PMID:18799682   PMID:19029980   PMID:19056373   PMID:19100254   PMID:19109233   PMID:19122665   PMID:19223390  
PMID:19273836   PMID:19304890   PMID:19357274   PMID:19407245   PMID:19422820   PMID:19429033   PMID:19472217   PMID:19517566   PMID:19561609   PMID:19683085   PMID:19952108   PMID:19955443  
PMID:20533175   PMID:20578145   PMID:20643644   PMID:20646667   PMID:20660756   PMID:20848190   PMID:20954080   PMID:21094676   PMID:21110116   PMID:21209331   PMID:21363934   PMID:21447550  
PMID:21552265   PMID:21931618   PMID:22095825   PMID:22179047   PMID:22402346   PMID:22573687   PMID:22771389   PMID:23271286   PMID:23325464   PMID:23740243   PMID:23967143   PMID:23981041  
PMID:24240054   PMID:24264724   PMID:24388991   PMID:24472833   PMID:24528677   PMID:24533105   PMID:25502463   PMID:25504432   PMID:25582777   PMID:25613906   PMID:25639508   PMID:26218245  
PMID:26340267   PMID:26348666   PMID:26552406   PMID:26607632   PMID:26658865   PMID:26722433   PMID:27035418   PMID:27237094   PMID:27579669   PMID:27639396   PMID:28560441   PMID:29721855  
PMID:30306574   PMID:30391523   PMID:30502245   PMID:31432117   PMID:31968603  


Genomics

Comparative Map Data
Shh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.246,954,017 - 6,963,170 (+)NCBI
Rnor_6.0 Ensembl4718,538 - 727,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04718,538 - 727,691 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04711,420 - 720,573 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.442,200,504 - 2,209,657 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.142,200,503 - 2,209,657 (+)NCBI
Celera43,316,537 - 3,325,690 (-)NCBICelera
Cytogenetic Map4q11NCBI
SHH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7155,799,980 - 155,812,463 (-)EnsemblGRCh38hg38GRCh38
GRCh387155,799,980 - 155,812,463 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377155,595,558 - 155,604,967 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh377155,592,674 - 155,605,157 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367155,288,319 - 155,297,728 (-)NCBINCBI36hg18NCBI36
Build 347155,095,033 - 155,104,443NCBI
Celera7150,021,217 - 150,030,626 (-)NCBI
Cytogenetic Map7q36.3NCBI
HuRef7149,327,101 - 149,336,513 (-)NCBIHuRef
CHM1_17155,601,138 - 155,613,409 (-)NCBICHM1_1
CRA_TCAGchr7v27154,827,119 - 154,836,528 (-)NCBI
Shh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39528,661,838 - 28,672,099 (-)NCBIGRCm39mm39
GRCm38528,456,840 - 28,467,101 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl528,456,815 - 28,467,256 (-)EnsemblGRCm38mm10GRCm38
MGSCv37528,783,380 - 28,793,641 (-)NCBIGRCm37mm9NCBIm37
MGSCv36528,787,627 - 28,797,875 (-)NCBImm8
Celera525,997,895 - 26,008,156 (-)NCBICelera
Cytogenetic Map5B1NCBI
cM Map514.39NCBI
Shh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554918,647,133 - 8,657,381 (-)NCBIChiLan1.0ChiLan1.0
SHH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17159,116,966 - 159,126,660 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7159,114,666 - 159,126,651 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07147,400,112 - 147,414,036 (-)NCBIMhudiblu_PPA_v0panPan3
SHH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1618,484,809 - 18,662,903 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11618,650,553 - 18,663,571 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Shh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493652710,033,095 - 10,042,713 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl182,545,718 - 2,555,484 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1182,546,202 - 2,555,484 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2182,664,794 - 2,673,805 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHH
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121123,929,937 - 123,942,451 (-)NCBI
ChlSab1.1 Ensembl21123,932,900 - 123,942,395 (-)Ensembl
Shh
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248002,202,986 - 2,215,309 (+)NCBI

Position Markers
Shh  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04718,627 - 718,886NCBIRnor6.0
Rnor_5.04711,509 - 711,768UniSTSRnor5.0
RGSC_v3.442,209,309 - 2,209,568UniSTSRGSC3.4
Celera43,316,626 - 3,316,885UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4125545519Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4125545519Rat
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4125545519Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4126654881Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4126803291Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4128352196Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4128352196Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4128352196Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4128352196Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4129778604Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4129778604Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4131554484Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)4142118977Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:64
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000008497
Prediction methods: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 8 10 4 3
Low 2 64 22 13 8
Below cutoff 1 2 12 7 5 7 5 6 13 8 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008497   ⟹   ENSRNOP00000008497
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4718,538 - 727,691 (-)Ensembl
RefSeq Acc Id: NM_017221   ⟹   NP_058917
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.246,954,017 - 6,963,170 (+)NCBI
Rnor_6.04718,538 - 727,691 (-)NCBI
Rnor_5.04711,420 - 720,573 (-)NCBI
RGSC_v3.442,200,504 - 2,209,657 (+)RGD
Celera43,316,537 - 3,325,690 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058917 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA20999 (Get FASTA)   NCBI Sequence Viewer  
  AAD45373 (Get FASTA)   NCBI Sequence Viewer  
  EDL86418 (Get FASTA)   NCBI Sequence Viewer  
  Q63673 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058917   ⟸   NM_017221
- Peptide Label: precursor
- UniProtKB: Q63673 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008497   ⟸   ENSRNOT00000008497
Protein Domains
HintC   HintN

Transcriptome

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

Promoters
RGD ID:13692770
Promoter ID:EPDNEW_R3293
Type:single initiation site
Name:Shh_1
Description:sonic 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_6.04727,716 - 727,776EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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
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 (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
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
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
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
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
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3673 AgrOrtholog
Ensembl Genes ENSRNOG00000006120 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008497 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008497 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.1380.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Hedgehog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hedgehog_Hint UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hedgehog_sig/DD-Pept_Zn-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hedgehog_signalling_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hint_dom_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hint_dom_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hint_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intein_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29499 UniProtKB/Swiss-Prot
NCBI Gene 29499 ENTREZGENE
Pfam HH_signal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hint UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SHH RGD
PhenoGen Shh PhenoGen
PIRSF Peptidase_C46 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS SONICHHOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE INTEIN_N_TER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HintC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HintN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51294 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55166 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC214872
UniProt G3V6T0_RAT UniProtKB/TrEMBL
  Q63673 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-12-04 Shh  sonic hedgehog signaling molecule  Shh  sonic hedgehog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Shh  sonic hedgehog  Shh  sonic hedgehog homolog (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Shh  sonic hedgehog homolog (Drosophila)    sonic hedgehog homolog (Drosophila)   Symbol and Name status set to approved 1299863 APPROVED
2002-06-10 Shh  sonic hedgehog homolog (Drosophila)       Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease mutations activating the Shh pathway are associated with medulloblastoma 628387
gene_process important mitogen for cerebellar granule neuron precursors (GNPs) produced by the Purkinje neurons 628387
gene_regulation mitogenic activity stimulates DNA synthesis 628387