Shh (sonic hedgehog signaling molecule) - Rat Genome Database

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Gene: Shh (sonic hedgehog signaling molecule) Rattus norvegicus
Symbol: Shh
Name: sonic hedgehog signaling molecule
RGD ID: 3673
Description: Predicted to enable several functions, including cholesterol-protein transferase activity; laminin-1 binding activity; and metal ion binding activity. Involved in several processes, including nervous system development; positive regulation of cell differentiation; and reproductive structure development. Acts upstream of or within ventral spinal cord interneuron specification. Located in several cellular components, including dendrite; neuronal cell body; and synaptic vesicle. Used to study Parkinsonism and 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
Previously 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
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.246,954,017 - 6,963,170 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl46,954,017 - 6,963,170 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx411,962,609 - 11,971,762 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.047,776,827 - 7,785,980 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.046,123,054 - 6,132,207 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04718,538 - 727,691 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4718,538 - 727,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04711,420 - 720,573 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.442,200,504 - 2,209,657 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)

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)
chronic kidney disease  (IEP,ISO)
cleft palate  (ISO)
colorectal cancer  (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)
Failure to Thrive  (ISO)
Fluoride Poisoning  (IEP)
focal segmental glomerulosclerosis  (ISO)
gastrointestinal stromal tumor  (ISO)
genetic disease  (ISO)
hepatocellular carcinoma  (ISO)
Hirschsprung's disease  (ISO)
holoprosencephaly  (ISO)
holoprosencephaly 3  (ISO,ISS)
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)
neurodevelopmental disorder with dysmorphic facies and distal limb anomalies  (ISO)
nevoid basal cell carcinoma syndrome  (ISO)
ocular hypertension  (IEP)
pancreatic cancer  (ISO)
Parkinsonism  (IMP)
Partial Agenesis of Corpus Callosum  (ISO)
Patterson Stevenson Syndrome  (ISO)
Peripheral Nerve Injuries  (IEP)
Persistent Cloaca  (ISO)
polydactyly  (ISO)
pre-malignant neoplasm  (IEP)
Preaxial Polydactyly II  (ISO)
primary progressive multiple sclerosis  (ISO)
Schizencephaly  (ISO)
secondary Parkinson disease  (ISO)
septooptic dysplasia  (ISO)
solitary median maxillary central incisor  (ISO)
Spinal Cord Injuries  (IMP)
stomach cancer  (ISO)
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)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
Ac-Ser-Asp-Lys-Pro-OH  (EXP,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  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzylpenicillin  (ISO)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
captopril  (EXP,ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
curcumin  (EXP)
Cyclopamine  (EXP,ISO)
D-glucose  (ISO)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
ethanol  (ISO)
Ethylenethiourea  (EXP)
flavonoids  (EXP)
folic acid  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
glucose  (ISO)
goralatide  (EXP,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)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (EXP)
oxidopamine  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenytoin  (ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-galactopyranoside  (EXP)
resveratrol  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (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)
thyroxine  (EXP)
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
alpha-beta T cell differentiation  (IEA,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)
astrocyte differentiation  (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 migration  (ISO)
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  (ISO)
epithelial cell proliferation involved in prostate gland development  (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 epithelial 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)
gene expression  (ISO)
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 apoptotic process  (IEA,ISO)
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  (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  (ISS)
negative regulation of cell migration  (IEA,ISO,ISS)
negative regulation of cellular process  (IMP)
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 differentiation  (ISO)
negative regulation of proteasomal ubiquitin-dependent protein catabolic process  (IEA,ISO)
negative regulation of protein catabolic process  (ISO)
negative regulation of T cell differentiation in thymus  (IEA,ISO)
negative regulation of T cell proliferation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription elongation by RNA polymerase II  (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  (ISO,ISS)
neural tube formation  (IMP)
neuroblast proliferation  (IEA,ISO,ISS)
neuron differentiation  (ISO)
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 astrocyte differentiation  (IEA,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  (IEA,ISO)
positive regulation of DNA-templated transcription  (ISO,ISS)
positive regulation of endothelial cell chemotaxis  (IDA)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of epithelial cell proliferation involved in prostate gland development  (IEA,ISO)
positive regulation of gene expression  (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 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 import into nucleus  (IEA,ISO)
protein localization to nucleus  (ISO)
regulation of cell population proliferation  (IDA,ISS)
regulation of DNA-templated transcription  (ISO)
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 glial cell proliferation  (IEA,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 stem cell proliferation  (IEA,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)
self proteolysis  (IEA,ISO,ISS)
skeletal muscle cell proliferation  (IEA,ISO)
skeletal muscle fiber differentiation  (IEA,ISO)
skeletal muscle tissue development  (ISO)
skin development  (ISO)
smooth muscle tissue development  (IEA,ISO)
smoothened signaling pathway  (IBA,ISO,ISS)
somite development  (IEA,ISO)
spinal cord dorsal/ventral patterning  (IDA,IEA,ISO)
spinal cord motor neuron differentiation  (IEA,ISO)
stem cell development  (ISO,ISS)
stem cell proliferation  (IEA,ISO)
striated muscle cell differentiation  (ISO)
striated muscle tissue development  (IEA,ISO)
T cell differentiation in thymus  (ISO,ISS)
T cell proliferation  (IEA,ISO)
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)
trunk neural crest cell migration  (IEA,ISO)
vasculature development  (ISO)
vasculogenesis  (IEA,ISO,ISS)
ventral spinal cord interneuron specification  (IDA)
zona limitans intrathalamica formation  (IDA)

Cellular Component

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


References - curated
# Reference Title Reference Citation
1. Sonic Hedgehog gene delivery to the rodent heart promotes angiogenesis via iNOS/netrin-1/PKC pathway. Ahmed RP, etal., PLoS One. 2010 Jan 5;5(1):e8576. doi: 10.1371/journal.pone.0008576.
2. The upregulated expression of sonic hedgehog in motor neurons after rat facial nerve axotomy. Akazawa C, etal., J Neurosci. 2004 Sep 8;24(36):7923-30.
3. Relationship between Sonic hedgehog protein, brain-derived neurotrophic factor and oxidative stress in autism spectrum disorders. Al-Ayadhi LY, Neurochem Res. 2012 Feb;37(2):394-400. doi: 10.1007/s11064-011-0624-x. Epub 2011 Oct 9.
4. A novel mutation in the SHH long-range regulator (ZRS) is associated with preaxial polydactyly, triphalangeal thumb, and severe radial ray deficiency. Al-Qattan MM, etal., Am J Med Genet A. 2012 Oct;158A(10):2610-5. doi: 10.1002/ajmg.a.35584. Epub 2012 Aug 17.
5. Identification of two novel mutations in Shh long-range regulator associated with familial pre-axial polydactyly. Albuisson J, etal., Clin Genet. 2011 Apr;79(4):371-7. doi: 10.1111/j.1399-0004.2010.01465.x.
6. Sonic hedgehog is neuroprotective in the cavernous nerve with crush injury. Angeloni N, etal., J Sex Med. 2013 May;10(5):1240-50. doi: 10.1111/j.1743-6109.2012.02930.x. Epub 2012 Sep 20.
7. Fetal ethanol exposure activates protein kinase A and impairs Shh expression in prechordal mesendoderm cells in the pathogenesis of holoprosencephaly. Aoto K, etal., Birth Defects Res A Clin Mol Teratol. 2008 Apr;82(4):224-31. doi: 10.1002/bdra.20447.
8. Sonic hedgehog directs specialised mesoderm differentiation in the intestine and pancreas. Apelqvist A, etal., Curr Biol. 1997 Oct 1;7(10):801-4.
9. Improvement of neurological recovery and stimulation of neural progenitor cell proliferation by intrathecal administration of Sonic hedgehog. Bambakidis NC, etal., J Neurosurg. 2012 May;116(5):1114-20. doi: 10.3171/2012.1.JNS111285. Epub 2012 Feb 10.
10. Interactions between Hedgehog proteins and their binding partners come into view. Beachy PA, etal., Genes Dev. 2010 Sep 15;24(18):2001-12.
11. Processing-dependent trafficking of Sonic hedgehog to the regulated secretory pathway in neurons. Beug ST, etal., Mol Cell Neurosci. 2011 Mar;46(3):583-96. Epub 2010 Dec 21.
12. Sonic Hedgehog regulates brain-derived neurotrophic factor in normal and regenerating cavernous nerves. Bond CW, etal., J Sex Med. 2013 Mar;10(3):730-7. doi: 10.1111/jsm.12030. Epub 2012 Dec 13.
13. Epigenetic changes in Basal Cell Carcinoma affect SHH and WNT signaling components. Brinkhuizen T, etal., PLoS One. 2012;7(12):e51710. doi: 10.1371/journal.pone.0051710. Epub 2012 Dec 17.
14. Dynamic changes of Sonic Hedgehog signaling pathway in gastric mucosa of rats with MNNG-induced gastric precancerous lesions. Cai D, etal., J Cell Physiol. 2019 Jul;234(7):10827-10834. doi: 10.1002/jcp.27908. Epub 2018 Dec 7.
15. Intrastriatal sonic hedgehog injection increases Patched transcript levels in the adult rat subventricular zone. Charytoniuk D, etal., Eur J Neurosci 2002 Dec;16(12):2351-7.
16. Upregulation of Shh and Ptc1 in hyperoxia-induced acute lung injury in neonatal rats. Dang H, etal., Mol Med Rep. 2012 Aug;6(2):297-302. doi: 10.3892/mmr.2012.929. Epub 2012 May 28.
17. Sonic hedgehog signaling mediates epithelial-mesenchymal communication and promotes renal fibrosis. Ding H, etal., J Am Soc Nephrol. 2012 May;23(5):801-13. doi: 10.1681/ASN.2011060614. Epub 2012 Feb 2.
18. Pax6 controls progenitor cell identity and neuronal fate in response to graded Shh signaling. Ericson J, etal., Cell. 1997 Jul 11;90(1):169-80.
19. Increased expression of sonic hedgehog in temporal lobe epileptic foci in humans and experimental rats. Fang M, etal., Neuroscience. 2011 May 19;182:62-70. doi: 10.1016/j.neuroscience.2011.02.060. Epub 2011 Mar 3.
20. Abnormal Sonic hedgehog signaling in the lung of rats with esophageal atresia induced by adriamycin. Fragoso AC, etal., Pediatr Res. 2014 Oct;76(4):355-62. doi: 10.1038/pr.2014.105. Epub 2014 Jul 8.
21. Sonic hedgehog regulates prostatic growth and epithelial differentiation. Freestone SH, etal., Dev Biol. 2003 Dec 15;264(2):352-62.
22. A variant in the sonic hedgehog regulatory sequence (ZRS) is associated with triphalangeal thumb and deregulates expression in the developing limb. Furniss D, etal., Hum Mol Genet. 2008 Aug 15;17(16):2417-23. doi: 10.1093/hmg/ddn141. Epub 2008 May 7.
23. [Mutation and expression of WNT8b gene and SHH gene in Hirschsprung disease]. Gao H, etal., Zhonghua Wei Chang Wai Ke Za Zhi. 2010 Oct;13(10):758-61.
24. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
25. Notochord anomalies in the adriamycin rat model: A morphologic and molecular basis for the VACTERL association. Gillick J, etal., J Pediatr Surg. 2003 Mar;38(3):469-73; discussion 469-73.
26. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
27. Correlation Between Hedgehog (Hh) Protein Family and Brain-Derived Neurotrophic Factor (BDNF) in Autism Spectrum Disorder (ASD). Halepoto DM, etal., J Coll Physicians Surg Pak. 2015 Dec;25(12):882-5. doi: 12.2015/JCPSP.882885.
28. Significance of sonic hedgehog signaling after massive hepatectomy in a rat. Hanaoka J, etal., Surg Today. 2013 Mar;43(3):300-7. doi: 10.1007/s00595-012-0248-z. Epub 2012 Jul 12.
29. Expression of sonic hedgehog regulates morphological changes of rat developing cerebellum in hypothyroidism. Hasebe M, etal., J Toxicol Sci. 2008 Oct;33(4):473-7.
30. Extreme variability of expression of a Sonic Hedgehog mutation: attention difficulties and holoprosencephaly. Heussler HS, etal., Arch Dis Child. 2002 Apr;86(4):293-6.
31. Left cardiac isomerism in the Sonic hedgehog null mouse. Hildreth V, etal., J Anat. 2009 Jun;214(6):894-904. doi: 10.1111/j.1469-7580.2009.01087.x.
32. Hypermethylation of SHH in the pathogenesis of congenital anorectal malformations. Huang Y, etal., J Pediatr Surg. 2014 Sep;49(9):1400-4. doi: 10.1016/j.jpedsurg.2014.03.007.
33. Hypoxia-induced compensatory effect as related to Shh and HIF-1alpha in ischemia embryo rat heart. Hwang JM, etal., Mol Cell Biochem. 2008 Apr;311(1-2):179-87. Epub 2008 Jan 29.
34. Bone marrow-derived mesenchymal stem cells expressing the Shh transgene promotes functional recovery after spinal cord injury in rats. Jia Y, etal., Neurosci Lett. 2014 Jun 24;573:46-51. doi: 10.1016/j.neulet.2014.05.010. Epub 2014 May 15.
35. Sonic hedgehog (SHH) and glioblastoma-2 (Gli-2) expressions are associated with poor jaundice-free survival in biliary atresia. Jung HY, etal., J Pediatr Surg. 2015 Mar;50(3):371-6. doi: 10.1016/j.jpedsurg.2014.08.025. Epub 2014 Dec 20.
36. The conserved barH-like homeobox-2 gene barhl2 acts downstream of orthodentricle-2 and together with iroquois-3 in establishment of the caudal forebrain signaling center induced by Sonic Hedgehog. Juraver-Geslin HA, etal., Dev Biol. 2014 Dec 1;396(1):107-20. doi: 10.1016/j.ydbio.2014.09.027. Epub 2014 Oct 2.
37. Regionalization within the mammalian telencephalon is mediated by changes in responsiveness to Sonic Hedgehog. Kohtz JD, etal., Development. 1998 Dec;125(24):5079-89.
38. Replicated anterior zeugopod (raz): a polydactylous mouse mutant with lowered Shh signaling in the limb bud. Krebs O, etal., Development. 2003 Dec;130(24):6037-47.
39. Sonic hedgehog regulates adult neural progenitor proliferation in vitro and in vivo. Lai K, etal., Nat Neurosci 2003 Jan;6(1):21-7.
40. Sonic hedgehog promotes rod photoreceptor differentiation in mammalian retinal cells in vitro. Levine EM, etal., J Neurosci. 1997 Aug 15;17(16):6277-88.
41. Expression of hedgehog signal pathway in articular cartilage is associated with the severity of cartilage damage in rats with adjuvant-induced arthritis. Li R, etal., J Inflamm (Lond). 2015 Mar 28;12:24. doi: 10.1186/s12950-015-0072-5. eCollection 2015.
42. The role of the sonic hedgehog signaling pathway in early brain injury after experimental subarachnoid hemorrhage in rats. Li T, etal., Neurosci Lett. 2013 Sep 27;552:81-6. doi: 10.1016/j.neulet.2013.07.042. Epub 2013 Aug 7.
43. Sonic hedgehog exerts distinct, stage-specific effects on tongue and taste papilla development. Liu HX, etal., Dev Biol. 2004 Dec 15;276(2):280-300.
44. Molecular mechanisms of Sonic hedgehog mutant effects in holoprosencephaly. Maity T, etal., Proc Natl Acad Sci U S A. 2005 Nov 22;102(47):17026-31. Epub 2005 Nov 10.
45. Sonic hedgehog, BMP4, and Hox genes in the development of anorectal malformations in Ethylenethiourea-exposed fetal rats. Mandhan P, etal., J Pediatr Surg. 2006 Dec;41(12):2041-5.
46. Sonic hedgehog expression in the development of hindgut in ETU-exposed fetal rats. Mandhan P, etal., Pediatr Surg Int. 2006 Jan;22(1):31-6.
47. Sonic hedgehog ligand partners with caveolin-1 for intracellular transport. Mao H, etal., Lab Invest. 2009 Mar;89(3):290-300. Epub 2009 Jan 12.
48. Intrinsic facilitation of adult peripheral nerve regeneration by the Sonic hedgehog morphogen. Martinez JA, etal., Exp Neurol. 2015 Sep;271:493-505. doi: 10.1016/j.expneurol.2015.07.018. Epub 2015 Jul 22.
49. Attenuation of experimental autoimmune encephalomyelitis and nonimmune demyelination by IFN-beta plus vitamin B12: treatment to modify notch-1/sonic hedgehog balance. Mastronardi FG, etal., J Immunol. 2004 May 15;172(10):6418-26.
50. The amount of sonic hedgehog in multiple sclerosis white matter is decreased and cleavage to the signaling peptide is deficient. Mastronardi FG, etal., Mult Scler. 2003 Aug;9(4):362-71.
51. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
52. Frequent deregulations in the hedgehog signaling network and cross-talks with the epidermal growth factor receptor pathway involved in cancer progression and targeted therapies. Mimeault M and Batra SK, Pharmacol Rev. 2010 Sep;62(3):497-524.
53. Cyclopamine and jervine in embryonic rat tongue cultures demonstrate a role for Shh signaling in taste papilla development and patterning: fungiform papillae double in number and form in novel locations in dorsal lingual epithelium. Mistretta CM, etal., Dev Biol 2003 Feb 1;254(1):1-18.
54. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
55. Pituitary adenylate cyclase-activating polypeptide and sonic hedgehog interact to control cerebellar granule precursor cell proliferation. Nicot A, etal., J Neurosci 2002 Nov 1;22(21):9244-54.
56. An inversion involving the mouse Shh locus results in brachydactyly through dysregulation of Shh expression. Niedermaier M, etal., J Clin Invest. 2005 Apr;115(4):900-9.
57. Expression of the Sonic hedgehog (SHH ) gene during early human development and phenotypic expression of new mutations causing holoprosencephaly. Odent S, etal., Hum Mol Genet. 1999 Sep;8(9):1683-9.
58. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
59. Basal cell carcinomas in mice overexpressing sonic hedgehog. Oro AE, etal., Science. 1997 May 2;276(5313):817-21.
60. Sonic hedgehog induces response of commissural axons to Semaphorin repulsion during midline crossing. Parra LM and Zou Y, Nat Neurosci. 2010 Jan;13(1):29-35. doi: 10.1038/nn.2457. Epub 2009 Nov 29.
61. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
62. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
63. Sonic hedgehog cascade is required for penile postnatal morphogenesis, differentiation, and adult homeostasis. Podlasek CA, etal., Biol Reprod. 2003 Feb;68(2):423-38.
64. Regulation of cavernous nerve injury-induced apoptosis by sonic hedgehog. Podlasek CA, etal., Biol Reprod. 2007 Jan;76(1):19-28. Epub 2006 Sep 20.
65. Retinoic acid is essential for Shh/Hoxd signaling during rat limb outgrowth but not for limb initiation. Power SC, etal., Dev Dyn. 1999 Dec;216(4-5):469-80.
66. Sonic hedgehog-patched Gli signaling in the developing rat prostate gland: lobe-specific suppression by neonatal estrogens reduces ductal growth and branching. Pu Y, etal., Dev Biol 2004 Sep 15;273(2):257-75.
67. GOA pipeline RGD automated data pipeline
68. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
69. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
70. Floor plate and motor neuron induction by vhh-1, a vertebrate homolog of hedgehog expressed by the notochord. Roelink H, etal., Cell 1994 Feb 25;76(4):761-75.
71. Mutations in the human Sonic Hedgehog gene cause holoprosencephaly. Roessler E, etal., Nat Genet. 1996 Nov;14(3):357-60.
72. Defining the molecular pathologies in cloaca malformation: similarities between mouse and human. Runck LA, etal., Dis Model Mech. 2014 Apr;7(4):483-93. doi: 10.1242/dmm.014530. Epub 2014 Feb 13.
73. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Sagai T, etal., Development. 2005 Feb;132(4):797-803.
74. Temporal and spatial expression of Pax9 and Sonic hedgehog during development of normal mouse palates and cleft palates in TGF-beta3 null embryos. Sasaki Y, etal., Arch Oral Biol. 2007 Mar;52(3):260-7. Epub 2006 Nov 13.
75. Activation of the sonic hedgehog pathway and its prognostic impact in patients with gastric cancer. Saze Z, etal., Dig Surg. 2012;29(2):115-23. doi: 10.1159/000336949. Epub 2012 Mar 27.
76. Differential expression of sonic hedgehog immunoreactivity during lesion evolution in autoimmune encephalomyelitis. Seifert T, etal., J Neuropathol Exp Neurol. 2005 May;64(5):404-11.
77. Identification of sonic hedgehog as a candidate gene responsible for the polydactylous mouse mutant Sasquatch. Sharpe J, etal., Curr Biol. 1999 Jan 28;9(2):97-100.
78. High frequency stimulation induces sonic hedgehog release from hippocampal neurons. Su Y, etal., Sci Rep. 2017 Mar 6;7:43865. doi: 10.1038/srep43865.
79. Triphalangeal thumb-polysyndactyly syndrome and syndactyly type IV are caused by genomic duplications involving the long range, limb-specific SHH enhancer. Sun M, etal., J Med Genet. 2008 Sep;45(9):589-95. doi: 10.1136/jmg.2008.057646. Epub 2008 Apr 16.
80. Extracellular and intracellular regulation of oligodendrocyte development: roles of Sonic hedgehog and expression of E proteins. Sussman CR, etal., Glia. 2002 Oct;40(1):55-64.
81. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
82. Spatial expression of Sonic hedgehog in the lung epithelium during branching morphogenesis. Urase K, etal., Biochem Biophys Res Commun. 1996 Aug 5;225(1):161-6.
83. Expression and clinical significance of hedgehog signaling pathway related components in colorectal cancer. Wang H, etal., Asian Pac J Cancer Prev. 2012;13(5):2319-24. doi: 10.7314/apjcp.2012.13.5.2319.
84. Paradoxical dysregulation of the neural stem cell pathway sonic hedgehog-Gli1 in autoimmune encephalomyelitis and multiple sclerosis. Wang Y, etal., Ann Neurol. 2008 Oct;64(4):417-27. doi: 10.1002/ana.21457.
85. A specific mutation in the distant sonic hedgehog (SHH) cis-regulator (ZRS) causes Werner mesomelic syndrome (WMS) while complete ZRS duplications underlie Haas type polysyndactyly and preaxial polydactyly (PPD) with or without triphalangeal thumb. Wieczorek D, etal., Hum Mutat. 2010 Jan;31(1):81-9. doi: 10.1002/humu.21142.
86. Pancreatic cancer: molecular pathogenesis and new therapeutic targets. Wong HH and Lemoine NR, Nat Rev Gastroenterol Hepatol. 2009 Jul;6(7):412-22. Epub 2009 Jun 9.
87. Erythropoietin and sonic hedgehog mediate the neuroprotective effects of brain-derived neurotrophic factor against mitochondrial inhibition. Wu CL, etal., Neurobiol Dis. 2010 Oct;40(1):146-54. doi: 10.1016/j.nbd.2010.05.019. Epub 2010 May 23.
88. Neuroprotective effect of up-regulated Sonic hedgehog in retinal ganglion cells following chronic ocular hypertension. Wu J, etal., Invest Ophthalmol Vis Sci. 2010 Jan 13.
89. Expressions of sonic hedgehog, patched, smoothened and Gli-1 in human intestinal stromal tumors and their correlation with prognosis. Yoshizaki A, etal., World J Gastroenterol. 2006 Sep 21;12(35):5687-91. doi: 10.3748/wjg.v12.i35.5687.
90. Down-regulation of SHH/BMP4 signalling in human anorectal malformations. Zhang J, etal., J Int Med Res. 2009 Nov-Dec;37(6):1842-50.
91. Lentivirus-mediated delivery of sonic hedgehog into the striatum stimulates neuroregeneration in a rat model of Parkinson disease. Zhang Y, etal., Neurol Sci. 2014 Dec;35(12):1931-40. doi: 10.1007/s10072-014-1866-6. Epub 2014 Jul 17.
92. [Expression of sonic hedgehog signaling pathw ay and its inhibition by cyclopamine in rat liver with chronic fluorosis]. Zhao L, etal., Zhonghua Bing Li Xue Za Zhi. 2014 Dec;43(12):814-9.
93. Sonic hedgehog is a novel tubule-derived growth factor for interstitial fibroblasts after kidney injury. Zhou D, etal., J Am Soc Nephrol. 2014 Oct;25(10):2187-200. doi: 10.1681/ASN.2013080893. Epub 2014 Apr 17.
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:31734396   PMID:31968603   PMID:32298032   PMID:32980902   PMID:33012205   PMID:35147838   PMID:36906487   PMID:37815888  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.246,954,017 - 6,963,170 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl46,954,017 - 6,963,170 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx411,962,609 - 11,971,762 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.047,776,827 - 7,785,980 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.046,123,054 - 6,132,207 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04718,538 - 727,691 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4718,538 - 727,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04711,420 - 720,573 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.442,200,504 - 2,209,657 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.142,200,503 - 2,209,657 (+)NCBI
Celera43,316,537 - 3,325,690 (-)NCBICelera
Cytogenetic Map4q11NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh387155,799,980 - 155,812,463 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7155,799,980 - 155,812,463 (-)EnsemblGRCh38hg38GRCh38
GRCh377155,592,674 - 155,605,157 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367155,288,319 - 155,297,728 (-)NCBINCBI36Build 36hg18NCBI36
Build 347155,095,033 - 155,104,443NCBI
Celera7150,021,217 - 150,030,626 (-)NCBICelera
Cytogenetic Map7q36.3NCBI
HuRef7149,327,101 - 149,336,513 (-)NCBIHuRef
CHM1_17155,604,000 - 155,613,409 (-)NCBICHM1_1
T2T-CHM13v2.07156,983,127 - 156,995,607 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27154,827,119 - 154,836,528 (-)NCBI
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm39528,661,838 - 28,672,099 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl528,661,813 - 28,672,254 (-)EnsemblGRCm39 Ensembl
GRCm38528,456,840 - 28,467,101 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl528,456,815 - 28,467,256 (-)EnsemblGRCm38mm10GRCm38
MGSCv37528,783,380 - 28,793,641 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36528,787,627 - 28,797,875 (-)NCBIMGSCv36mm8
Celera525,997,895 - 26,008,156 (-)NCBICelera
Cytogenetic Map5B1NCBI
cM Map514.39NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0NW_0049554918,647,133 - 8,657,381 (-)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan1744,237,491 - 44,251,151 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07147,400,112 - 147,414,036 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17159,116,966 - 159,126,660 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7159,114,666 - 159,126,651 (-)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.11618,650,553 - 18,663,571 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1618,484,809 - 18,662,903 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1619,286,449 - 19,295,913 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01620,382,879 - 20,392,367 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1620,382,707 - 20,392,037 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11618,753,210 - 18,762,671 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01619,333,131 - 19,342,583 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01619,386,812 - 19,396,258 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_0244051182,860,455 - 2,871,247 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493652710,033,299 - 10,042,599 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493652710,033,095 - 10,042,713 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl182,545,994 - 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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.121123,929,937 - 123,942,451 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21123,932,900 - 123,942,395 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607220,134,625 - 20,147,164 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_0046248002,203,393 - 2,212,068 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248002,202,986 - 2,215,309 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Shh
14 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:64
Interacting mature miRNAs:68
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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
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)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
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)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.246,962,821 - 6,963,081 (-)MAPPERmRatBN7.2
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


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
Medium 8 10 4 3
Low 2 64 22 13 8
Below cutoff 1 2 12 7 5 7 5 6 13 8 5


RefSeq Acc Id: ENSRNOT00000008497   ⟹   ENSRNOP00000008497
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl46,954,017 - 6,963,170 (+)Ensembl
Rnor_6.0 Ensembl4718,538 - 727,691 (-)Ensembl
RefSeq Acc Id: NM_017221   ⟹   NP_058917
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
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  
Ensembl Protein ENSRNOP00000008497
GenBank Protein Q63673 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_058917   ⟸   NM_017221
- Peptide Label: precursor
- UniProtKB: Q63673 (UniProtKB/Swiss-Prot),   A6KJL6 (UniProtKB/TrEMBL),   G3V6T0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008497   ⟸   ENSRNOT00000008497
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63673-F1-model_v2 AlphaFold Q63673 1-437 view protein structure


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

RGD ID:13692770
Promoter ID:EPDNEW_R3293
Type:single initiation site
Description:sonic hedgehog
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.04727,716 - 727,776EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3673 AgrOrtholog
BioCyc Gene G2FUF-46140 BioCyc
Ensembl Genes ENSRNOG00000006120 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008497 ENTREZGENE
  ENSRNOT00000008497.3 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1380.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hedgehog/Intein (Hint) domain 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
Pfam HH_signal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hint UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Shh PhenoGen
PIRSF Peptidase_C46 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006120 RatGTEx
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
  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