Gli3 (GLI family zinc finger 3) - Rat Genome Database

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Gene: Gli3 (GLI family zinc finger 3) Rattus norvegicus
Symbol: Gli3
Name: GLI family zinc finger 3
RGD ID: 620272
Description: Predicted to enable several functions, including beta-catenin binding activity; enzyme binding activity; and mediator complex binding activity. Involved in liver regeneration; prostate gland development; and response to estrogen. Predicted to be located in axoneme; cytosol; and nuclear lumen. Predicted to be part of GLI-SUFU complex and transcription repressor complex. Predicted to be active in cilium and nucleus. Biomarker of clubfoot; hypospadias; and pre-malignant neoplasm. Human ortholog(s) of this gene implicated in Greig cephalopolysyndactyly syndrome; Pallister-Hall syndrome; anodontia; polydactyly; and syndactyly. Orthologous to human GLI3 (GLI family zinc finger 3); PARTICIPATES IN altered Hedgehog signaling pathway; Hedgehog signaling pathway; pancreatic cancer pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GLI-Kruppel family member GLI3; GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome); LOC307001; transcriptional activator GLI3
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
mRatBN7.21749,438,567 - 49,709,712 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1749,438,567 - 49,709,712 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1752,630,120 - 52,901,404 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01756,633,008 - 56,904,289 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01750,730,889 - 51,002,171 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01752,294,942 - 52,569,036 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1752,294,942 - 52,569,036 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01750,360,049 - 50,629,477 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41757,594,102 - 57,867,710 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11757,781,069 - 57,856,545 (-)NCBI
Celera1745,497,321 - 45,768,089 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-hydroxypropanoic acid  (ISO)
6-propyl-2-thiouracil  (EXP)
Ac-Ser-Asp-Lys-Pro-OH  (EXP,ISO)
aflatoxin B1  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
captopril  (EXP,ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dorsomorphin  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
fenpyroximate  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
goralatide  (EXP,ISO)
iron atom  (ISO)
iron(0)  (ISO)
L-methionine  (ISO)
melphalan  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
miconazole  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
ochratoxin A  (ISO)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
picoxystrobin  (ISO)
potassium chromate  (ISO)
Ptaquiloside  (ISO)
pyrimidifen  (ISO)
rac-lactic acid  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
sodium arsenite  (ISO)
succimer  (ISO)
sunitinib  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vismodegib  (ISO)
zinc oxide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
alpha-beta T cell differentiation  (ISO)
anatomical structure development  (ISO)
anatomical structure formation involved in morphogenesis  (ISO)
anterior semicircular canal development  (ISO)
anterior/posterior pattern specification  (ISO)
apoptotic process  (ISO)
artery development  (ISO)
axon guidance  (ISO)
brain development  (ISO)
branching involved in ureteric bud morphogenesis  (ISO)
branching morphogenesis of an epithelial tube  (ISO)
camera-type eye development  (ISO)
camera-type eye morphogenesis  (ISO)
cell differentiation involved in kidney development  (ISO)
cell population proliferation  (ISO)
central nervous system development  (ISO)
cerebral cortex radial glia-guided migration  (ISO)
chondrocyte differentiation  (ISO)
developmental growth  (ISO)
dorsal/ventral pattern formation  (ISO)
embryonic digestive tract development  (ISO)
embryonic digestive tract morphogenesis  (ISO)
embryonic digit morphogenesis  (ISO)
embryonic limb morphogenesis  (ISO)
embryonic morphogenesis  (ISO)
embryonic neurocranium morphogenesis  (ISO)
embryonic skeletal system morphogenesis  (ISO)
forebrain development  (ISO)
forebrain dorsal/ventral pattern formation  (ISO)
forebrain radial glial cell differentiation  (ISO)
frontal suture morphogenesis  (ISO)
gene expression  (ISO)
heart development  (ISO)
hindgut morphogenesis  (ISO)
hippocampus development  (ISO)
in utero embryonic development  (ISO)
inner ear development  (ISO)
kidney development  (ISO)
lambdoid suture morphogenesis  (ISO)
larynx morphogenesis  (ISO)
lateral ganglionic eminence cell proliferation  (ISO)
lateral semicircular canal development  (ISO)
layer formation in cerebral cortex  (ISO)
limb development  (ISO)
limb morphogenesis  (ISO)
liver regeneration  (IEP)
lung development  (ISO)
mammary gland development  (ISO)
mammary gland specification  (ISO)
melanocyte differentiation  (ISO)
metanephros development  (ISO)
negative regulation of alpha-beta T cell differentiation  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of chondrocyte differentiation  (ISO)
negative regulation of DNA-templated transcription  (ISO)
negative regulation of neuron differentiation  (ISO)
negative regulation of smoothened signaling pathway  (ISO)
negative regulation of stem cell proliferation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative thymic T cell selection  (ISO)
neural tube development  (ISO)
neuroblast proliferation  (ISO)
neuron differentiation  (ISO)
neuron fate commitment  (ISO)
odontogenesis of dentin-containing tooth  (ISO)
oligodendrocyte differentiation  (ISO)
optic nerve morphogenesis  (ISO)
osteoblast differentiation  (ISO)
pallium development  (ISO)
pattern specification process  (ISO)
positive regulation of alpha-beta T cell differentiation  (ISO)
positive regulation of chondrocyte differentiation  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of neuroblast proliferation  (ISO)
positive regulation of osteoblast differentiation  (ISO)
positive regulation of protein import into nucleus  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
prostate gland development  (IEP)
protein import into nucleus  (ISO)
protein processing  (ISO)
proximal/distal pattern formation  (ISO)
regulation of apoptotic process  (ISO)
regulation of bone development  (ISO)
regulation of cell differentiation  (ISO)
regulation of cell population proliferation  (ISO)
regulation of DNA-templated transcription  (ISO)
regulation of gene expression  (ISO)
regulation of smoothened signaling pathway  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
response to estrogen  (IEP)
roof of mouth development  (ISO)
sagittal suture morphogenesis  (ISO)
smoothened signaling pathway  (IBA,ISO,TAS)
smoothened signaling pathway involved in dorsal/ventral neural tube patterning  (ISO)
smoothened signaling pathway involved in spinal cord motor neuron cell fate specification  (ISO)
smoothened signaling pathway involved in ventral spinal cord interneuron specification  (ISO)
spinal cord dorsal/ventral patterning  (ISO)
spinal cord motor neuron differentiation  (ISO)
stem cell proliferation  (ISO)
subpallium development  (ISO)
T cell differentiation in thymus  (ISO)
telencephalon development  (ISO)
thymocyte apoptotic process  (ISO)
tongue development  (ISO)
tube development  (ISO)
vocalization behavior  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View

References - curated
# Reference Title Reference Citation
1. Pallister-Hall syndrome phenotype in mice mutant for Gli3. Böse J, etal., Hum Mol Genet. 2002 May 1;11(9):1129-35.
2. 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.
3. The role of hedgehog signaling pathway in liver regeneration. Cai Y, etal., Hepatogastroenterology. 2011 Nov-Dec;58(112):2071-6. doi: 10.5754/hge11155.
4. The expression of Gli3, regulated by HOXD13, may play a role in idiopathic congenital talipes equinovarus. Cao D, etal., BMC Musculoskelet Disord. 2009 Nov 19;10:142. doi: 10.1186/1471-2474-10-142.
5. Crossed polydactyly type I caused by a point mutation in the GLI3 gene in a large Chinese pedigree. Cheng B, etal., J Clin Lab Anal. 2006;20(4):133-8.
6. Hedgehog signaling update. Cohen MM, Am J Med Genet A. 2010 Aug;152A(8):1875-914. doi: 10.1002/ajmg.a.32909.
7. New insights into genotype-phenotype correlation for GLI3 mutations. Démurger F, etal., Eur J Hum Genet. 2015 Jan;23(1):92-102. doi: 10.1038/ejhg.2014.62. Epub 2014 Apr 16.
8. Molecular analysis of non-syndromic preaxial polydactyly: preaxial polydactyly type-IV and preaxial polydactyly type-I. Fujioka H, etal., Clin Genet. 2005 May;67(5):429-33.
9. 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.
10. Gli3-deficient mice exhibit cleft palate associated with abnormal tongue development. Huang X, etal., Dev Dyn. 2008 Oct;237(10):3079-87. doi: 10.1002/dvdy.21714.
11. Expanded mutational spectrum of the GLI3 gene substantiates genotype-phenotype correlations. Jamsheer A, etal., J Appl Genet. 2012 Nov;53(4):415-22. doi: 10.1007/s13353-012-0109-x. Epub 2012 Aug 18.
12. Molecular and clinical analyses of Greig cephalopolysyndactyly and Pallister-Hall syndromes: robust phenotype prediction from the type and position of GLI3 mutations. Johnston JJ, etal., Am J Hum Genet. 2005 Apr;76(4):609-22. Epub 2005 Feb 28.
13. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Jones S, etal., Science. 2008 Sep 26;321(5897):1801-6. Epub 2008 Sep 4.
14. Point mutations throughout the GLI3 gene cause Greig cephalopolysyndactyly syndrome. Kalff-Suske M, etal., Hum Mol Genet. 1999 Sep;8(9):1769-77.
15. GLI3 frameshift mutations cause autosomal dominant Pallister-Hall syndrome. Kang S, etal., Nat Genet. 1997 Mar;15(3):266-8.
16. Murine models of VACTERL syndrome: Role of sonic hedgehog signaling pathway. Kim PC, etal., J Pediatr Surg. 2001 Feb;36(2):381-4. doi: 10.1053/jpsu.2001.20722.
17. 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.
18. Gli3 is a novel downstream target of miR‑200a with an anti‑fibrotic role for progression of liver fibrosis in vivo and in vitro. Li L, etal., Mol Med Rep. 2020 Apr;21(4):1861-1871. doi: 10.3892/mmr.2020.10997. Epub 2020 Feb 21.
19. A case-control study of the association between tooth-development gene polymorphisms and non-syndromic hypodontia in the Chinese Han population. Liu H, etal., Eur J Oral Sci. 2012 Oct;120(5):378-85. doi: 10.1111/j.1600-0722.2012.00986.x. Epub 2012 Aug 18.
20. Genetic research and structural dysplasia assessment of anorectal malformations in neonatal male rats induced by di(n-butyl) phthalate. Liu ZH, etal., Environ Toxicol. 2016 Mar;31(3):261-8. doi: 10.1002/tox.22040. Epub 2014 Sep 12.
21. A sensitized mutagenesis screen identifies Gli3 as a modifier of Sox10 neurocristopathy. Matera I, etal., Hum Mol Genet. 2008 Jul 15;17(14):2118-31. doi: 10.1093/hmg/ddn110. Epub 2008 Apr 7.
22. 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.
23. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
25. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
26. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27. 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.
28. Mutation in GLI3 in postaxial polydactyly type A. Radhakrishna U, etal., Nat Genet. 1997 Nov;17(3):269-71.
29. GOA pipeline RGD automated data pipeline
30. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
32. Comprehensive gene review and curation RGD comprehensive gene curation
33. Sonic hedgehog expression and role in healing corneal epithelium. Saika S, etal., Invest Ophthalmol Vis Sci. 2004 Aug;45(8):2577-85.
34. The mouse mutation Pdn (Polydactyly Nagoya) is caused by the integration of a retrotransposon into the Gli3 gene. Thien H and Rüther U, Mamm Genome. 1999 Mar;10(3):205-9.
35. A novel GLI3 mutation affecting the zinc finger domain leads to preaxial-postaxial polydactyly-syndactyly complex. Volodarsky M, etal., BMC Med Genet. 2014 Sep 30;15:110. doi: 10.1186/s12881-014-0110-9.
36. A hypermorphic mouse Gli3 allele results in a polydactylous limb phenotype. Wang C, etal., Dev Dyn. 2007 Mar;236(3):769-76.
37. Novel frame-shift mutations of GLI3 gene in non-syndromic postaxial polydactyly patients. Wang Z, etal., Clin Chim Acta. 2014 Jun 10;433:195-9. doi: 10.1016/j.cca.2014.03.012. Epub 2014 Mar 22.
38. Maternal exposure to di-n-butyl phthalate (DBP) induces combined anorectal and urogenital malformations in male rat offspring. Zhu YP, etal., Reprod Toxicol. 2016 Jun;61:169-76. doi: 10.1016/j.reprotox.2016.04.007. Epub 2016 Apr 11.
Additional References at PubMed
PMID:2118997   PMID:8026071   PMID:8387379   PMID:9152009   PMID:9232833   PMID:9268572   PMID:9268579   PMID:9655803   PMID:9731531   PMID:10075717   PMID:10077605   PMID:10409502  
PMID:10625551   PMID:10693670   PMID:10693759   PMID:11053430   PMID:11238441   PMID:11485934   PMID:12142027   PMID:12435361   PMID:12435627   PMID:12435628   PMID:12435629   PMID:14602680  
PMID:14723851   PMID:15065125   PMID:15136151   PMID:15215207   PMID:15315762   PMID:15728667   PMID:15855276   PMID:15880651   PMID:16168404   PMID:16247775   PMID:16254602   PMID:16284117  
PMID:16342201   PMID:16364285   PMID:16396903   PMID:16571630   PMID:16611981   PMID:16720875   PMID:16914490   PMID:16968815   PMID:17000779   PMID:17043310   PMID:17191253   PMID:17328886  
PMID:17331723   PMID:17395647   PMID:17400206   PMID:17714700   PMID:17764085   PMID:18298960   PMID:18478223   PMID:18559511   PMID:18582859   PMID:18799682   PMID:19036983   PMID:19048639  
PMID:19084012   PMID:19422820   PMID:19592253   PMID:19667090   PMID:19684112   PMID:19809516   PMID:20042388   PMID:20159594   PMID:20360384   PMID:20570969   PMID:20943929   PMID:21209331  
PMID:21289087   PMID:21525285   PMID:21552265   PMID:22235033   PMID:22547067   PMID:22841643   PMID:23042389   PMID:23955340   PMID:24548465   PMID:24927541   PMID:27395007   PMID:28177282  
PMID:29487109   PMID:31957704  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.21749,438,567 - 49,709,712 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1749,438,567 - 49,709,712 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1752,630,120 - 52,901,404 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01756,633,008 - 56,904,289 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01750,730,889 - 51,002,171 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01752,294,942 - 52,569,036 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1752,294,942 - 52,569,036 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01750,360,049 - 50,629,477 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41757,594,102 - 57,867,710 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11757,781,069 - 57,856,545 (-)NCBI
Celera1745,497,321 - 45,768,089 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh38741,960,949 - 42,264,268 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl741,960,949 - 42,264,100 (-)EnsemblGRCh38hg38GRCh38
GRCh37742,000,547 - 42,276,808 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36741,967,072 - 42,243,137 (-)NCBINCBI36Build 36hg18NCBI36
Build 34741,776,919 - 42,036,135NCBI
Celera741,991,319 - 42,267,350 (-)NCBICelera
Cytogenetic Map7p14.1NCBI
HuRef741,885,427 - 42,162,362 (-)NCBIHuRef
CHM1_1742,003,855 - 42,280,223 (-)NCBICHM1_1
T2T-CHM13v2.0742,119,298 - 42,422,619 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2742,040,400 - 42,316,460 (-)NCBI
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391315,638,308 - 15,904,611 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1315,637,820 - 15,904,611 (+)EnsemblGRCm39 Ensembl
GRCm381315,463,723 - 15,730,026 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1315,463,235 - 15,730,026 (+)EnsemblGRCm38mm10GRCm38
MGSCv371315,555,556 - 15,821,859 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361315,254,867 - 15,517,860 (+)NCBIMGSCv36mm8
Celera1315,745,941 - 16,017,370 (+)NCBICelera
Cytogenetic Map13A1NCBI
cM Map135.43NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_0049554601,528,412 - 1,805,918 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554601,528,457 - 1,805,584 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan1794,528,190 - 94,804,051 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0742,004,965 - 42,280,772 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1742,056,566 - 42,322,865 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl742,056,565 - 42,322,865 (+)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.1187,800,817 - 8,071,531 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl187,801,394 - 8,068,132 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha187,651,291 - 7,921,706 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0187,847,548 - 8,118,213 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl187,846,935 - 8,116,066 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1187,829,563 - 8,099,968 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0187,798,494 - 8,068,961 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0187,912,805 - 8,183,294 (+)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_02440511897,915,181 - 98,191,969 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647817,126,911 - 17,403,011 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493647817,129,922 - 17,403,630 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl1852,404,072 - 52,697,900 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11852,403,463 - 52,697,906 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21857,616,734 - 57,801,327 (+)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.12116,386,700 - 16,665,648 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2116,549,789 - 16,662,238 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660625,800,697 - 6,080,257 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_00462474018,975,596 - 19,235,900 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474018,961,395 - 19,238,760 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Gli3
479 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:29
Interacting mature miRNAs:32
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (
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
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172702794956836890Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172738994653481766Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173199078450909196Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174135465160463643Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174207316069599340Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174207316069599340Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,567,911 - 49,568,080 (+)MAPPERmRatBN7.2
Rnor_6.01752,424,553 - 52,424,721NCBIRnor6.0
Rnor_5.01750,489,557 - 50,489,725UniSTSRnor5.0
RGSC_v3.41757,727,026 - 57,727,194UniSTSRGSC3.4
RGSC_v3.41757,724,764 - 57,724,932UniSTSRGSC3.4
RGSC_v3.41757,724,628 - 57,724,943RGDRGSC3.4
RGSC_v3.11757,729,867 - 57,730,035RGD
Celera1745,626,649 - 45,626,817UniSTS
RH 3.4 Map17510.39UniSTS
RH 3.4 Map17510.39RGD
RH 2.0 Map17440.5RGD
SHRSP x BN Map1730.3699RGD
FHH x ACI Map1735.5899RGD
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,598,572 - 49,598,803 (+)MAPPERmRatBN7.2
Rnor_6.01752,455,214 - 52,455,444NCBIRnor6.0
Rnor_5.01750,520,243 - 50,520,473UniSTSRnor5.0
RGSC_v3.41757,756,111 - 57,756,341UniSTSRGSC3.4
Celera1745,657,144 - 45,657,374UniSTS
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,574,157 - 49,574,256 (+)MAPPERmRatBN7.2
Rnor_6.01752,430,785 - 52,430,883NCBIRnor6.0
Rnor_5.01750,495,789 - 50,495,887UniSTSRnor5.0
RGSC_v3.41757,731,080 - 57,731,178UniSTSRGSC3.4
Celera1745,632,829 - 45,632,927UniSTS
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,438,394 - 49,438,488 (+)MAPPERmRatBN7.2
Rnor_6.01752,294,770 - 52,294,863NCBIRnor6.0
Rnor_5.01750,359,877 - 50,359,970UniSTSRnor5.0
RGSC_v3.41757,593,930 - 57,594,023UniSTSRGSC3.4
Celera1745,497,149 - 45,497,242UniSTS
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,468,514 - 49,468,734 (+)MAPPERmRatBN7.2
Rnor_6.01752,324,888 - 52,325,107NCBIRnor6.0
Rnor_5.01750,389,995 - 50,390,214UniSTSRnor5.0
RGSC_v3.41757,624,048 - 57,624,267UniSTSRGSC3.4
Celera1745,527,219 - 45,527,438UniSTS
RH 3.4 Map17508.89UniSTS
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,438,469 - 49,438,669 (+)MAPPERmRatBN7.2
Rnor_6.01752,294,845 - 52,295,044NCBIRnor6.0
Rnor_5.01750,359,952 - 50,360,151UniSTSRnor5.0
RGSC_v3.41757,594,005 - 57,594,204UniSTSRGSC3.4
Celera1745,497,224 - 45,497,423UniSTS
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,470,611 - 49,470,813 (+)MAPPERmRatBN7.2
Rnor_6.01752,326,985 - 52,327,186NCBIRnor6.0
Rnor_5.01750,392,092 - 50,392,293UniSTSRnor5.0
RGSC_v3.41757,626,145 - 57,626,346UniSTSRGSC3.4
Celera1745,529,316 - 45,529,517UniSTS
RH 3.4 Map17508.39UniSTS
Cytogenetic Map17q12.1UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21749,511,446 - 49,511,567 (+)MAPPERmRatBN7.2
Rnor_6.01752,367,811 - 52,367,931NCBIRnor6.0
Rnor_5.01750,432,815 - 50,432,935UniSTSRnor5.0
RGSC_v3.41757,668,340 - 57,668,460UniSTSRGSC3.4
Celera1745,570,326 - 45,570,446UniSTS
Cytogenetic Map17q12.1UniSTS


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 4 2 2 37 16 29 2
Low 3 42 36 22 19 22 8 9 37 17 10 9 8
Below cutoff 1 16 16 16 2 2 2


RefSeq Acc Id: ENSRNOT00000019396   ⟹   ENSRNOP00000019396
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1749,438,567 - 49,709,712 (-)Ensembl
Rnor_6.0 Ensembl1752,294,942 - 52,569,036 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081290   ⟹   ENSRNOP00000070877
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1752,295,004 - 52,477,575 (-)Ensembl
RefSeq Acc Id: NM_080405   ⟹   NP_536330
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
mRatBN7.21749,438,567 - 49,709,712 (-)NCBI
Rnor_6.01752,294,942 - 52,569,036 (-)NCBI
Rnor_5.01750,360,049 - 50,629,477 (-)NCBI
RGSC_v3.41757,594,102 - 57,867,710 (-)RGD
Celera1745,497,321 - 45,768,089 (-)RGD
Protein Sequences
Protein RefSeqs NP_536330 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB71724 (Get FASTA)   NCBI Sequence Viewer  
  EDL87409 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019396
RefSeq Acc Id: NP_536330   ⟸   NM_080405
- UniProtKB: F1M9H1 (UniProtKB/TrEMBL),   A6K9B6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019396   ⟸   ENSRNOT00000019396
RefSeq Acc Id: ENSRNOP00000070877   ⟸   ENSRNOT00000081290
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M9H1-F1-model_v2 AlphaFold F1M9H1 1-1582 view protein structure


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

RGD ID:13700512
Promoter ID:EPDNEW_R11034
Type:initiation region
Description:GLI family zinc finger 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.01752,568,951 - 52,569,011EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620272 AgrOrtholog
BioCyc Gene G2FUF-9082 BioCyc
Ensembl Genes ENSRNOG00000014395 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019396 ENTREZGENE
  ENSRNOT00000019396.8 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/TrEMBL
InterPro GLI-like UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:140588 UniProtKB/TrEMBL
  PTHR45718:SF5 UniProtKB/TrEMBL
Pfam zf-C2H2 UniProtKB/TrEMBL
PhenoGen Gli3 PhenoGen
RatGTEx ENSRNOG00000014395 RatGTEx
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-11-18 Gli3  GLI family zinc finger 3  Gli3  GLI-Kruppel family member GLI3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-04-27 Gli3  GLI-Kruppel family member GLI3  Gli3_predicted  GLI-Kruppel family member GLI3 (predicted)  Data merged from RGD:1306122 737654 APPROVED
2005-01-20 Gli3  GLI-Kruppel family member GLI3    GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome)  Name updated 1299863 APPROVED
2005-01-12 Gli3_predicted  GLI-Kruppel family member GLI3 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Gli3  GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome)      Symbol and Name status set to provisional 70820 PROVISIONAL