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Gene Detail
sonic hedgehog
Synonyms Hhg1, Hx, Hxl3, M100081
Feature Type protein coding gene
Genetic Map
Chromosome 5
14.39 cM
Detailed Genetic Map ± 1 cM

Mapping data(24)
Sequence Map
Chr5:28456815-28467101 bp, - strand
From VEGA annotation of GRCm38

  10287 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer

Mouse Genome Browser
HomoloGene:30961  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 rhesus macaque; 1 cattle; 1 dog; 1 chicken; 1 western clawed frog; 2 zebrafish

Protein SuperFamily: hedgehog protein
Gene Tree: Shh

Human Homolog SHH, sonic hedgehog
NCBI Gene ID 6469
neXtProt AC  NX_Q15465
Human Synonyms  HHG1, HLP3, HPE3, MCOPCB5, SMMCI, TPT, TPTPS
Human Chr (Location)  7q36; chr7:155802864-155812273 (-)  GRCh38
Disease Associations  (4) Diseases Associated with Human SHH
alleles, and
All mutations/alleles(33) : Chemically induced (ENU)(8) Radiation induced(4) Spontaneous(1) Targeted(20)
Genomic Mutations involving Shh (3)
Heterozygotes exhibit shortening of all digits, holes between the frontal bones, dyssymphyses between cervical vertebrae and bony plates over many ribs. Homozygotes usually die before E12, are short-limbed dwarfs and lack forefeet, hindfeet, eyes, ears, external genetalia and a mouth.
Human Diseases Modeled Using Mouse Shh (2)    Alleles Annotated to Human Diseases(4)    Phenotype Images(2)
Shh interacts with 196 markers (Mir7-1, Mir9-1, Mir9-2, ...)
Gene Ontology
All GO classifications: (312 annotations)
Process anatomical structure development, anatomical structure formation involved in morphogenesis, ...
Component axon, cell surface, ...
Function calcium ion binding, glycoprotein binding, ...
External Resources: FuncBase
Literature Summary: (1261 records)
Data Summary: Results (2514)    Tissues (693)    Images (1145)
Theiler Stages: 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28
Assay TypeResults
Immunohistochemistry 94
RNA in situ 2249
In situ reporter (knock in) 2
Northern blot 36
Western blot 16
RT-PCR 117
cDNA source data(35)
External Resources: Allen Institute   GENSAT   GEO   Expression Atlas
All nucleic(163) Genomic(1) cDNA(58) Primer pair(19) Other(85)
Microarray probesets(4)
Other database
VEGA Gene ModelOTTMUSG00000021299 (Evidence)
Ensembl Gene ModelENSMUSG00000002633 (Evidence)
Entrez Gene20423 (Evidence)
PDB1VHH, 2WFX, 3D1M, 3N1R, 4C4M, 4C4N, 2WG4
Consensus CDS ProjectCCDS19146.1
International Mouse Knockout Project StatusShh
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000021299 VEGA Gene Model | MGI Sequence Detail 10287 C57BL/6J ±  kb
transcript OTTMUST00000050499 VEGA | MGI Sequence Detail 2692 Not Applicable 
polypeptide OTTMUSP00000023583 VEGA | MGI Sequence Detail 437 Not Applicable 

For the selected sequences
All sequences(22) RefSeq(6) UniProt(3)
Polymorphisms RFLP(2) : SNPs within 2kb(35 from dbSNP Build 137)
InterPro IPR000320 Hedgehog, N-terminal signaling domain
InterPro IPR001657 Hedgehog protein
InterPro IPR009045 Hedgehog signalling/DD-peptidase zinc-binding domain
InterPro IPR001767 Hint domain
InterPro IPR003586 Hint domain C-terminal
InterPro IPR003587 Hint domain N-terminal
InterPro IPR006141 Intein splice site
Protein Ontology PR:000014841 sonic hedgehog protein
References (Earliest) J:13476 Dickie MM, Hemimelic extra toes, Hx. Mouse News Lett. 1968;38:24
(Latest) J:212084 Herriges MJ, et al., Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev. 2014 Jun 15;28(12):1363-79
All references(1587)
Disease annotation references (3)
accession IDs
MGD-MRK-11020, MGD-MRK-14403, MGD-MRK-19573, MGD-MRK-8906, MGI:3051411, MGI:94931, MGI:96290

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
MGI 5.19
The Jackson Laboratory