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Shh Gene Detail
Summary
  • Symbol
    Shh
  • Name
    sonic hedgehog
  • Synonyms
    Hhg1
  • Feature Type
    protein coding gene
  • IDs
    MGI:98297
    NCBI Gene: 20423
  • Alliance
    gene page
  • Transcription Start Sites
    5 TSS
  • Regulated by
    Rr117, Rr119, Rr204 ... (21 regulatory regions)
Location &
Maps
more
  • Sequence Map
    Chr5:28661838-28672099 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 5, 14.39 cM
  • Mapping Data
    26 experiments
Strain
Comparison
more
  • SNPs within 2kb
    226 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98297
 protein coding gene Chr5:28661813-28672254 (-)
129S1/SvImJ MGP_129S1SvImJ_G0029372
 protein coding gene Chr5:26360358-26370774 (-)
A/J MGP_AJ_G0029338
 protein coding gene Chr5:25470334-25480765 (-)
AKR/J MGP_AKRJ_G0029289
 protein coding gene Chr5:26505717-26516151 (-)
BALB/cJ MGP_BALBcJ_G0029349
 protein coding gene Chr5:26024712-26035135 (-)
C3H/HeJ MGP_C3HHeJ_G0029070
 protein coding gene Chr5:26548359-26558778 (-)
C57BL/6NJ MGP_C57BL6NJ_G0029802
 protein coding gene Chr5:27992485-28007939 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0027040
 protein coding gene Chr5:23080710-23091145 (-)
CAST/EiJ MGP_CASTEiJ_G0028481
 protein coding gene Chr5:25654644-25665152 (-)
CBA/J MGP_CBAJ_G0029038
 protein coding gene Chr5:28476941-28492189 (-)
DBA/2J MGP_DBA2J_G0029187
 protein coding gene Chr5:25697222-25707719 (-)
FVB/NJ MGP_FVBNJ_G0029145
 protein coding gene Chr5:25129691-25140123 (-)
LP/J MGP_LPJ_G0029272
 protein coding gene Chr5:26819013-26829433 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0029174
 protein coding gene Chr5:29509969-29520403 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0029836
 protein coding gene Chr5:26137330-26147744 (-)
PWK/PhJ MGP_PWKPhJ_G0028205
 protein coding gene Chr5:24818474-24829042 (-)
SPRET/EiJ MGP_SPRETEiJ_G0028036
 protein coding gene Chr5:25421952-25432358 (-)
WSB/EiJ MGP_WSBEiJ_G0028561
 protein coding gene Chr5:26149082-26159510 (-)



Homology
more
  • Human Ortholog
    SHH, sonic hedgehog signaling molecule
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SHH, sonic hedgehog signaling molecule
  • Synonyms
    HHG1, HLP3, HPE3, MCOPCB5, ShhNC, SMMCI, TPT, TPTPS
  • Links
    NCBI Gene ID: 6469
    UniProt: Q15465

  • Chr Location
    7q36.3; chr7:155799980-155812463 (-)  GRCh38
Human Diseases
more
  • Diseases
    2 with Shh mouse models; 10 with human SHH associations

Human Disease Mouse Models
      
IDs
 View 3 models
      
IDs
 View 1 model
      
IDs
IDs
IDs
IDs
IDs
IDs
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    4 with disease annotations
  • References
    7 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    309 phenotypes from 16 alleles in 25 genetic backgrounds
    278 phenotypes from multigenic genotypes
    794 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
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 genitalia and a mouth.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    426
  • GO References
    153
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    5923
  • Tissues
    1130
  • cDNA Data
    58
  • Literature Summary
    1908
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 20423 NCBI Gene Model | MGI Sequence Detail 10262 C57BL/6J ±  kb
    transcript NM_009170 RefSeq | MGI Sequence Detail 2667 C57BL/6  
    polypeptide Q62226 UniProt | EBI | MGI Sequence Detail 437 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 444
      Genomic 1
      cDNA 91
      Primer pair 75
      Other 277

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-11020, MGD-MRK-14403, MGD-MRK-19573, MGD-MRK-8906, MGI:3051411, MGI:94931, MGI:96290
    References
    more
    • Summaries
      All 2754
      Developmental Gene Expression 1908
      Diseases 7
      Gene Ontology 153
      Phenotypes 794
    • Earliest
      J:5021 Batchelor AL, et al., A comparison of the mutagenic effectiveness of chronic neutron- and gamma-irradiation of mouse spermatogonia. Mutat Res. 1966 Jun;3(3):218-29
    • Latest
      J:374451 Negretti NM, et al., Epithelial outgrowth through mesenchymal rings drives lung alveologenesis. JCI Insight. 2025 Jan 7;10(4)
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/30/2025
    MGI 6.24     		The Jackson Laboratory