U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SHH sonic hedgehog signaling molecule [ Homo sapiens (human) ]

Gene ID: 6469, updated on 11-Jun-2025
Official Symbol
SHHprovided by HGNC
Official Full Name
sonic hedgehog signaling moleculeprovided by HGNC
Primary source
HGNC:HGNC:10848
See related
Ensembl:ENSG00000164690 MIM:600725; AllianceGenome:HGNC:10848
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TPT; HHG1; HLP3; HPE3; SMMCI; ShhNC; TPTPS; MCOPCB5
Summary
This gene encodes a protein that is instrumental in patterning the early embryo. It has been implicated as the key inductive signal in patterning of the ventral neural tube, the anterior-posterior limb axis, and the ventral somites. Of three human proteins showing sequence and functional similarity to the sonic hedgehog protein of Drosophila, this protein is the most similar. The protein is made as a precursor that is autocatalytically cleaved; the N-terminal portion is soluble and contains the signalling activity while the C-terminal portion is involved in precursor processing. More importantly, the C-terminal product covalently attaches a cholesterol moiety to the N-terminal product, restricting the N-terminal product to the cell surface and preventing it from freely diffusing throughout the developing embryo. Defects in this protein or in its signalling pathway are a cause of holoprosencephaly (HPE), a disorder in which the developing forebrain fails to correctly separate into right and left hemispheres. HPE is manifested by facial deformities. It is also thought that mutations in this gene or in its signalling pathway may be responsible for VACTERL syndrome, which is characterized by vertebral defects, anal atresia, tracheoesophageal fistula with esophageal atresia, radial and renal dysplasia, cardiac anomalies, and limb abnormalities. Additionally, mutations in a long range enhancer located approximately 1 megabase upstream of this gene disrupt limb patterning and can result in preaxial polydactyly. [provided by RefSeq, Jul 2008]
Expression
Biased expression in stomach (RPKM 3.1), urinary bladder (RPKM 2.9) and 10 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table
See SHH in Genome Data Viewer
Location:
7q36.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (155799980..155812463, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (156983127..156995607, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (155592674..155605157, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155436294-155437248 Neighboring gene RBM33 divergent transcript Neighboring gene RNA binding motif protein 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26899 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:155520719-155521219 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:155534138-155535337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26901 Neighboring gene VISTA enhancer hs1268 Neighboring gene Sharpr-MPRA regulatory region 9615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26902 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155561116-155561309 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:155567610-155568809 Neighboring gene Sharpr-MPRA regulatory region 3765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155574696-155575231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155575232-155575766 Neighboring gene MPRA-validated peak6863 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155597860-155598829 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155598830-155599798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155607457-155608100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155608399-155608900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155628074-155629066 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:155632935-155634134 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155638472-155638619 Neighboring gene MPRA-validated peak6864 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:155661375-155662574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26904 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:155678617-155679816 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:155743904-155745103 Neighboring gene uncharacterized LOC124901788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155745489-155745989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155747182-155747910 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:155754590-155755789 Neighboring gene uncharacterized LOC389602

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Associated conditions

Description Tests
Holoprosencephaly 3
MedGen: C1840529 OMIM: 142945 GeneReviews: Holoprosencephaly Overview
Compare labs
Microphthalmia, isolated, with coloboma 5
MedGen: C1968843 OMIM: 611638 GeneReviews: Not available
Compare labs
Solitary median maxillary central incisor syndrome
MedGen: C1840235 OMIM: 147250 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-06-24)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-06-24)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.
EBI GWAS Catalog
Identification of a candidate gene for astigmatism.
EBI GWAS Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables cholesterol-protein transferase activity IEA
Inferred from Electronic Annotation
more info
 
enables cholesterol-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables endopeptidase activity TAS
Traceable Author Statement
more info
 
enables glycosaminoglycan binding IEA
Inferred from Electronic Annotation
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables laminin-1 binding IEA
Inferred from Electronic Annotation
more info
 
enables laminin-1 binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables morphogen activity NAS
Non-traceable Author Statement
more info
PubMed 
enables morphogen activity TAS
Traceable Author Statement
more info
PubMed 
enables patched binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables patched binding IDA
Inferred from Direct Assay
more info
PubMed 
enables patched binding IEA
Inferred from Electronic Annotation
more info
 
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
 
enables peptidase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within Bergmann glial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in CD4-positive or CD8-positive, alpha-beta T cell lineage commitment IDA
Inferred from Direct Assay
more info
PubMed 
involved_in CD4-positive or CD8-positive, alpha-beta T cell lineage commitment IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell differentiation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within androgen metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in androgen metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within angiogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in animal organ development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within animal organ formation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
involved_in apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in apoptotic signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within artery development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of astrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within axon guidance IEA
Inferred from Electronic Annotation
more info
 
involved_in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within blood coagulation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within branching involved in blood vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in branching involved in blood vessel morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within branching involved in prostate gland morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within branching involved in salivary gland morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within branching morphogenesis of an epithelial tube IEA
Inferred from Electronic Annotation
more info
 
involved_in branching morphogenesis of an epithelial tube ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within bud outgrowth involved in lung branching IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in cell development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in cell fate specification IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within cell fate specification IEA
Inferred from Electronic Annotation
more info
 
involved_in cell fate specification ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of cell migration IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell proliferation in external granule layer IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell-cell signaling IEA
Inferred from Electronic Annotation
more info
 
involved_in cell-cell signaling IEA
Inferred from Electronic Annotation
more info
 
involved_in cell-cell signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within cellular response to lithium ion IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within central nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in central nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in central nervous system development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of cerebellar granule cell precursor proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in cerebellar granule cell precursor proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in determination of left/right asymmetry in lateral mesoderm IEA
Inferred from Electronic Annotation
more info
 
involved_in determination of left/right asymmetry in lateral mesoderm ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in determination of left/right asymmetry in lateral mesoderm NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within determination of left/right symmetry IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within developmental growth IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within digestive tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in dopaminergic neuron differentiation TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within dorsal/ventral neural tube patterning IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within dorsal/ventral pattern formation IEA
Inferred from Electronic Annotation
more info
 
involved_in dorsal/ventral pattern formation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within ectoderm development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic digestive tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic digit morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic digit morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within embryonic foregut morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic limb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic limb morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within embryonic morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic organ development IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic pattern specification TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within endocytosis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of epithelial cell proliferation involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within epithelial cell proliferation involved in salivary gland morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within epithelial tube branching involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within epithelial-mesenchymal cell signaling IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within epithelial-mesenchymal cell signaling IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within epithelial-mesenchymal signaling involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within establishment of epithelial cell polarity IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within forebrain development IEA
Inferred from Electronic Annotation
more info
 
involved_in forebrain development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within forebrain regionalization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within formation of anatomical boundary IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within gene expression IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within hair follicle development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within hair follicle morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within heart development IEA
Inferred from Electronic Annotation
more info
 
involved_in heart development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within heart looping IEA
Inferred from Electronic Annotation
more info
 
involved_in heart looping ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within hindbrain development IEA
Inferred from Electronic Annotation
more info
 
involved_in hindbrain development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within hindgut morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within inner ear development IEA
Inferred from Electronic Annotation
more info
 
involved_in intein-mediated protein splicing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within intermediate filament organization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within kidney development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within left lung development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within limb bud formation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within limb development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lung development IEA
Inferred from Electronic Annotation
more info
 
involved_in lung development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within lung epithelium development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lung lobe morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lung morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lung-associated mesenchyme development IEA
Inferred from Electronic Annotation
more info
 
involved_in lymphoid progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in lymphoid progenitor cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within male genitalia development IEA
Inferred from Electronic Annotation
more info
 
involved_in male genitalia development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of mesenchymal cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mesenchymal cell proliferation involved in lung development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mesenchymal smoothened signaling pathway involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in metanephric collecting duct development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in metanephric mesenchymal cell proliferation involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
involved_in metanephric mesenchymal cell proliferation involved in metanephros development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in metanephros development IEA
Inferred from Electronic Annotation
more info
 
involved_in metanephros development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within midbrain development IEA
Inferred from Electronic Annotation
more info
 
involved_in midbrain development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within myoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within myotube differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of cholesterol efflux IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cholesterol efflux ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of dopaminergic neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of kidney smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of kidney smooth muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of transcription elongation by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of ureter smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of ureter smooth muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative thymic T cell selection IEA
Inferred from Electronic Annotation
more info
 
involved_in negative thymic T cell selection ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within neural crest cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in neural crest cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in neuroblast proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within neuron fate commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron fate commitment ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within odontogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within oligodendrocyte development IEA
Inferred from Electronic Annotation
more info
 
involved_in oligodendrocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within osteoblast development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within pancreas development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within pattern specification process IEA
Inferred from Electronic Annotation
more info
 
involved_in pattern specification process IEA
Inferred from Electronic Annotation
more info
 
involved_in pattern specification process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in polarity specification of anterior/posterior axis IEA
Inferred from Electronic Annotation
more info
 
involved_in polarity specification of anterior/posterior axis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of T cell differentiation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of alpha-beta T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of astrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cell division IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of cerebellar granule cell precursor proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of epithelial cell proliferation involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of immature T cell proliferation in thymus IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of immature T cell proliferation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of kidney smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of kidney smooth muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of mesenchymal cell proliferation involved in ureter development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of mesenchymal cell proliferation involved in ureter development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of sclerotome development IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of skeletal muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of skeletal muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of smoothened signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of striated muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of ureter smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of ureter smooth muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive thymic T cell selection IEA
Inferred from Electronic Annotation
more info
 
involved_in positive thymic T cell selection ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within primary prostatic bud elongation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within prostate epithelial cord elongation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within prostate gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in prostate gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein autoprocessing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within protein localization to nucleus IEA
Inferred from Electronic Annotation
more info
 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of developmental process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of epithelial cell proliferation involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of glial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of mesenchymal cell proliferation involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of nodal signaling pathway NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of odontogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of odontogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within regulation of prostatic bud formation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of protein localization to nucleus IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of proteolysis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of proteolysis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within regulation of stem cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within respiratory tube development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within right lung development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within salivary gland cavitation IEA
Inferred from Electronic Annotation
more info
 
involved_in self proteolysis IEA
Inferred from Electronic Annotation
more info
 
involved_in self proteolysis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of skeletal muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within skeletal muscle fiber differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of skeletal muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within skin development IEA
Inferred from Electronic Annotation
more info
 
involved_in smooth muscle tissue development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in smoothened signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in smoothened signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in smoothened signaling pathway IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in somite development IEA
Inferred from Electronic Annotation
more info
 
involved_in somite development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within spinal cord dorsal/ventral patterning IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within spinal cord motor neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in stem cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in stem cell development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within stem cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within striated muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within striated muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within telencephalon regionalization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within thalamus development IEA
Inferred from Electronic Annotation
more info
 
involved_in thymus development IEA
Inferred from Electronic Annotation
more info
 
involved_in thymus development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within thyroid gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in tissue development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within trachea development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within trachea morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within tracheoesophageal septum formation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of trunk neural crest cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in tube development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within vasculature development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within vasculogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in vasculogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in ventral midline development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
located_in cell surface IEA
Inferred from Electronic Annotation
more info
 
located_in cell surface ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular matrix HDA PubMed 
located_in extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region TAS
Traceable Author Statement
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in membrane raft IEA
Inferred from Electronic Annotation
more info
 
located_in membrane raft ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
Preferred Names
sonic hedgehog protein
Names
shh unprocessed N-terminal signaling and C-terminal autoprocessing domains
sonic hedgehog homolog

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007504.2 RefSeqGene

    Range
    4811..17294
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000193.4NP_000184.1  sonic hedgehog protein isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_000184.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC078834, BX109787, BX452210, BY797055, L38518
    Consensus CDS
    CCDS5942.1
    UniProtKB/Swiss-Prot
    A4D247, Q15465, Q75MC9
    UniProtKB/TrEMBL
    D9ZGF9
    Related
    ENSP00000297261.2, ENST00000297261.7
    Conserved Domains (3) summary
    cd00081
    Location:198363
    Hint; Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, ...
    pfam01079
    Location:187448
    Hint; Hint module
    pfam01085
    Location:39184
    HH_signal; Hedgehog amino-terminal signalling domain
  2. NM_001310462.2NP_001297391.1  sonic hedgehog protein isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' and 3' UTRs and has multiple coding region differences, compared to variant 1. It encodes isoform 2 which has a shorter and distinct N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC078834, AI192528, AY927452, AY927455
    UniProtKB/TrEMBL
    C9JC48
    Related
    ENSP00000396621.1, ENST00000430104.5
    Conserved Domains (1) summary
    pfam01085
    Location:1297
    HH_signal; Hedgehog amino-terminal signalling domain

RNA

  1. NR_132318.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC078834, AI192528, AY927453, AY927454, L38518
    Related
    ENST00000441114.5
  2. NR_132319.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC078834, AI192528, AY927453
    Related
    ENST00000435425.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    155799980..155812463 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420718.1XP_047276674.1  sonic hedgehog protein isoform X2

  2. XM_011516479.3XP_011514781.1  sonic hedgehog protein isoform X1

    See identical proteins and their annotated locations for XP_011514781.1

    Conserved Domains (3) summary
    cd00081
    Location:111276
    Hint; Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, ...
    pfam01079
    Location:100361
    Hint; Hint module
    pfam01085
    Location:1297
    HH_signal; Hedgehog amino-terminal signalling domain
  3. XM_011516480.3XP_011514782.1  sonic hedgehog protein isoform X1

    See identical proteins and their annotated locations for XP_011514782.1

    Conserved Domains (3) summary
    cd00081
    Location:111276
    Hint; Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, ...
    pfam01079
    Location:100361
    Hint; Hint module
    pfam01085
    Location:1297
    HH_signal; Hedgehog amino-terminal signalling domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    156983127..156995607 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358808.1XP_054214783.1  sonic hedgehog protein isoform X2

  2. XM_054358806.1XP_054214781.1  sonic hedgehog protein isoform X1

  3. XM_054358807.1XP_054214782.1  sonic hedgehog protein isoform X1