shha sonic hedgehog signaling molecule a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: shhaprovided by ZNC
Official Full Name: sonic hedgehog signaling molecule aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-166
See related: Ensembl:ENSDARG00000068567 AllianceGenome:ZFIN:ZDB-GENE-980526-166
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: shh; syu; vhh1; ShhNC; vhh-1; fc83d08; wu:fc83d08
Summary: Predicted to enable calcium ion binding activity and patched binding activity. Involved in regulation of gene expression. Acts upstream of or within several processes, including animal organ development; chordate embryonic development; and neurogenesis. Predicted to be located in plasma membrane. Predicted to be active in extracellular space. Is expressed in several structures, including central nervous system; digestive system; fin; head; and mesoderm. Human ortholog(s) of this gene implicated in several diseases, including Hirschsprung's disease; holoprosencephaly (multiple); hypoplastic or aplastic tibia with polydactyly; middle cerebral artery infarction; and polydactyly. Orthologous to human SHH (sonic hedgehog signaling molecule). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 7

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (40884012..40891326)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (40597844..40611254)

Chromosome 7 - NC_007118.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ccn2a-FGFR1-SHH signaling is necessary for intervertebral disc homeostasis and regeneration in adult zebrafish.
Title: Ccn2a-FGFR1-SHH signaling is necessary for intervertebral disc homeostasis and regeneration in adult zebrafish.
Functional analysis of Sonic Hedgehog variants associated with holoprosencephaly in humans using a CRISPR/Cas9 zebrafish model.
Title: Functional analysis of Sonic Hedgehog variants associated with holoprosencephaly in humans using a CRISPR/Cas9 zebrafish model.
Sonic hedgehog expression in zebrafish forebrain identifies the teleostean pallidal signaling center and shows preglomerular complex and posterior tubercular dopamine cells to arise from shh cells.
Title: Sonic hedgehog expression in zebrafish forebrain identifies the teleostean pallidal signaling center and shows preglomerular complex and posterior tubercular dopamine cells to arise from shh cells.
Basal epidermis collective migration and local Sonic hedgehog signaling promote skeletal branching morphogenesis in zebrafish fins.
Title: Basal epidermis collective migration and local Sonic hedgehog signaling promote skeletal branching morphogenesis in zebrafish fins.
Variation in phenotypes from a Bmp-Gata3 genetic pathway is modulated by Shh signaling.
Title: Variation in phenotypes from a Bmp-Gata3 genetic pathway is modulated by Shh signaling.
Sulf2a controls Shh-dependent neural fate specification in the developing spinal cord.
Title: Sulf2a controls Shh-dependent neural fate specification in the developing spinal cord.
Shh-signaling-dependent regulation of matrix metalloproteinase9, in turn, regulates Shha levels and genes essential for retina regeneration, such as lin28a, zic2b, and foxn4.
Title: let-7 MicroRNA-Mediated Regulation of Shh Signaling and the Gene Regulatory Network Is Essential for Retina Regeneration.
Mutation of hmgcs1 had no effect on Shh signaling at 2 and 3 days post fertilization (dpf), but did result in a decrease in the expression of gli1, a known Shh target gene, at 4 dpf, after morphological deficits in craniofacial development and chondrocyte differentiation were observed in hmgcs1 mutants.
Title: Functional analysis of the zebrafish ortholog of HMGCS1 reveals independent functions for cholesterol and isoprenoids in craniofacial development.
Shha/Smo is functionally dedicated to ray branching during fin regeneration.
Title: Shh promotes direct interactions between epidermal cells and osteoblast progenitors to shape regenerated zebrafish bone.
Shh and Rx3 govern formation of a distinct progenitor domain that elaborates patterning through its anisotropic growth and differentiation.
Title: Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus.

Submit: New GeneRIF Correction See all GeneRIFs (62)

General gene information

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Markers

fd07h09.y1 (e-PCR)
- UniSTS:204085

fb08b12 (e-PCR)
- UniSTS:204646

shh (e-PCR), detects polymorphism
- UniSTS:187033

fc83d08.x1 (e-PCR)
- UniSTS:188313

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables cholesterol-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity, acting on ester bonds	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables patched binding	IBA Inferred from Biological aspect of Ancestor 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 transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adenohypophysis development	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within adenohypophysis development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood circulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cardioblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within caudal fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell-cell signaling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within diencephalon development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic digestive tract morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic neurocranium morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic neurocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endocardial cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within endocrine pancreas development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within endocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within floor plate development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within floor plate formation	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within floor plate formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glial cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gliogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within gliogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glomerulus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within habenula development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear development	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within intein-mediated protein splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within midbrain-hindbrain boundary development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within muscle cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural plate morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron fate commitment	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within odontogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in oligodendrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within oligodendrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within oligodendrocyte progenitor proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pancreas development	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within pancreas development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within pancreas development	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within pectoral fin development	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smoothened signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within post-embryonic foregut morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pronephros development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein autoprocessing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within proteolysis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of BMP signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cardiac muscle tissue regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cartilage development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of vascular endothelial growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in self proteolysis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within skeletal muscle fiber development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within skeletal muscle fiber development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in smoothened signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within smoothened signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somitogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within spinal cord motor neuron cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within striated muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within swim bladder morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sonic hedgehog protein

Names: shh unprocessed N-terminal signaling and C-terminal autoprocessing domains; sonic hedgehog a; sonic hedgehog protein A; sonic-you

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_131063.3 → NP_571138.1 sonic hedgehog protein precursor

See identical proteins and their annotated locations for NP_571138.1

Status: VALIDATED

Source sequence(s)

CT668143, CU041319, L27585

UniProtKB/Swiss-Prot

O13170, O13171, O13208, O13209, O13245, O13246, Q92008

UniProtKB/TrEMBL

Q1MTB5

Related

ENSDARP00000125090.1, ENSDART00000149395.3

Conserved Domains (3) summary

cd00081
Location:198 → 343

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:187 → 404

Hint; Hint module

pfam01085
Location:39 → 184

HH_signal; Hedgehog amino-terminal signalling domain