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SHH Gene

protein-coding GIFtS: 74

GC07M149327

sonic hedgehog
(Previous names: sonic hedgehog (Drosophila) homolog, sonic hedgehog homolog (Drosophila) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: HPE3, HLP3)

		Products

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases & Descriptions
sonic hedgehog¹ ²		HLP3² ⁵
MCOPCB5¹ ² ⁵		sonic hedgehog (Drosophila) homolog¹
SMMCI¹ ² ⁵		sonic hedgehog homolog (Drosophila)¹
TPT¹ ²		sonic hedgehog homolog²
TPTPS¹ ²		sonic hedgehog protein²
HHG1¹ ²		HHG-1³
HPE3² ⁵

External Ids:	HGNC: 10848¹	Entrez Gene: 6469²	Ensembl: ENSG00000164690⁷	UniProtKB: Q15465³

Export aliases for SHH gene to outside databases

Previous GC identifers: GC07M153825 GC07M154898 GC07M155013 GC07M155014 GC07M155095 GC07M155288 GC07M155592

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SHH:

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)

UniProtKB/Swiss-Prot: SHH_HUMAN, Q15465

Function: Binds to the patched (PTC) receptor, which functions in association with smoothened (SMO), to activate the

transcription of target genes. In the absence of SHH, PTC represses the constitutive signaling activity of SMO. Also

regulates another target, the gli oncogene. Intercellular signal essential for a variety of patterning events during

development: signal produced by the notochord that induces ventral cell fate in the neural tube and somites, and the

polarizing signal for patterning of the anterior-posterior axis of the developing limb bud. Displays both floor plate-

and motor neuron-inducing activity. The threshold concentration of N-product required for motor neuron induction is

5-fold lower than that required for floor plate induction (By similarity)

summary for SHH:

The hedgehog (Hh) signaling pathway is crucial in the development of all known animals. In the embryo, it

regulates morphogenesis of a variety of tissues and organs, in the adult, it controls stem cell

proliferation. There are three human Hh proteins; Sonic hedgehog (Shh), Desert hedgehog (Dhh) and Indian

hedgehog (Ihh). Each is expressed at different times of development and in specific cell types and they are

tightly controlled by highly complex, yet divergent transcriptional enhancers. Hh protein release and

diffusion is controlled by various proteins including Skinny hedgehog (Sit), Dispatched (Disp), Tout-velu

(Ttv) and Hedgehog-interacting protein (Hip). Hh proteins bind to the twelve transmembrane domain protein,

Patched (Ptc). In the absence of Hh proteins, Ptc catalytically inhibits Smo. Hh-Ptc binding results in loss

of Ptc activity and activation of Smo, which transduces the Hh signal to the cytoplasm. This leads to the

activation of the Ci/GLI family of transcription factors, through complex interactions of Costal2 (Cos2),

Fused (Fu) and Suppressor of fu [Su(fu)]. Furthermore, PKA, CK1, GSK-3 and Slimb modulate this signal

transduction pathway. Abberant activation of the Hh pathway has been linked to multiple types of human

cancer, particularly basal cell carcinoma. Disruption of Hh signaling during embryonic development, either

through congenital mutation or maternal teratogen consumption, can lead to severe developmental disorders

such as holoprosencephaly.

Gene Wiki entry for SHH (Sonic hedgehog)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SHH gene promoter:
         NF-kappaB   NF-kappaB1   Sox9   CUTL1   SRF   LUN-1   AhR   c-Myb   PPAR-gamma2   PPAR-gamma1
         Other transcription factors

Search SABiosciences Chromatin IP Primers for SHH

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for SHH

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7q36 Ensembl cytogenetic band: 7q36.3 HGNC cytogenetic band: 7q36

SHH Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHH gene location

GeneLoc gene densities for chromosome 7 GeneLoc Exon Structure

GeneLoc location for GC07M149327: view genomic region (about GC identifiers)

Start:	149,327,101 bp from pter
End:	149,336,513 bp from pter
Size:	9,413 bases
Orientation:	minus strand

1 alternative location:

Chr7- 155,592,680-155,604,967

RefSeq DNA sequence:

NC_000007.13 NT_007741.14 NT_079596.2

(According to ¹UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

UniProtKB/Swiss-Prot: SHH_HUMAN, Q15465 (See protein sequence)

Recommended Name: Sonic hedgehog protein precursor

Size: 462 amino acids; 49607 Da

Subunit: Interacts with HHATL/GUP1 which negatively regulates HHAT-mediated palmitoylation of the SHH N-terminus.

N-product is active as a multimer (By similarity)

Subcellular location: Sonic hedgehog protein C-product: Secreted, extracellular space (By similarity). Note=The

C-terminal peptide diffuses from the cell (By similarity)

Subcellular location: Sonic hedgehog protein N-product: Cell membrane; Lipid-anchor (By similarity). Note=The N-product

either remains associated with lipid rafts at the cell surface, or forms freely diffusible active multimers with its

hydrophobic lipid-modified N- and C-termini buried inside (By similarity)

Mass spectrometry: Mass=19.560; Method=Electrospray; Range=24-197; Note=Soluble N-product, purified from insect cells;

Source=PubMed:9593755;

Mass spectrometry: Mass=20.167; Method=Electrospray; Range=24-197; Note=Membrane-bound N-product, purified from insect

cells; Source=PubMed:9593755;

PDB structures from and Proteopedia :

3HO5 (3D)

3M1N (3D)

3MXW (3D)

Secondary accessions: A4D247 Q75MC9

Explore the universe of human proteins at neXtProt for SHH: NX_Q15465

Post-translational modifications:

The C-terminal domain displays an autoproteolysis activity and a cholesterol transferase activity. Both activities

result in the cleavage of the full-length protein and covalent attachment of a cholesterol moiety to the C-terminal of

the newly generated N-terminal fragment (N-product). The N-product is the active species in both local and long-range

signaling, whereas the C-product has no signaling activity¹

Cholesterylation is required for N-product targeting to lipid rafts and multimerization (By similarity)¹

N-palmitoylation of Cys-24 by HHAT is required for N-product multimerization and full activity (By similarity)¹

REFSEQ proteins: NP_000184.1

ENSEMBL proteins:

ENSP00000297261 ENSP00000396621 ENSP00000410546 ENSP00000413871

Human Recombinant Proteins

	Browse Purified and Recombinant Proteins at Millipore
	Browse Human Recombinant Proteins at Sigma-Aldrich
	R&D Systems Recombinant & Natural Proteins for SHH (Sonic Hedgehog/Shh)
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells OriGene Protein Over-expression Lysate: SHH
	GenScript Custom Purified and Recombinant Proteins Services for SHH
	Novus Biologicals Proteins for SHH
	Novus Biologicals Lysate for SHH
	Browse Sino Biological Recombinant Proteins
	ProSpec Recombinant Protein for SHH

5/11 Gene Ontology (GO) cellular component terms (GO ID links to tree view) (see all 11):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005615	extracellular space	ISS	--
GO:0005624	membrane fraction	IEA	--
GO:0005634	nucleus	IEA	--
GO:0005783	endoplasmic reticulum	IEA	--

About this table

SHH for ontologies About GeneDecksing

Antibodies for SHH:

	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for SHH
	R&D Systems Antibodies for SHH (Sonic Hedgehog/Shh)
	Cell Signaling Technology (CST) Antibodies for SHH
	OriGene Antibodies (see all 3): SHH
	GenScript Custom Superior Antibodies Services for SHH
	Novus Biologicals Antibodies for SHH
	Epitomics antibodies for SHH

Assays for SHH:

	Browse Kits and Assays available from Millipore
	Browse ELISAs at Sigma-Aldrich
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for SHH
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for SHH

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

SHH for domains About GeneDecksing

5/7 InterPro domains/families (see all 7):

IPR003586 Hedgehog_hint_C

IPR001657 Peptidase_C46

IPR009045 Hedgehog/DD-pept_Zn-bd

IPR000320 Hedgehog_signaling_dom

IPR006141 Intein_splice_site

Graphical View of Domain Structure for InterPro Entry Q15465

ProtoNet protein and cluster: Q15465

5 Blocks protein families:

IPB000320 Hedgehog amino-terminal signaling domain

IPB001657 Sonic hedgehog protein signature

IPB001767 Hedgehog protein

IPB003586 Hedgehog/Intein hint domain

IPB009045 Hedgehog/DD-peptidase

UniProtKB/Swiss-Prot: SHH_HUMAN, Q15465

Similarity: Belongs to the hedgehog family

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section

UniProtKB/Swiss-Prot: SHH_HUMAN, Q15465

Function: Binds to the patched (PTC) receptor, which functions in association with smoothened (SMO), to activate the

transcription of target genes. In the absence of SHH, PTC represses the constitutive signaling activity of SMO. Also

regulates another target, the gli oncogene. Intercellular signal essential for a variety of patterning events during

development: signal produced by the notochord that induces ventral cell fate in the neural tube and somites, and the

polarizing signal for patterning of the anterior-posterior axis of the developing limb bud. Displays both floor plate-

and motor neuron-inducing activity. The threshold concentration of N-product required for motor neuron induction is

5-fold lower than that required for floor plate induction (By similarity)

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich siRNA Panels and siRNA for SHH Sigma-Aldrich shRNA Panels for SHH
		OriGene 29mer shRNA kits in GFP-retroviral vector: SHH OriGene shRNA RFP: SHH OriGene basic RS shRNA: SHH OriGene siRNA: SHH
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of SHH

miRNA:		Browse microRNA Mimics at Sigma-Aldrich Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of SHH
		Search SABiosciences for Assays for microRNAs that regulate SHH

Gene
Editing:

Sigma-Aldrich CompoZr Knockout ZFN for SHH

Clones:		Browse Clones for the Expression of Recombinant Proteins Available from Millipore
		Browse iPSC Reprogramming Factors at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: SHH OriGene Myc/DDK tagged cDNA clones in CMV expression vector: SHH OriGene untagged cDNA clones in CMV expression vector: SHH Browse 3'-UTR reporter clones for miRNA target validation Browse MicroRNA Expression Plasmids
		GenScript cDNA clone with any tag delivered in your preferred vector: SHH
		Sino Biological Human cDNA Clone for SHH

Cell
Lines:

GenScript Custom overexpressing Cell Line Services for SHH

Genatlas biochemistry entry for SHH:

embryonic patterning gene,Drosophila segment polarity gene Sonic hedgehog homolog,general ventralizing signal,expressed

in the notochord and floor plate cells,gut endoderm,posterior limb buds,inductive signal for somite differentiation

and limb development at the anteroposterior axis,targetting BMP2 and HOXD genes through a FGF4 positive feedback

loop,also expressed in fetal liver,lung and kidney and in hair follicle,involved in signal transduction,SHH pathway

5/10 Gene Ontology (GO) molecular function terms (GO ID links to tree view) (see all 10):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001948	glycoprotein binding	IEA	--
GO:0004871	signal transducer activity	IDA	19561609
GO:0005113	patched binding	IEA	--
GO:0005509	calcium ion binding	IDA	19561609
GO:0005515	protein binding	IPI	19561609

About this table

SHH for ontologies About GeneDecksing

Animal Models: 15/27 MGI mutant phenotypes (inferred from 24 alleles) (MGI details for Shh) (see all 27):

behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary
embryogenesis	endocrine/exocrine gland	growth/size	hearing/vestibular/ear	homeostasis/metabolism
lethality-postnatal	lethality-prenatal/perinatal	life span-post-weaning/aging	limbs/digits/tail	muscle

SHH for phenotypes About GeneDecksing

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section

SHH for pathways About GeneDecksing

1 Millipore Pathway for SHH

Development Hedgehog and PTH signaling pathways in bone and cartilage development

5/6 Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Pathways for SHH (see all 6)

	Basal Cell Carcinoma Signaling
	Corticotropin Releasing Hormone Signaling
	Sonic Hedgehog Signaling
	Axonal Guidance Signaling
	Molecular Mechanisms of Cancer

3 Kegg Pathways (Kegg details for SHH):

	hsa04340 Hedgehog signaling pathway
	hsa05200 Pathways in cancer
	hsa05217 Basal cell carcinoma

SABiosciences Pathway-Focused PCR Arrays including SHH (see all 4): PAHS-049A PAHS-059A

Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Molecular Interaction Network for SHH

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for SHH

5/20 Interacting proteins for SHH (ENSP00000297261³) via UniProtKB, MINT, and/or STRING (see all 20)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
BOC	ENSP00000273395³	STRING: ENSP00000273395
CDON	ENSP00000263577³	STRING: ENSP00000263577
FOXA1	ENSP00000250448³	STRING: ENSP00000250448
GLI2	ENSP00000354586³	STRING: ENSP00000354586
GPC3	ENSP00000359854³	STRING: ENSP00000359854

About this table

5/173 Gene Ontology (GO) biological process terms (GO ID links to tree view) (see all 173):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001525	angiogenesis	--	--
GO:0001569	patterning of blood vessels	ISS	--
GO:0001570	vasculogenesis	ISS	--
GO:0001656	metanephros development	ISS	--
GO:0001658	branching involved in ureteric bud morphogenesis	ISS	--

About this table

SHH for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

SHH for compounds About GeneDecksing

Browse Small Molecules at Sigma-Aldrich

Browse drugs & compounds from Enzo Life Sciences

Compounds for SHH available from Tocris Bioscience

Compound	Action	CAS number
SANT-1	Inhibitor of hedgehog (Hh) signaling; antagonizes smoothened activity	[304909-07-7]

About this table

2 Novoseek chemical compound relationships for SHH gene

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
cyclopamine	89.5	8	17300775 (1), 19788370 (1), 20025076 (1), 20087349 (1)
cholesterol	0	2	10799401 (1), 15539288 (1)

About this table

2 PharmGKB drug compound relationship for SHH gene

Drug compound	PharmGKB Relations	PubMed IDs for articles supporting these relationships
statin	PD	15546153

About this table

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich siRNA Panels and siRNA for SHH Sigma-Aldrich shRNA Panels for SHH
		OriGene 29mer shRNA kits in GFP-retroviral vector: SHH OriGene shRNA RFP: SHH OriGene basic RS shRNA: SHH OriGene siRNA: SHH
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of SHH

miRNA:		Browse microRNA Mimics at Sigma-Aldrich Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of SHH
		Search SABiosciences for Assays for microRNAs that regulate SHH

Clones:		Browse FLAG tag genes at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: SHH OriGene Myc/DDK tagged cDNA clones in CMV expression vector: SHH OriGene untagged cDNA clones in CMV expression vector: SHH Browse 3'-UTR reporter clones for miRNA target validation Browse OriGene MicroRNA Expression Plasmids
		GenScript cDNA clone with any tag delivered in your preferred vector: SHH

Primers:		OriGene genome-wide validated SYBR primer pairs: SHH Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for SHH: PPH02405A

REFSEQ mRNAs for SHH gene:

NM_000193.2

Additional cDNA sequence:

AY927450.1 AY927451.1 AY927452.1 AY927453.1 AY927454.1 AY927455.1 L38518.1

3 DOTS entries:

DT.121093532 DT.305318 DT.405095

4 AceView cDNA sequences:

NM_000193 L38518 AA076750 BX452210

highest scoring ESTs for SHH:

L38518 AA076750 BX452210 NM_000193 AA076861 AA077592 AA503654 AA904572 AI192528 AW969518

Unigene Cluster for SHH:

Sonic hedgehog

Hs.164537 [show with all ESTs]

Unigene Representative Sequence: NM_000193

GeneLoc Exon Structure

5 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000297261(uc003wmj.1 uc003wmk.1) ENST00000472308 ENST00000430104

ENST00000441114(uc003wmh.1 uc003wmi.1) ENST00000435425

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

SHH expression in normal and diseased human tissues

¹ / ² / ³

6 probe-sets matching SHH gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
59360_at²^{, 3}	U95-B	1	0.81	1.00	0.92	0.90	AA503654	0.40	1.00	0.76	1
31724_at²^{, 3}	U95-A	1	0.38	1.00	0.89	1.11	L38518	1.00	1.00	1.00	1
236263_at²^{, 3}	U133-B	1	0.64	1.00	--	--	AI192528	0.40	1.00	0.76	1
207586_at²^{, 3}	U133-A	1	0.27	1.00	--	--	NM_000193	0.60	1.00	0.82	1
236263_at²	U133Plus2	1	0.64	1.00	--	--	--	--	--	--	--
207586_at²	U133Plus2	1	0.27	1.00	--	--	--	--	--	--	--

About this table

SHH for expression About GeneDecksing

Data from Genenote (Publications) and GNF BioGPS
About these images

About these images

CGAP SAGE TAG: GCGGTCAAGT

SOURCE GeneReport for Unigene cluster: Hs.164537

Expression variation in blood from EXPOLDB for SHH

UniProtKB/Swiss-Prot: SHH_HUMAN, Q15465

Tissue specificity: Expressed in fetal intestine, liver, lung, and kidney. Not expressed in adult tissues

Primers:		OriGene genome-wide validated SYBR primer pairs: SHH Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for SHH: PPH02405A

SABiosciences Expression via Pathway-Focused PCR Arrays including SHH (see all 4): PAHS-049A PAHS-059A

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for SHH gene from 5/10 species (see all 10)

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	SHH¹	--	sonic hedgehog homolog (Drosophila)	91.06(n) 95.38(a)	608860 XM_845357.1 XP_850450.1
chimpanzee (Pan troglodytes)	SHH¹	--	sonic hedgehog homolog (Drosophila)	97.92(n) 97.29(a)	743371 XM_001147185.1 XP_001147185.1
cow (Bos taurus)	SHH¹	--	sonic hedgehog homolog (Drosophila)	91.98(n) 97.33(a)	286821 XM_614193.3 XP_614193.3
rat (Rattus norvegicus)	Shh¹	--	sonic hedgehog	87.28(n) 93.1(a)	29499 NM_017221.1 NP_058917.1
mouse (Mus musculus)	Shh^{1 , 5}	5 (14.39 cM)⁵	sonic hedgehog^{1, 5}	87.84(n)¹ 92.66(a)¹	20423¹ NM_009170.2¹ NP_033196.1¹ AK052447⁵ AK077688⁵ (see all 9)

About this table Species with no ortholog for SHH

ENSEMBL Gene Tree for SHH (if available)

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for SHH gene

IHH² DHH²

SHH for paralogs About GeneDecksing

(SNPs according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

SNP ID	Valid	Chr 7 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
rs288745^1,2	C,H,	155606336(+)	`tttttA/Taaaaa`	1	--	ng5¹ trp³		0	--	--	--	--
rs288746^1,2	C,F,O,H,	155606672(-)	`CCTCTT/CATGCC`	1	--	ng5¹		30		NS EA NA MN WA	3036
rs756884^1,2	C,F,H,	155604099(+)	`ACAGTG/ACCAGG`	1	--	int¹		13		NS NA WA	904
rs872723^1,2	C,F,	155605744(+)	`CTGCTC/TTTTTA`	1	--	ng5¹		9		NS EA NA WA	2120
rs1233553^1,2	C,F,	155598145(+)	`GGGAAA/GCCTGG`	1	--	int¹		7		NS MN NA WA	344
rs1233554^1,2	C,F,A,	155598879(+)	`CAGCGC/ACCCTG`	1	--	int¹		16		NA EA MN NS WA	2176
rs1233555^1,2	C,F,A,H,	155599300(+)	`GGCAAT/CCGCCA`	1	--	int¹		5		NS NA	1020
rs1233556^1,2	C,F,A,H,	155600417(+)	`GGACAC/TGGGAT`	1	--	int¹		21		NS EA NA WA	1646
rs1233557^1,2	C,F,	155601653(+)	`CCCCAC/AGCTTG`	1	--	int¹		8		NA NS EA WA	390
rs1233561^1,2	C,F,	155603157(+)	`ACGCAC/ACGGGC`	1	--	int¹		7		NS MN NA WA	412

About this table

HapMap Linkage Disequilibrium images for SHH (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SHH: --

QIAGEN SeqTarget long-range PCR primers for resequencing SHH

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SHH for disorders About GeneDecksing

OMIM: 600725 disorders: 142945 147250 120200 611638

UniProtKB/Swiss-Prot: SHH_HUMAN, Q15465

Defects in SHH are the cause of microphthalmia isolated with coloboma type 5 (MCOPCB5) [MIM:611638].

Microphthalmia is a clinically heterogeneous disorder of eye formation, ranging from small size of a single eye to

complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of

the retina and choroid, cataract and other abnormalities like cataract may also be present. Ocular colobomas are a set

of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure

(optic fissure)

Defects in SHH are the cause of holoprosencephaly type 3 (HPE3) [MIM:142945]. Holoprosencephaly (HPE)

[MIM:236100] is the most common structural anomaly of the brain, in which the developing forebrain fails to correctly

separate into right and left hemispheres. Holoprosencephaly is genetically heterogeneous and associated with several

distinct facies and phenotypic variability. The majority of HPE3 cases are apparently sporadic, although clear

examples of autosomal dominant inheritance have been described. Interestingly, up to 30% of obligate carriers of HPE3

gene in autosomal dominant pedigrees are clinically unaffected

Defects in SHH are a cause of solitary median maxillary central incisor (SMMCI) [MIM:147250]. SMMCI is a rare

dental anomaly characterized by the congenital absence of one maxillary central incisor

Defects in SHH are the cause of triphalangeal thumb-polysyndactyly syndrome (TPTPS) [MIM:174500]. TPTPS is an

autosomal dominant syndrome characterized by a wide spectrum of pre- and post-axial abnormalities due to altered SHH

expression pattern during limb development. TPTPS mutations have been mapped to the 7q36 locus in the LMBR1 gene which

contains in its intron 5 a long-range cis-regulatory element of SHH expression

10/15 Novoseek disease relationships for SHH gene (see all 15)

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
holoprosencephaly	94.3	16	10594002 (2), 11479728 (2), 10441331 (1), 15107988 (1) (see all 13)
cyclopia	82.8	1	16282375 (1)
semilobar holoprosencephaly	73.4	2	17556830 (2)
polydactyly	70.7	4	17300775 (1), 9600232 (1), 18178536 (1)
cleft lip	62.8	1	11112334 (1)
smith-lemli-opitz syndrome	59.8	1	10799401 (1)
microcephaly	55.9	1	15107988 (1)
carcinoma basal cell	49.9	2	10504535 (1), 15547729 (1)
craniofacial anomaly	47.9	1	11460262 (1)
mental retardation	28.1	1	15107988 (1)

About this table

0 PharmGKB disease relationship for SHH gene

Disease	PharmGKB Relations	PubMed IDs for articles supporting these relationships
Abnormalities, Drug-Induced	PD	15546153

About this table

GeneTests: SHH

Holoprosencephaly

Human Gene Mutation Database (HGMD): SHH
Genetic Association Database (GAD): SHH
Human Genome Epidemiology (HuGE) Navigator: SHH (11 documents)

Export disorders and mutations for SHH gene to outside databases

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶UniProtKB/TrEMBL, and/or ⁷Novoseek)
About This Section

10/300 PubMed articles for SHH gene, integrated from 7 sources (see all 300):
(articles sorted by number of sources associating them with SHH)

Cloning, expression, and chromosomal location of SHH and IHH: two human homologues of the Drosophila segment polarity gene hedgehog. (PubMed id 7590746)^{1, 2, 3, 7} Marigo V.... Tabin C. (1995)
SONIC HEDGEHOG mutations causing human holoprosencephaly impair neural patterning activity. (PubMed id 12709790)^{1, 4, 7} Schell-Apacik C....Ming J.E. (2003)
Expression of the Sonic hedgehog (SHH) gene during early human development and phenotypic expression of new mutations causing holoprosencephaly. (PubMed id 10441331)^{1, 2, 7} Odent S....Vekemans M. (1999)
The mutational spectrum of the sonic hedgehog gene in holoprosencephaly: SHH mutations cause a significant proportion of autosomal dominant holoprosencephaly. (PubMed id 10556296)^{1, 2, 7} Nanni L.... Muenke M. (1999)
The mutational spectrum of holoprosencephaly-associat ed changes within the SHH gene in humans predicts loss-of-function through eith er key structural alterations of the ligand or its altered synthesis. (PubMed id 19603532)^{1, 2, 7} Roessler E....Muenke M. (2009)
Molecular mechanisms of Sonic hedgehog mutant effects in holoprosencephaly. (PubMed id 16282375)^{1, 2, 7} Maity T.... Beachy P.A. (2005)
Molecular screening of SHH, ZIC2, SIX3, and TGIF genes in patients with features of holoprosencephaly spectrum: mutation review and genotype-phenotype correlations. (PubMed id 15221788)^{1, 2, 7} Dubourg C.... David V. (2004)
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)^{1, 2} Liu T.... Smith R.D. (2005)
Mutation analysis of the Sonic hedgehog promoter and putative enhancer elements in Parkinson's disease patients. (PubMed id 15249145)^{1, 4} Bak M....Tommerup N. (2004)
Novel mutation in sonic hedgehog in non-syndromic colobomatous microphthalmia. (PubMed id 12503095)^{1, 2} Schimmenti L.A.... Muenke M. (2003)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 6469	HGNC: 10848	AceView: SHH	Ensembl:ENSG00000164690	euGenes: HUgn6469
ECgene: SHH	Kegg: 6469	H-InvDB: SHH

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
ATLAS Chromosomes in Cancer entry for SHH	Genetics and Cytogenetics in Oncology and Haematology
GeneReviews	http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SHH
NIEHS-SNPs	http://egp.gs.washington.edu/data/shh/

Intellectual Property for SHH gene
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Patent Information for SHH gene:
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GeneCards and IP:
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