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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 IDQualified GO termEvidencePubMed 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 IDQualified GO termEvidencePubMed IDs
    GO:0001948 glycoprotein binding IEA--
    GO:0004871 signal transducer activity IDA19561609
    GO:0005113 patched binding IEA--
    GO:0005509 calcium ion binding IDA19561609
    GO:0005515 protein binding IPI19561609
    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/neurologicalcardiovascular systemcellularcraniofacialdigestive/alimentary
    embryogenesisendocrine/exocrine glandgrowth/sizehearing/vestibular/earhomeostasis/metabolism
    lethality-postnatallethality-prenatal/perinatallife span-post-weaning/aginglimbs/digits/tailmuscle

    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 CentralTM Interacting Genes and Proteins Network for SHH

    5/20 Interacting proteins for SHH (ENSP000002972613) via UniProtKB, MINT, and/or STRING (see all 20)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BOCENSP000002733953STRING: ENSP00000273395
    CDONENSP000002635773STRING: ENSP00000263577
    FOXA1ENSP000002504483STRING: ENSP00000250448
    GLI2ENSP000003545863STRING: ENSP00000354586
    GPC3ENSP000003598543STRING: ENSP00000359854
    About this table

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

    GO IDQualified GO termEvidencePubMed 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
    CompoundAction CAS number
    SANT-1Inhibitor 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
    statinPD  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  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    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
    SHH gene expression
    SHH gene electronic northern expression
    SHH gene sage expression
    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)
    Shh1 , 5 5 (14.39 cM)5
    sonic hedgehog1, 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

    10/164 NCBI SNPs in SHH are shown (see all 164)
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidChr 7 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ----------
    rs2887451,2
    C,H,155606336(+) tttttA/Taaaaa 1 -- ng51 trp30--------
    rs2887461,2
    C,F,O,H,155606672(-) CCTCTT/CATGCC 1 -- ng5130Minor allele frequency- C:0.10NS EA NA MN WA 3036
    rs7568841,2
    C,F,H,155604099(+) ACAGTG/ACCAGG 1 -- int113Minor allele frequency- A:0.10NS NA WA 904
    rs8727231,2
    C,F,155605744(+) CTGCTC/TTTTTA 1 -- ng519Minor allele frequency- T:0.07NS EA NA WA 2120
    rs12335531,2
    C,F,155598145(+) GGGAAA/GCCTGG 1 -- int17Minor allele frequency- G:0.08NS MN NA WA 344
    rs12335541,2
    C,F,A,155598879(+) CAGCGC/ACCCTG 1 -- int116Minor allele frequency- A:0.21NA EA MN NS WA 2176
    rs12335551,2
    C,F,A,H,155599300(+) GGCAAT/CCGCCA 1 -- int15Minor allele frequency- C:0.47NS NA 1020
    rs12335561,2
    C,F,A,H,155600417(+) GGACAC/TGGGAT 1 -- int121Minor allele frequency- T:0.15NS EA NA WA 1646
    rs12335571,2
    C,F,155601653(+) CCCCAC/AGCTTG 1 -- int18Minor allele frequency- A:0.06NA NS EA WA 390
    rs12335611,2
    C,F,155603157(+) ACGCAC/ACGGGC 1 -- int17Minor allele frequency- A:0.06NS 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-InducedPD  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)
    1. 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)
    2. SONIC HEDGEHOG mutations causing human holoprosencephaly impair neural patterning activity. (PubMed id 12709790)1, 4, 7 Schell-Apacik C....Ming J.E. (2003)
    3. 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)
    4. 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)
    5. 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)
    6. Molecular mechanisms of Sonic hedgehog mutant effects in holoprosencephaly. (PubMed id 16282375)1, 2, 7 Maity T.... Beachy P.A. (2005)
    7. 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)
    8. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)1, 2 Liu T.... Smith R.D. (2005)
    9. 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)
    10. 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)
    About This Section
     ANDOR
    Aliases
    Disorders
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      Query String
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      (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)
    About This Section
    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)
    About This Section
    NameDescription
    ATLAS Chromosomes in Cancer entry for SHH Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SHH
    NIEHS-SNPshttp://egp.gs.washington.edu/data/shh/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from XenneX, Inc.)
    About This Section
    Patent Information for SHH gene:
    Search GeneIP for patents involving SHH

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