General Information
Symbol
Dmel\shf
Species
D. melanogaster
Name
shifted
Annotation Symbol
CG3135
Feature Type
FlyBase ID
FBgn0003390
Gene Model Status
Stock Availability
Gene Snapshot
Shifted is a secreted protein that positively modulates Hedgehog signaling. It controls the diffusion of lipid-modified hh protein by stabilizing its interaction with the heparan sulfate proteoglycans. [Date last reviewed: 2016-06-30]
Genomic Location
Cytogenetic map
Sequence location
X:6,771,463..6,779,659 [-]
Recombination map
1-18
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Molecular Function (see GO section for details)
Experimental Evidence
Predictions / Assertions
-
Summaries
Gene Group Membership
Positive Regulators of Hedgehog Signaling Pathway -
Positive regulators of hedgehog signaling down-regulation the pathway, enhancing the activation of transcription of hh-responsive genes.
UniProt Contributed Function Data
Required for normal accumulation and movement of lipid-modified hedgehog (hh) morphogen. May act by stabilizing the interaction between heparan sulfate proteoglycans (HSPGs) and hh, HSPGs being required for diffusion of hh morphogen. Not involved in wingless (wg) morphogen movement, suggesting that it may provide HSPG specificity for Hh.
(UniProt, Q9W3W5)
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
*shf: shifted
Vein L3 fails to reach wing margin and is shifted toward L4. Anterior crossvein usually lacking. Wings divergent. Postscutellar bristles small and erect. Body small. Viability 60% wild type. Female often sterile. RK2.
shf2
Veins closer together than in wild type. L3 and L4 tend to fuse near anterior crossvein; anterior crossvein shortened, knotted, or absent. Phenotypic effect visible in prepupal wing bud, the two longitudinal veins diverging at a smaller-than-normal angle [Waddington, 1940, J. Genet. 41: 75-139 (fig.)]. Eyes sometimes slightly rough. Scutellar bristles often absent. Scutellum short. Wings narrow and often warped downward. Fertility and viability good. RK2.
*shf3
thumb
shf3: shifted-3
From Bridges and Brehme, 1944, Carnegie Inst. Washington Publ. No. 552: 173.
Like shf2 but more extreme. Viability about 70% wild type. Frequently infertile. RK2.
shfov: shifted-oval
Eyes rough and narrow. First basal wing cell absent because L3 and L4 veins close. Wings narrow and pointed. Viability and fertility low. RK2.
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
4

Please see the GBrowse view of Dmel\shf or the JBrowse view of Dmel\shf for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Gene model reviewed during 5.50
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.55
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0070978
1784
456
FBtr0340088
1796
460
FBtr0340089
1733
439
FBtr0340090
1745
443
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0070939
50.7
456
8.85
FBpp0309087
51.1
460
8.80
FBpp0309088
49.0
439
8.95
FBpp0309089
49.3
443
8.90
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Interacts with hh.
(UniProt, Q9W3W5)
Crossreferences
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\shf using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (9 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:Q02936
(assigned by UniProt )
Terms Based on Predictions or Assertions (0 terms)
Biological Process (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
(assigned by UniProt )
inferred from genetic interaction with UniProtKB:P18502
(assigned by UniProt )
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
Terms Based on Predictions or Assertions (0 terms)
Expression Data
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
shf transcript is expressed in the wing disc in parts of the presumptive notum, and in the anterior and posterior edges of the wing pouch.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
shf protein has a distribution similar to that of shf transcript, and is localized to parts of the presumptive notum, to the presumptive wing hinge, and to the anterior and posterior edges of the wing pouch. The wing pouch expression is stronger at the anterior- and posterior-most edges, and more pronounced in the posterior compartment. Immunoreactivity appears to be associated with the cell surface.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\shf in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 11-12
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 11 )
For All Classical and Insertion Alleles Show
 
Allele of shf
Class
Mutagen
Associated Insertion
Stocks
Known lesion
    0
    Yes
      0
      --
      Other relevant insertions
      miscellaneous insertions
      Transgenic Constructs ( 14 )
      For All Alleles Carried on Transgenic Constructs Show
      Transgenic constructs containing/affecting coding region of shf
      Allele of shf
      Mutagen
      Associated Transgenic Construct
      Stocks
      Transgenic constructs containing regulatory region of shf
      Deletions and Duplications ( 13 )
      Summary of Phenotypes
      Orthologs
      Human Orthologs (via DIOPT v7.1)
      Homo sapiens (Human) (1)
      Species\Gene Symbol
      Score
      Best Score
      Best Reverse Score
      Alignment
      Complementation?
      Transgene?
      13 of 15
      Yes
      Yes
       
      Model Organism Orthologs (via DIOPT v7.1)
      Mus musculus (laboratory mouse) (1)
      Species\Gene Symbol
      Score
      Best Score
      Best Reverse Score
      Alignment
      Complementation?
      Transgene?
      12 of 15
      Yes
      Yes
      Rattus norvegicus (Norway rat) (2)
      11 of 13
      Yes
      Yes
      1 of 13
      No
      No
      Xenopus tropicalis (Western clawed frog) (2)
      9 of 12
      Yes
      Yes
      1 of 12
      No
      Yes
      Danio rerio (Zebrafish) (1)
      12 of 15
      Yes
      Yes
      Caenorhabditis elegans (Nematode, roundworm) (7)
      1 of 15
      Yes
      Yes
      1 of 15
      Yes
      Yes
      1 of 15
      Yes
      Yes
      1 of 15
      Yes
      No
      1 of 15
      Yes
      Yes
      1 of 15
      Yes
      No
      1 of 15
      Yes
      Yes
      Arabidopsis thaliana (thale-cress) (0)
      No orthologs reported.
      Saccharomyces cerevisiae (Brewer's yeast) (0)
      No orthologs reported.
      Schizosaccharomyces pombe (Fission yeast) (0)
      No orthologs reported.
      Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919073G )
      Organism
      Common Name
      Gene
      AAA Syntenic Ortholog
      Multiple Dmel Genes in this Orthologous Group
      Drosophila melanogaster
      fruit fly
      Drosophila suzukii
      Spotted wing Drosophila
      Drosophila simulans
      Drosophila sechellia
      Drosophila erecta
      Drosophila yakuba
      Drosophila ananassae
      Drosophila pseudoobscura pseudoobscura
      Drosophila persimilis
      Drosophila willistoni
      Drosophila virilis
      Drosophila mojavensis
      Drosophila grimshawi
      Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091505W0 )
      Organism
      Common Name
      Gene
      Multiple Dmel Genes in this Orthologous Group
      Musca domestica
      House fly
      Glossina morsitans
      Tsetse fly
      Lucilia cuprina
      Australian sheep blowfly
      Mayetiola destructor
      Hessian fly
      Aedes aegypti
      Yellow fever mosquito
      Anopheles darlingi
      American malaria mosquito
      Anopheles gambiae
      Malaria mosquito
      Culex quinquefasciatus
      Southern house mosquito
      Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W05V0 )
      Organism
      Common Name
      Gene
      Multiple Dmel Genes in this Orthologous Group
      Bombyx mori
      Silkmoth
      Danaus plexippus
      Monarch butterfly
      Heliconius melpomene
      Postman butterfly
      Apis florea
      Little honeybee
      Apis mellifera
      Western honey bee
      Bombus impatiens
      Common eastern bumble bee
      Bombus terrestris
      Buff-tailed bumblebee
      Linepithema humile
      Argentine ant
      Linepithema humile
      Argentine ant
      Megachile rotundata
      Alfalfa leafcutting bee
      Nasonia vitripennis
      Parasitic wasp
      Dendroctonus ponderosae
      Mountain pine beetle
      Tribolium castaneum
      Red flour beetle
      Pediculus humanus
      Human body louse
      Rhodnius prolixus
      Kissing bug
      Cimex lectularius
      Bed bug
      Cimex lectularius
      Bed bug
      Acyrthosiphon pisum
      Pea aphid
      Zootermopsis nevadensis
      Nevada dampwood termite
      Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X05QS )
      Organism
      Common Name
      Gene
      Multiple Dmel Genes in this Orthologous Group
      Strigamia maritima
      European centipede
      Ixodes scapularis
      Black-legged tick
      Stegodyphus mimosarum
      African social velvet spider
      Tetranychus urticae
      Two-spotted spider mite
      Daphnia pulex
      Water flea
      Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G08T8 )
      Organism
      Common Name
      Gene
      Multiple Dmel Genes in this Orthologous Group
      Strongylocentrotus purpuratus
      Purple sea urchin
      Strongylocentrotus purpuratus
      Purple sea urchin
      Ciona intestinalis
      Vase tunicate
      Gallus gallus
      Domestic chicken
      Gallus gallus
      Domestic chicken
      Human Disease Model Data
      FlyBase Human Disease Model Reports
        Alleles Reported to Model Human Disease (Disease Ontology)
        Download
        Models ( 0 )
        Allele
        Disease
        Evidence
        References
        Interactions ( 0 )
        Allele
        Disease
        Interaction
        References
        Comments ( 0 )
         
        Human Orthologs (via DIOPT v7.1)
        Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
        Homo sapiens (Human)
        Gene name
        Score
        OMIM
        OMIM Phenotype
        Complementation?
        Transgene?
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        esyN Network Diagram
        Show neighbor-neighbor interactions:
        Select Layout:
        Legend:
        Protein
        RNA
        Selected Interactor(s)
        Interactions Browser

        Please look at the Interaction Group reports for full details of the physical interactions
        protein-protein
        Interacting group
        Assay
        References
        Summary of Genetic Interactions
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement

        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Interacts with hh.
        (UniProt, Q9W3W5 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        Pathways
        Gene Group - Pathway Membership (FlyBase)
        Positive Regulators of Hedgehog Signaling Pathway -
        Positive regulators of hedgehog signaling down-regulation the pathway, enhancing the activation of transcription of hh-responsive genes.
        External Data
        Linkouts
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        SignaLink - A signaling pathway resource with multi-layered regulatory networks.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        X
        Recombination map
        1-18
        Cytogenetic map
        Sequence location
        X:6,771,463..6,779,659 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        6C13-6D1
        Limits computationally determined from genome sequence between P{EP}Ctr1AEP1364&P{EP}EP1445 and P{EP}C3GEP1613
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Determined by deletion analysis (details unspecified).
        Experimentally Determined Recombination Data
        Location
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (6)
        Genomic Clones (9)
         

        Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

        cDNA Clones (21)
         

        Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

        cDNA clones, fully sequences
        BDGP DGC clones
        Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         
        polyclonal
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of
        Source for database merge of
        Source for merge of: shf CG3135
        Additional comments
        Other Comments
        Mutants display hyperplastic phenotype, with tissue overgrowth in mitotic recombination clones.
        Mutations in shf cause extra longitudinal or transverse veins with plexated vein phenotypes. kn, fu and shf act synergistically against Px, px, net, dsr and emc.
        Origin and Etymology
        Discoverer
        Bridges, Jan. 1913.
        Etymology
        Identification
        External Crossreferences and Linkouts ( 46 )
        Crossreferences
        NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
        GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
        GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        Linkouts
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
        DPiM - Drosophila Protein interaction map
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        FlyMine - An integrated database for Drosophila genomics
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        KEGG Genes - Molecular building blocks of life in the genomic space.
        modMine - A data warehouse for the modENCODE project
        SignaLink - A signaling pathway resource with multi-layered regulatory networks.
        Synonyms and Secondary IDs (12)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (83)