Open Close
General Information
Symbol
Dmel\pip
Species
D. melanogaster
Name
pipe
Annotation Symbol
CG9614
Feature Type
FlyBase ID
FBgn0003089
Gene Model Status
Stock Availability
Gene Snapshot
pipe (pip) encodes a sulfotransferase that contributes to the formation and polarity of the embryonic dorsal-ventral axis. [Date last reviewed: 2019-03-14]
Key Links
Genomic Location
Cytogenetic map
Sequence location
3L:19,298,623..19,337,609 [-]
Recombination map

3-45

RefSeq locus
NT_037436 REGION:19298623..19337609
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (14 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:O44342
(assigned by UniProt )
inferred from mutant phenotype
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000951070
(assigned by GO_Central )
Biological Process (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
inferred from genetic interaction with FLYBASE:ea; FB:FBgn0000533
inferred from genetic interaction with FLYBASE:gd; FB:FBgn0000808
inferred from genetic interaction with FLYBASE:ndl; FB:FBgn0002926
inferred from genetic interaction with FLYBASE:wbl; FB:FBgn0004003
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in chromosome
inferred from direct assay
located_in Golgi apparatus
inferred from direct assay
located_in nucleus
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
non-traceable author statement
(assigned by UniProt )
inferred from electronic annotation with InterPro:IPR005331, InterPro:IPR007734
(assigned by InterPro )
Protein Family (UniProt)
Belongs to the sulfotransferase 3 family. (Q86BJ3)
Summaries
Gene Group (FlyBase)
DORSAL GROUP -
The Dorsal group genes encode components of the Toll pathway and were initially identified by maternal effect mutations resulting in the dorsalization of the embryo. (Adapted from FBrf0091014 and FBrf0223077).
OTHER SULFOTRANSFERASES -
Other sulfotransferases is a collection of transferases that do not fit into any of the other major sulfotransferases.
Pathway (FlyBase)
Extracellular Spatzle Activating Pathway Core Components -
In Drosophila, activation of the Toll pathway is controlled by the generation of a cleaved, active, Toll-binding form of spatzle ligand. Proteolytic activation of spatzle ligand lies downstream of several zymogen activation cascades that are initiated by different cues. In dorsal-ventral patterning, localized activation of spz results in ventral nuclear accumulation of dl. During viral and fungal and gram positive bacterial immune challenge, zymogen cascades are activated by extracellular pattern recognition receptors or virulence factor-mediated cleavage of the zymogen persephone (psh). (Adapted from FBrf0091014 and FBrf0223077).
Protein Function (UniProtKB)
Sulfotransferase involved in dorsoventral axis patterning in early embryos. Required for the specific ventral activation of a series of proteases acting in the perivitelline space between the embryonic membrane and the eggshell. Probably acts by mediating the sulfation of some glycoprotein or glycosaminoglycan stably deposited in the egg, whose ventrally localized modification leads to spatially restricted activation of the protease cascade.
(UniProt, Q86BJ3)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
pip: pipe
Maternal-effect lethal; homozygous females are sterile. As in the mutant dl, lethal embryos produced by pip females lack ventral and lateral elements; all cells differentiate like the dorsal-most cells of normal embryos (Anderson and Nusslein-Volhard, 1984). Dorsalization is also observed in the pattern of ftz stripes in pip embryos (Carroll et al., 1987). Embryos are not rescued by injection of wild-type cytoplasm; injection of cytoplasm from ventralized embryos of Tl5/+ females, however, partially restores the pip+ embryonic pattern, resulting in differentiation of filzkorper in 25-40% of the treated pip embryos (Anderson et al., 1985).
Summary (Interactive Fly)

heparan sulfate 2-O-sulfotransferase - functions in follicle cells to set up the spatially restricted signal responsible for activating the spatially delimited protease cascade triggering Toll and the establishment of dorsal/ventral polarity during early development.

Gene Model and Products
Number of Transcripts
11
Number of Unique Polypeptides
11

Please see the JBrowse view of Dmel\pip 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 5.43

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.46

Gene model reviewed during 5.55

Gene model reviewed during 6.25

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0075003
1724
413
FBtr0075004
1397
403
FBtr0075005
1509
418
FBtr0075007
1441
397
FBtr0075008
1614
407
FBtr0075009
1532
405
FBtr0075010
1377
358
FBtr0075011
1490
401
FBtr0075012
1478
406
FBtr0075013
1848
514
FBtr0333897
1845
513
Additional Transcript Data and Comments
Reported size (kB)

1.7, 1.5 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0074770
48.1
413
8.76
FBpp0074771
48.2
403
9.76
FBpp0074772
48.7
418
8.34
FBpp0074774
46.7
397
7.99
FBpp0074775
48.2
407
9.19
FBpp0074776
47.8
405
9.70
FBpp0074777
41.9
358
9.85
FBpp0074778
47.7
401
10.07
FBpp0074779
47.8
406
8.83
FBpp0074780
60.3
514
7.30
FBpp0306029
60.1
513
7.20
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)

403, 392 (aa)

Comments
External Data
Subunit Structure (UniProtKB)

Interacts directly with windbeutel (wbl).

(UniProt, Q86BJ3)
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\pip using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
salivary gland body primordium

Comment: reported as salivary gland anlage

salivary gland body primordium

Comment: reported as salivary gland primordium

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Use of isoform-specific oligonucleotides shows that all the major pip isoforms are abundantly expressed in embryos, presumably in salivary glands. Isoforms containing the first 7 alternative exons (after the 3 common amino-terminal exons) are detected in ovaries at a lower level.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
epitope tag
Stage
Tissue/Position (including subcellular localization)
Reference
immuno-electron microscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in chromosome
inferred from direct assay
located_in Golgi apparatus
inferred from direct assay
located_in nucleus
inferred from direct assay
Expression Deduced from Reporters
Reporter: P{pip-lacZ.5'}
Stage
Tissue/Position (including subcellular localization)
Reference
Stage
Tissue/Position (including subcellular localization)
Reference
adult brain

Comment: low expression throughout adult brain

High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\pip 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
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) 13-16
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 31 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of pip
Transgenic constructs containing regulatory region of pip
Aberrations (Deficiencies and Duplications) ( 27 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
5 of 15
Yes
Yes
2 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
5 of 15
Yes
Yes
2 of 15
No
No
Rattus norvegicus (Norway rat) (2)
4 of 13
Yes
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (1)
1 of 12
Yes
No
Danio rerio (Zebrafish) (3)
5 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
3 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091906Y2 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila sechellia
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091503ZC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W03RG )
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
Megachile rotundata
Alfalfa leafcutting bee
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G05MH )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
4 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    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
    DO term
    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 see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    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 directly with windbeutel (wbl).
    (UniProt, Q86BJ3 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Extracellular Spatzle Activating Pathway Core Components -
    In Drosophila, activation of the Toll pathway is controlled by the generation of a cleaved, active, Toll-binding form of spatzle ligand. Proteolytic activation of spatzle ligand lies downstream of several zymogen activation cascades that are initiated by different cues. In dorsal-ventral patterning, localized activation of spz results in ventral nuclear accumulation of dl. During viral and fungal and gram positive bacterial immune challenge, zymogen cascades are activated by extracellular pattern recognition receptors or virulence factor-mediated cleavage of the zymogen persephone (psh). (Adapted from FBrf0091014 and FBrf0223077).
    Metabolic Pathways
    External Data
    Linkouts
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map

    3-45

    Cytogenetic map
    Sequence location
    3L:19,298,623..19,337,609 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    76A5-76A6
    Limits computationally determined from genome sequence between P{EP}MESR6EP3142 and P{lacW}l(3)L3809L3809
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (15)
    Genomic Clones (28)
    cDNA Clones (86)
     

    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 sequenced
    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)
    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
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of
    Additional comments
    Other Comments

    pip may promote 6-0- and/or N-sulfation of heparan sulfate but is not required for heparan sulfate 2-0-sulfation.

    pip protein does not show any heparan sulfate-sulfotransferase or chondroitin sulfate-sulfotransferase activity in vitro.

    Embryonic extracts derived from a cross between pip mutant mothers and Oregon R males lack the 80 kD ea-Spn27A protein complex seen in wild type embryonic extracts.

    dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

    A follicular cell marker system that yields a visible phenotype within the mature egg shell allows direct comparison of a clone and its effect on the dorsal ventral pattern of the embryos. Wild type wbl activity is required only in the cells on the ventral side of the follicular epithelium and is restricted along the A/P axis.

    Double mutant combinations of pip with ea alleles demonstrate that spatial regulation of ea activity by localized zymogen activation is a key initial event in defining the polarity of the dorsal-ventral embryonic pattern.

    Strong dorsalizing mutants of ndl, snk, gd or pip have wild type axial ratios in pupae.

    Mutations in maternal dorsal class gene pip do not interact with RpII140wimp.

    Analysis of mosaic females indicates that the expression of ndl, pip and wbl is required in the somatic tissue, in the follicle cells that surround the oocyte, for the production of embryos with the correct dorsoventral axis.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 75 )
    Sequence 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
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DPiM - Drosophila Protein interaction map
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (6)
    Reported As
    Secondary FlyBase IDs
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (238)