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General Information
Symbol
Dmel\Chi
Species
D. melanogaster
Name
Chip
Annotation Symbol
CG3924
Feature Type
FlyBase ID
FBgn0013764
Gene Model Status
Stock Availability
Gene Snapshot
Chip (Chi) encodes a transcriptional co-factor that regulates gene expression. It contributes to the regulation of Notch signaling, leg development and axon guidance. [Date last reviewed: 2019-09-12]
Also Known As
dLdb, Ldb
Key Links
Genomic Location
Cytogenetic map
Sequence location
2R:24,031,538..24,033,943 [-]
Recombination map
2-106
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Gene Group (FlyBase)
WNT ENHANCEOSOME -
The Wnt enhanceosome complex binds to Wnt/wg-enhancer elements via the TCF/LEF protein, pan. In the absence nuclear β-catenin (arm), Wnt/wg-responsive genes are silenced by the repressor gro binding to the enhanceosome. Activation of the canonical Wnt signaling pathway leads to arm accumulation in the nucleus, incorporation into the enhanceosome and the stimulation of transcription. (Adapted from FBrf0235074 and FBrf0229654).
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Chi or the JBrowse view of Dmel\Chi 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.46
Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0072191
2156
577
FBtr0072192
2125
596
Additional Transcript Data and Comments
Reported size (kB)
2.2 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0072100
62.6
577
8.29
FBpp0072101
64.8
596
7.99
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Chi 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 (24 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:Bx; FB:FBgn0265598
inferred from physical interaction with FLYBASE:Iswi; FB:FBgn0011604
inferred from physical interaction with FLYBASE:tou; FB:FBgn0033636
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000822352
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR030174
(assigned by InterPro )
Biological Process (16 terms)
Terms Based on Experimental Evidence (12 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001623859
(assigned by GO_Central )
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
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Chi transcript is expressed in all developmental stages. Expression in early embryos (0-30 min) is tenfold higher than in later developmental stages.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Chi protein is detected in embryonic and larval cell nuclei. Staining is also detected along salivary gland chromosomes.
Chi is expressed in many cells surrounding the antennal lobe at 18hrs APF.
From early cellular blastoderm through the end of embryogenesis, Chi protein is detected in all nuclei, including pole cells. Nuclei of larval tissues, including fat body, imaginal discs, and salivary gland, also stain for Chi protein.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Chi 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
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 16 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 27 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Chi
Transgenic constructs containing regulatory region of Chi
Deletions and Duplications ( 14 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
 
12 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
11 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
9 of 13
Yes
Yes
9 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
9 of 12
Yes
Yes
6 of 12
No
Yes
Danio rerio (Zebrafish) (4)
11 of 15
Yes
Yes
11 of 15
Yes
Yes
8 of 15
No
Yes
2 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (4)
1 of 9
Yes
Yes
1 of 9
Yes
Yes
1 of 9
Yes
Yes
1 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (1)
2 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919060W )
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) ( EOG091503FN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W08AP )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
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
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
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0869 )
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
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) ( EOG091G0A0P )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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 ( 1 )
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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
    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
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-106
    Cytogenetic map
    Sequence location
    2R:24,031,538..24,033,943 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    60B5-60B5
    Limits computationally determined from genome sequence between P{lacW}Phmk07623&P{lacW}tsrk05633 and P{EP}EP503
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    60A-60A
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (17)
    Genomic Clones (13)
     

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

    cDNA Clones (227)
     

    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)
    Other 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
     
    monoclonal
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for identity of: Chi CG3924
    Source for database merge of
    Source for merge of: Chi Ldb
    Additional comments
    "Ldb" may correspond to "Chi".
    Other Comments
    Gene expression is increased in response to the presence of two copies of Scer\GAL4hs.PB.
    S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.
    tou, pnr and Chi co-operate during neural development.
    Ssdp interacts with Chi to regulate development.
    The ap :Chi complex may act as a tetramer.
    Chi has a role in segmentation.
    Chi is an essential cofactor for ap in the regulation of axon guidance.
    ap activity depends on the formation of a LIM homeodomain dimer bridged by a dimer of Chi cofactor.
    Chi has roles in wing development beyond mediating ap activity and regulating ct.
    Chi acts as a cofactor for ap in wing development.
    Lack and excess of Chi gene product cause the same phenotype as lack of ap function: dorsal to ventral transformations, generation of new wing margins, wing outgrowths.
    The normal function of ap in dorso-ventral compartmentalization in the wing requires the correct proportion of Chi and ap gene product.
    Chi is identified as a ubiquitously expressed gene whose protein product interacts with ap LIM domains in the yeast two-hybrid assay.
    Mutations in Chi show strong genetic interaction with ap. In spite of its generalized expression, lack of Chi function in genetic mosaics produces specific phenotypes identical to the phenotype of ap mutant clones; i.e., dorsoventral transformation, generation of new wing margins and wing outgrowths. Overexpression of Chi produces a new wing margin, but only where ap is expressed.
    Gene isolated in a screen of the second chromosome identifying mutants affecting disc morphology.
    In analogy to their vertebrate counterparts, the gene products of Bx, ap and Chi form a DNA-binding complex, that regulates wing development.
    Chi cooperates with different LIM domain proteins and other factors to structurally support enhancer-promoter interactions.
    Chi, but not mam, modulates expression of a gypsy insertion into Ubx. Chi and mam regulate ct alleles lacking gypsy insertions. sd, mam and Chi cooperate synergistically to regulate ct expression.
    Genetic analysis suggests that Chi is involved in facilitating long-distance communication between the wing margin enhancer and the promoter of ct.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 47 )
    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/TrEMBL - Automatically annotated and unreviewed 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
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    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
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    InterPro - A database of protein families, domains and functional sites
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    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
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    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
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (12)
    Reported As
    Secondary FlyBase IDs
    • FBgn0020536
    • FBgn0024338
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (145)