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General Information
Symbol
Dmel\opa
Species
D. melanogaster
Name
odd paired
Annotation Symbol
CG1133
Feature Type
FlyBase ID
FBgn0003002
Gene Model Status
Stock Availability
Gene Snapshot
odd paired (opa) encodes a transcription factor that acts as a pair rule gene during early embryogenesis, as well as being involved in midgut morphogenesis. After embryogenesis, it contributes to adult head morphogenesis, neural stem cell development, and circadian rhythm. [Date last reviewed: 2018-09-20]
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:4,852,813..4,869,979 [+]
Recombination map

3-47.1

RefSeq locus
NT_033777 REGION:4852813..4869979
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (12 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with FLYBASE:ci; FB:FBgn0004859
inferred from sequence or structural similarity with HGNC:4319
inferred from biological aspect of ancestor with PANTHER:PTN001803442
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001803442
(assigned by GO_Central )
Biological Process (6 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from expression pattern
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002500429
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001803442
(assigned by GO_Central )
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001803442
(assigned by GO_Central )
Protein Family (UniProt)
Belongs to the GLI C2H2-type zinc-finger protein family. (P39768)
Summaries
Gene Group (FlyBase)
C2H2 ZINC FINGER TRANSCRIPTION FACTORS -
Zinc finger C2H2 transcription factors are sequence-specific DNA binding proteins that regulate transcription. They possess DNA-binding domains that are formed from repeated Cys2His2 zinc finger motifs. (Adapted from PMID:1835093, FBrf0220103 and FBrf0155739).
Protein Function (UniProtKB)
Transcription factor essential for parasegmental subdivision of the embryo. It is involved in the activation of wingless (wg) in odd parasegments. It is also required for the timely activation of wg in the remaining parasegments and for the timely activation of engrailed (en) in all parasegments.
(UniProt, P39768)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
opa: odd paired
Deletes alternate metasegments, as defined by a line separating the anterior from the posterior parts of the anterior compartments; portions of denticle bands of T2, A1, A3, A5, and A7 and naked cuticle of T3, A2, A4 and A6 missing. Pattern of Ubx protein distribution in the double-sized units reveals them to be composite, the anterior half being derived from an odd-numbered parasegment and the posterior half from an even-numbered parasegment (read metasegment) (Ingham and Martinez-Arias, Nature 324: 592-97). Without discernable effect on ftz expression (Carrol and Scott, 1980, Cell 45: 113-26). However, exhibits loss of en product with a consequent increase in Ubx expression in even-numbered parasegments (Martinez-Arias and White, 1988, Development 102: 325-38).
Summary (Interactive Fly)

transcription factor - zinc finger - pair rule gene - required for the timely activation of and during segmentation - controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\opa or the JBrowse view of Dmel\opa 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 5.49

gene_with_stop_codon_read_through ; SO:0000697

Stop-codon suppression (UGA) postulated; FBrf0243886.

Gene model reviewed during 6.32

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0078836
2939
609
FBtr0479794
2939
688
Additional Transcript Data and Comments
Reported size (kB)

3.0 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0078477
66.2
609
8.42
FBpp0428127
74.8
688
7.57
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)

609 (aa); 66 (kD predicted)

Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\opa using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
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
organism

Comment: maternally deposited

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

opa is expressed in a broad domain encompassing the entire segmented region of the embryo during stages 5-9. At stage 5, expression extends from 16%-78% egg length in ventrally located cells fated to become mesoderm and in dorsally located ectodermal cells. During gastrulation, expression becomes periodic, showing 14 stripes. By late stage 9, expression is no longer seen in the ectoderm or the mesoderm with the exception of a small number of cells in the neurogenic region, the tip of the germ band, and the head. Late in stage 11, opa expression initiates in the visceral mesoderm in seven discrete clusters of cells, arranged in two groups. In stage 12, expression becomes continuous in each region yielding at stage 13, two distinct domains of expression in the visceral mesoderm. The anterior domain corresponds to parasegment 5 and the posterior domain to parasegments 9-12. During stage 15, the 2nd midgut constriction forms between the opa expression domains. At stage 16, the first midgut constriction forms at the posterior boundary of the anterior opa expression domain and the third midgut constriction forms within the anterior margin of the posterior opa expression domain.

opa transcripts are detected in embryonic, larval, and pupal stages with peak levels between 2 and 12 hours of embryogenesis. opa transcripts are first detected in early stage 5 embryos in a 10 cell wide stripe at about 80% egg length. Expression extends posteriorly and becomes uniform over the region from 20% to 80% egg length with the posterior border being more sharply defined than the anterior border. Expression continues in this domain through gastrulation. During germ band extension, a pattern of 14 stripes develops over a low background level of expression.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

opa protein ispresent in a block from 20% to 80% egg length during cellularization andinto gastrulation. During germ band extension, a pattern of 14 stripesdevelops over a low background level of expression.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
Reporter: P{GAL4}opaGAL4
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\opa 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) 4-6
  • Stages(s) 7-8
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 34 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of opa
Transgenic constructs containing regulatory region of opa
Deletions and Duplications ( 13 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (11)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
9 of 15
Yes
Yes
9 of 15
Yes
Yes
7 of 15
No
Yes
7 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (7)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
9 of 15
Yes
Yes
8 of 15
No
Yes
7 of 15
No
Yes
7 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (9)
8 of 13
Yes
Yes
5 of 13
No
Yes
4 of 13
No
Yes
2 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (7)
8 of 12
Yes
Yes
8 of 12
Yes
Yes
5 of 12
No
Yes
5 of 12
No
Yes
3 of 12
No
Yes
1 of 12
No
No
1 of 12
No
Yes
Danio rerio (Zebrafish) (7)
9 of 15
Yes
Yes
8 of 15
No
Yes
8 of 15
No
Yes
8 of 15
No
Yes
7 of 15
No
Yes
7 of 15
No
Yes
5 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
8 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
2 of 15
Yes
Yes
1 of 15
No
Yes
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
1 of 12
Yes
Yes
1 of 12
Yes
No
1 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190AG9 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
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) ( EOG09150A77 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09Z6 )
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) ( EOG090X09UZ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
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) ( EOG091G0M59 )
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
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (3)
3 of 10
2 of 10
1 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 ( 3 )
    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.
    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 (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map

    3-47.1

    Cytogenetic map
    Sequence location
    3R:4,852,813..4,869,979 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    82D8-82E1
    Limits computationally determined from genome sequence between P{PZ}l(3)0273302733 and P{EP}EP974
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (12)
    Genomic Clones (27)
    cDNA Clones (29)
     

    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
    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
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of

    Source for identity of: opa CG1133

    Source for database merge of
    Additional comments
    Other Comments

    One of 42 Drosophila genes identified as being most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to human Mental Retardation disorders.

    Mutants exhibit pair-rule pattern defects.

    opa is required for formation of the three characteristic midgut constrictions. At the locations of the first and third constrictions, opa is positively regulated by Antp and abd-A, respectively, and negatively regulated by Ubx and dpp.

    opa activity is essential for the appropriate level and timing of en and wg expression in all parasegments, but does not determine their restricted spatial domains of expression.

    Deletes alternate metasegments, as defined by a line separating the anterior from the posterior parts of the anterior compartments; portions of denticle bands of T2, A1, A3, A5 and A7 and naked cuticle of T3, A2, A4 and A6 missing.

    Mutant analysis shows that wild type opa function is required to set up expression of ac in row B of the embryonic proneural cluster.

    Mutations in zygotic pair rule gene opa interact with RpII140wimp.

    The transition of prd RNA expression from the early 'pair-rule' pattern to the 'segment-polarity' pattern is regulated by the secondary pair-rule genes opa and odd.

    Genetic analysis demonstrates that opa is dispensable for efficient homeotic gene expression in the visceral mesoderm.

    opa mutants display pair-rule segmentation defects.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 39 )
    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
    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
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    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
    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 (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (8)
    Reported As
    Secondary FlyBase IDs
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (172)