FB2020_06, released Dec 22, 2020

Gene: Dmel\Or42a

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General Information
Symbol
Dmel\Or42a
Species
D. melanogaster
Name
Odorant receptor 42a
Annotation Symbol
CG17250
Feature Type
protein_coding_gene
FlyBase ID
FBgn0033041
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Snapshot
Odorant receptor 42a (Or42a) encodes a multi-transmembrane chemoreceptor that mediates response to volatile chemicals. [Date last reviewed: 2019-03-14]
Other Summaries
Also Known As

42a

Key Links
Genomic Location
Cytogenetic map
41F11-41F11
Sequence location
2R:5,791,441..5,792,967 [-]
Recombination map

2-55

RefSeq locus
NT_033778 REGION:5791441..5792967
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (7 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables odorant binding
inferred from sequence or structural similarity with FLYBASE:Or43b; FB:FBgn0026393
(FlyBase Curators, 2008--)
enables olfactory receptor activity
inferred from biological aspect of ancestor with PANTHER:PTN000474402
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in detection of chemical stimulus involved in sensory perception of smell
inferred from mutant phenotype
(Kreher et al., 2005)
involved_in olfactory behavior
inferred from mutant phenotype
(Syed et al., 2011, Fishilevich et al., 2005)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in detection of chemical stimulus involved in sensory perception of smell
inferred from biological aspect of ancestor with PANTHER:PTN000474402
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
located_in dendrite membrane
inferred from sequence or structural similarity with FLYBASE:Or22a; FB:FBgn0026398
(FlyBase Curators, 2008--)
located_in integral component of membrane
inferred from biological aspect of ancestor with PANTHER:PTN000474402
(assigned by GO_Central )
(Gaudet et al., 2011)
located_in plasma membrane
inferred from biological aspect of ancestor with PANTHER:PTN000474402
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the insect chemoreceptor superfamily. Heteromeric odorant receptor channel (TC 1.A.69) family. Or2a subfamily. (Q9V9I2)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
ODORANT RECEPTORS -
Insect odorant receptors (ORs) are a family of chemoreceptors activated by volatile chemicals. ORs form heteromeric complexes, believed to function as non-selective cation channels, comprising an OR and the co-receptor Orco. ORs are expressed in the dendrites of subsets of olfactory neurons in the antenna and maxillary palp. (Adapted from FBrf0168007 and FBrf0220463).
Protein Function (UniProtKB)
Odorant receptor which mediates acceptance or avoidance behavior, depending on its substrates. The odorant receptor repertoire encodes a large collection of odor stimuli that vary widely in identity, intensity, and duration. May form a complex with Orco to form odorant-sensing units, providing sensitive and prolonged odorant signaling and calcium permeability. Involved in the behavioral responses to butanol, ethyl acetate, propyl acetate, and pentyl acetate. Responds also to pyrazines.
(UniProt, Q9V9I2)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Or42a 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 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Or42a-RA
FBtr0086052
NM_078898
1280
406
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
Or42a-PA
FBpp0085388
46.9
406
8.18
NP_523622
AAF57307
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Orco. Complexes exist early in the endomembrane system in olfactory sensory neurons (OSNs), coupling these complexes to the conserved ciliary trafficking pathway (By similarity).

(UniProt, Q9V9I2)
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\Or42a 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
adult stage
maxillary palp olfactory receptor neuron | subset
(Goldman et al., 2005)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
Reporter: P{Or42a-GAL4.C}
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult olfactory receptor neuron Or42a
(Couto et al., 2005)
antennal lobe glomerulus VM7
(Couto et al., 2005)
Reporter: P{Or42a-GAL4.F}
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult olfactory receptor neuron Or42a
(Fishilevich and Vosshall, 2005)
antennal lobe glomerulus VM7
(Fishilevich and Vosshall, 2005)
larval stage
larval olfactory receptor neuron Or42a
(Masuda-Nakagawa et al., 2009)
larval antennal lobe glomerulus 42a
(Masuda-Nakagawa et al., 2009)
Reporter: P{Or42a-GAL4.G}
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
maxillary palp olfactory receptor neuron of maxillary palp basiconic sensillum pb1
(Goldman et al., 2005)
maxillary palp olfactory receptor neuron | subset
(Kreher et al., 2005)
adult olfactory receptor neuron Or42a
(Bai et al., 2009)
larval stage
olfactory receptor neuron of dorsal organ
(Kreher et al., 2005)
olfactory receptor neuron of terminal organ
(Kreher et al., 2005)
olfactory receptor neuron of embryonic/larval antennal lobe
(Kreher et al., 2005)
Reporter: P{Or42a-GAL4.W}
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult olfactory receptor neuron Or42a
(Komiyama et al., 2004)
antennal lobe glomerulus VM7
(Komiyama et al., 2004)
Reporter: P{Or42a-Mmus\Cd8a.GFP}
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult olfactory receptor neuron Or42a
(Couto et al., 2005)
antennal lobe glomerulus VM7
(Couto et al., 2005)
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Or42a in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Or42a
Transgenic constructs containing regulatory region of Or42a
Deletions and Duplications ( 0 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (0)
No records found.
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (0)
No records found.
Rattus norvegicus (Norway rat) (0)
No records found.
Xenopus tropicalis (Western clawed frog) (0)
No records found.
Danio rerio (Zebrafish) (0)
No records found.
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
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) ( EOG09190BUJ )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00012326
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00012327
Drosophila simulans
Dsim\GD10348
Drosophila sechellia
Dsec\GM16497
Drosophila erecta
Dere\GG10847
Drosophila yakuba
Dyak\GE11311
Drosophila ananassae
Dana\GF11032
Drosophila pseudoobscura pseudoobscura
Dpse\Or42a1
Drosophila pseudoobscura pseudoobscura
Dpse\Or42a2
Drosophila persimilis
Dper\GL20052
Drosophila persimilis
Dper\GL20053
Drosophila willistoni
Dwil\GK21762
Drosophila virilis
Dvir\GJ15103
Drosophila virilis
Dvir\GJ17804
Drosophila mojavensis
Dmoj\GI19947
Drosophila mojavensis
Dmoj\GI19935
Drosophila grimshawi
Dgri\GH21457
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091505DX )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Mayetiola destructor
Hessian fly
Mdes\Mdes019577
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W05AY )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Tribolium castaneum
Red flour beetle
Tcas\Or50
Tribolium castaneum
Red flour beetle
Tcas\Or34
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0573 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Tetranychus urticae
Two-spotted spider mite
Turt\tetur08g00530
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (59)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Or7a
3 of 10
Or22a
3 of 10
Or22b
3 of 10
Or42b
3 of 10
Or59b
3 of 10
Or1a
2 of 10
Or2a
2 of 10
Or9a
2 of 10
Or10a
2 of 10
Or13a
2 of 10
Or19a
2 of 10
Or19b
2 of 10
Or22c
2 of 10
Or23a
2 of 10
Or24a
2 of 10
Or30a
2 of 10
Or33a
2 of 10
Or33b
2 of 10
Or33c
2 of 10
Or35a
2 of 10
Or43a
2 of 10
Or43b
2 of 10
Or45a
2 of 10
Or45b
2 of 10
Or46a
2 of 10
Or47a
2 of 10
Or47b
2 of 10
Or49a
2 of 10
Or49b
2 of 10
Or59a
2 of 10
Or59c
2 of 10
Or63a
2 of 10
Or65a
2 of 10
Or65b
2 of 10
Or65c
2 of 10
Or67a
2 of 10
Or67b
2 of 10
Or67c
2 of 10
Or67d
2 of 10
Or69a
2 of 10
Or71a
2 of 10
Or74a
2 of 10
Or82a
2 of 10
Or83c
2 of 10
Or85a
2 of 10
Or85b
2 of 10
Or85c
2 of 10
Or85d
2 of 10
Or85f
2 of 10
Or88a
2 of 10
Or92a
2 of 10
Or94a
2 of 10
Or94b
2 of 10
Or98a
2 of 10
Or56a
1 of 10
Or83a
1 of 10
Or85e
1 of 10
Or98b
1 of 10
Orco
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 ( 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
    Interactions Browser
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement
    View in Interactions Browser
    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
    pdm3
    suppressible
    Or42a
    (Tichy et al., 2008)
    External Data
    Subunit Structure (UniProtKB)
    Interacts with Orco. Complexes exist early in the endomembrane system in olfactory sensory neurons (OSNs), coupling these complexes to the conserved ciliary trafficking pathway (By similarity).
    (UniProt, Q9V9I2 )
    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.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map

    2-55

    Cytogenetic map
    41F11-41F11
    Sequence location
    2R:5,791,441..5,792,967 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    41F11-41F11
    Limits computationally determined from genome sequence between P{PZ}l(2)0985109851&P{lacW}Src42Ak10108 and P{lacW}l(2)k09848k09848&P{EP}EP407
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-55

    (FlyBase, 2016)

    2-55.7

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (20)
    cDNA Clones (2)
     

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

        Source for identity of: Or42a CG17250

        (Warr and Vosshall, 2000.5.19)
        Source for database merge of
        Additional comments
        Other Comments

        Or42a is both necessary and sufficient for larval chemotaxis to several odours.

        (Fishilevich et al., 2005)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 21 )
        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
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        Flygut - An atlas of the Drosophila adult midgut
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        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
        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
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        Synonyms and Secondary IDs (8)
        Reported As
        Symbol Synonym
        41E.2
        (Warr and Vosshall, 2000.5.19)
        42a
        (Masuda-Nakagawa et al., 2009, Vogt et al., 2002)
        CG17250
        (Zhang et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Robertson, 2009)
        DOR117
        (Warr and Vosshall, 2000.5.19)
        OR42a
        (Störtkuhl and Fiala, 2011, Stocker, 2006)
        Or42A
        (Markstein et al., 2008)
        Or42a
        (Chepurwar et al., 2019, Golovin et al., 2019, Li et al., 2019, Si et al., 2019, Tastekin et al., 2018, Utashiro et al., 2018, Grabe et al., 2016, Newquist et al., 2016, Dweck et al., 2015, Hernandez-Nunez et al., 2015, Mansourian and Stensmyr, 2015, Grewal et al., 2014, Martin et al., 2013, Carey and Carlson, 2011, Endo et al., 2011, Gomez-Marin et al., 2011, Hartl et al., 2011, Hoare et al., 2011, Montague et al., 2011, Nagel and Wilson, 2011, Nagel and Wilson, 2011, Störtkuhl and Fiala, 2011, Syed et al., 2011, Tom et al., 2011, de Bruyne et al., 2010, Galizia et al., 2010, Guo and Kim, 2010, Larkin et al., 2010, Marshall et al., 2010, Olsen et al., 2010, Asahina et al., 2009, Bai et al., 2009, Masuda-Nakagawa et al., 2009, Robertson, 2009, Zhou et al., 2009, Asahina et al., 2008, Cayirlioglu et al., 2008, Chen and Hing, 2008, Hoare et al., 2008, Inomata et al., 2008, Kreher et al., 2008, Louis et al., 2008, Ray et al., 2008, Sambandan et al., 2008, Tichy et al., 2008, Lattemann et al., 2007, McBride et al., 2007, Olsen et al., 2007, Tunstall et al., 2007, de Bruyne and Warr, 2006, Stocker, 2006, Goldman et al., 2005, Kreher et al., 2005, Komiyama et al., 2004, Robertson et al., 2003)
        Name Synonyms
        Odorant receptor 42a
        Secondary FlyBase IDs
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (109)