FB2019_06, released Dec 19, 2019

Gene: Dmel\ninaD

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General Information
Symbol
Dmel\ninaD
Species
D. melanogaster
Name
neither inactivation nor afterpotential D
Annotation Symbol
CG31783
Feature Type
protein_coding_gene
FlyBase ID
FBgn0002939
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Snapshot
neither inactivation nor afterpotential D (ninaD) encodes a scavenger receptor involved in carotenoid transport, light detection and rhodopsin biosynthesis. [Date last reviewed: 2019-09-19]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
36E3-36E3
Sequence location
2L:18,081,628..18,083,608 [+]
Recombination map
2-53
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
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
scavenger receptor activity
Predictions / Assertions
scavenger receptor activity
Summaries
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
ninaD (J.C. Hall)
Basic physiological and rhodopsin-depleted phenotypes like those of ninaB mutants (e.g. rhodopsin levels reduced in all three classes of photoreceptors); ninaD mutants can be rescued by dietary supplement of vitamin A and several other retinoids. Measurements of light-induced "quantum bumps" (the basic "units" of the photoreceptor potential) in ninaD2 (rhodopsin content, 10-2 X wild-type) showed these responses to be basically normal (implying that, since extensive inter-rhodopsin molecular interactions are likely to be extremely rare, such interactions are not necessary for generation and adaptation of the bumps); yet, bump amplitudes approximately 4X normal (Johnson and Pak, 1986).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\ninaD or the JBrowse view of Dmel\ninaD 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
Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
ninaD-RA
FBtr0081031
NM_165237
1727
513
ninaD-RB
FBtr0302454
NM_001201907
1342
415
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
ninaD-PA
FBpp0080584
57.8
513
4.63
NP_724087
AAN11179
ninaD-PB
FBpp0291642
47.0
415
4.61
NP_001188836
ADV37085
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
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\ninaD 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 (7 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
scavenger receptor activity
inferred from mutant phenotype
(Kiefer et al., 2002)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
scavenger receptor activity
inferred from sequence or structural similarity
(Kiefer et al., 2002)
Biological Process (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
carotenoid transport
inferred from mutant phenotype
(Kiefer et al., 2002)
phototransduction
inferred from mutant phenotype
(Wang and Montell, 2005, Montell, 1999)
phototransduction, UV
inferred from mutant phenotype
(Stephenson et al., 1983)
phototransduction, visible light
inferred from mutant phenotype
(Stephenson et al., 1983)
rhodopsin biosynthetic process
inferred from mutant phenotype
(Ozaki et al., 1993, Stephenson et al., 1983)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
carotenoid transport
inferred from sequence or structural similarity
(Kiefer et al., 2002)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
membrane
inferred from electronic annotation with InterPro:IPR002159
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
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
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
Reporter: P{ninaD-GAL4.W}
Stage
Tissue/Position (including subcellular localization)
Reference
larval stage
embryonic/larval anterior midgut
(Wang et al., 2009)
embryonic/larval posterior midgut | restricted
(Wang et al., 2009)
Reporter: P{ninaD-GFP.Y}
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
neuron | subset of adult brain
• nucleus
(Yang and O'Tousa, 2007)
adult optic lobe neuron
(Yang and O'Tousa, 2007)
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\ninaD 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
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) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of ninaD
Transgenic constructs containing regulatory region of ninaD
Deletions and Duplications ( 16 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\SCARB1
6 of 15
Yes
No
 
Hsap\CD36
2 of 15
No
No
Hsap\SCARB2
2 of 15
No
No
 
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Scarb1
6 of 15
Yes
No
Mmus\Cd36
2 of 15
No
No
Mmus\Scarb2
2 of 15
No
No
Rattus norvegicus (Norway rat) (6)
Rnor\Scarb1
5 of 13
Yes
No
Rnor\LOC103690020
2 of 13
No
No
Rnor\RGD1565355
2 of 13
No
No
Rnor\Scarb2
2 of 13
No
No
Rnor\Cd36
1 of 13
No
No
Rnor\LOC100365047
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
Xtro\scarb1
5 of 12
Yes
No
Xtro\cd36
2 of 12
No
No
Xtro\scarb2
2 of 12
No
No
Xtro\cd36l
1 of 12
No
Yes
Danio rerio (Zebrafish) (5)
Drer\scarb1
4 of 15
Yes
No
Drer\cd36
2 of 15
No
No
Drer\scarb2a
2 of 15
No
No
Drer\scarb2b
2 of 15
No
No
Drer\wu:fj81e10
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (6)
Cele\scav-2
5 of 15
Yes
No
Cele\scav-1
4 of 15
No
No
Cele\scav-3
4 of 15
No
No
Cele\scav-5
4 of 15
No
No
Cele\scav-4
3 of 15
No
No
Cele\scav-6
3 of 15
No
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.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091905BC )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\ninaD
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00001151
Drosophila simulans
Dsim\GD24127
Drosophila sechellia
Dsec\GM17262
Drosophila erecta
Dere\GG21104
Drosophila yakuba
Dyak\GE12810
Drosophila ananassae
Dana\GF14812
Drosophila pseudoobscura pseudoobscura
Dpse\GA16473
Drosophila persimilis
Dper\GL14664
Drosophila willistoni
Dwil\GK18172
Drosophila virilis
Dvir\GJ17710
Drosophila mojavensis
Dmoj\GI17938
Drosophila grimshawi
Dgri\GH11637
Drosophila grimshawi
Dgri\GH23396
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504W9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17010510
Glossina morsitans
Tsetse fly
Gmor\GMOY006978
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_05644
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W092C )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Danaus plexippus
Monarch butterfly
Dple\DPOGS202796-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL009292
Heliconius melpomene
Postman butterfly
Hmel\SCR-like8
Apis florea
Little honeybee
Aflo\2213826500
Apis florea
Little honeybee
Aflo\2498852308
Apis mellifera
Western honey bee
Amel\GB53014
Apis mellifera
Western honey bee
Amel\GB44045
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP10581
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP10514
Bombus terrestris
Buff-tailed bumblebee
Bter\15204853
Bombus terrestris
Buff-tailed bumblebee
Bter\15204798
Linepithema humile
Argentine ant
Lhum\LH26186
Linepithema humile
Argentine ant
Lhum\LH17139
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0021b5
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:002bbc
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG007445
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG011340
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_04900
Tribolium castaneum
Red flour beetle
Tcas\crq
Pediculus humanus
Human body louse
Phum\PHUM351630
Rhodnius prolixus
Kissing bug
Rpro\RPRC006308
Cimex lectularius
Bed bug
Clec\CLEC008007
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI009159
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01894
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X08YJ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR010651
Strigamia maritima
European centipede
Smar\SMAR002938
Ixodes scapularis
Black-legged tick
Isca\ISCW010934
Ixodes scapularis
Black-legged tick
Isca\ISCW002412
Ixodes scapularis
Black-legged tick
Isca\ISCW023721
Stegodyphus mimosarum
African social velvet spider
Smim\KFM77785.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM63982.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM69030.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM60893.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur10g02420
Tetranychus urticae
Two-spotted spider mite
Turt\tetur03g08040
Tetranychus urticae
Two-spotted spider mite
Turt\tetur04g08760
Tetranychus urticae
Two-spotted spider mite
Turt\tetur13g00340
Tetranychus urticae
Two-spotted spider mite
Turt\tetur09g00840
Tetranychus urticae
Two-spotted spider mite
Turt\tetur11g04660
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_120417
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_303164
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_303163
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_237864
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0E0V )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000015724
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (13)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG31741
5 of 10
CG40006
5 of 10
CG3829
4 of 10
CG7227
4 of 10
CG10345
4 of 10
crq
4 of 10
dsb
4 of 10
emp
4 of 10
pes
4 of 10
santa-maria
4 of 10
Snmp1
4 of 10
Snmp2
4 of 10
CG2736
3 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 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?
    SCARB1; scavenger receptor class B member 1
    6 of 15
    601040
       
      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
      ninaE
      suppressible
      ninaD
      (Voolstra et al., 2010)
      Snmp1
      suppressible
      ninaD
      (Gomez-Diaz et al., 2016)
      External Data
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      2L
      Recombination map
      2-53
      Cytogenetic map
      36E3-36E3
      Sequence location
      2L:18,081,628..18,083,608 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      36E3-36E3
      Limits computationally determined from genome sequence between P{lacW}Aac11k06710 and P{EP}CG10413EP2164
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location
      2-53
      (FlyBase, 2016)
      2-53.2
      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (6)
      Genomic Clones (16)
       

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

      cDNA Clones (4)
       

      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
        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 database merge of
        Source for merge of: ninaD CG31783
        (FlyBase, 1996-)
        Additional comments
        Source for merge of ninaD CG31783 was sequence comparison ( date:030120 ).
        (FlyBase Genome Annotators, 2002-2003, FlyBase, 1996-)
        Other Comments
        ninaB and ninaD are not required in the retina, and exclusive retinal expression of either ninaB or ninaD, or both genes simultaneously, does not support rhodopsin biogenesis. Neuron-specific expression of ninaB and ninaD allows for rhodopsin biogenesis.
        (Gu et al., 2004)
        Major opsin genes can be transcribed in the absence of carotenoid, or retinoid. Expression of mature opsin is extremely depressed by carotenoid deprivation. The chromophore 11-cis-3-hydroxyretinal accelerates the synthesis of opsin by inducing its maturation.
        (Ozaki et al., 1993)
        Not the same gene as the very closely linked Arr1 (which produces a 'phototransduction protein'); this was shown by sequencing coding exons of genomic DNA from ninaD2, ninaD3 and ninaD5, all of which exhibited wild-type arrestin sequences in these ORFs (Smith et al., 1990).
        Basic physiological and rhodopsin-depleted phenotypes like those of ninaB mutants (e.g. rhodopsin levels reduced in all three classes of photoreceptors); ninaD mutants can be rescued by dietary supplement of vitamin A and several other retinoids. Measurements of light-induced 'quantum bumps' (the basic 'units' of the photoreceptor potential) in ninaD2 (rhodopsin content, 10-2 X wild-type) showed these responses to be basically normal (implying that, since extensive inter-rhodopsin molecular interactions are likely to be extremely rare, such interactions are not necessary for generation and adaptation of the bumps); yet, bump amplitudes approximately 4X normal (Johnson and Pak, 1986).
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 42 )
        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
        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
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Synonyms and Secondary IDs (5)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (69)