FB2021_02, released April 13, 2021

Gene: Dmel\Npc2d

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General Information
Symbol
Dmel\Npc2d
Species
D. melanogaster
Name
Niemann-Pick type C-2d
Annotation Symbol
CG12813
Feature Type
protein_coding_gene
FlyBase ID
FBgn0037782
Gene Model Status
Current
Stock Availability
1 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
85F8-85F8
Sequence location
3R:10,055,356..10,056,083 [-]
Recombination map
3-49
RefSeq locus
NT_033777 REGION:10055356..10056083
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 (3 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables sterol binding
inferred from sequence or structural similarity with HGNC:14537
(Huang et al., 2007)
inferred from biological aspect of ancestor with PANTHER:PTN000139325
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in intracellular cholesterol transport
inferred from electronic annotation with InterPro:IPR033916
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
involved_in sterol transport
inferred from biological aspect of ancestor with PANTHER:PTN000139325
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with FLYBASE:Npc2a; FB:FBgn0031381
(Huang et al., 2007)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
MD-2-RELATED LIPID-RECOGNITION PROTEINS -
Myeloid differentiation factor-2-related lipid-recognition (ML) domain-containing proteins are a broadly classed as lipid-binding proteins and have been implicated in processes such as lipid metabolism and innate immunity. (Adapted from FBrf0218672.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Npc2d 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 5.48

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Npc2d-RA
FBtr0082202
NM_141718
661
173
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
Npc2d-PA
FBpp0081680
19.0
173
4.41
NP_649975
AAF54488
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
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\Npc2d 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
embryonic stage 13 -- 17
embryonic/larval salivary gland
(Huang et al., 2007)
Additional Descriptive Data

Npc2d transcript is detected only in the embryonic salivary glands.

(Huang et al., 2007)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Npc2d 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, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Npc2d
Transgenic constructs containing regulatory region of Npc2d
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)Exel6155
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
short lived | heat sensitive, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
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\NPC2
7 of 15
Yes
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
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\Npc2
7 of 15
Yes
No
Rattus norvegicus (Norway rat) (1)
Rnor\Npc2
6 of 13
Yes
No
Xenopus tropicalis (Western clawed frog) (1)
Xtro\npc2
6 of 12
Yes
No
Danio rerio (Zebrafish) (2)
Drer\npc2
7 of 15
Yes
No
Drer\zgc:193725
5 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\heh-1
6 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (5)
Atha\AT1G45015
1 of 9
Yes
Yes
Atha\AT2G16005
1 of 9
Yes
Yes
Atha\AT3G11780
1 of 9
Yes
Yes
Atha\AT3G44100
1 of 9
Yes
Yes
Atha\AT5G06480
1 of 9
Yes
Yes
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) ( EOG09190H5A )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00013029
Drosophila simulans
Dsim\GD20738
Drosophila sechellia
Dsec\GM26189
Drosophila erecta
Dere\GG17305
Drosophila yakuba
Dyak\GE24707
Drosophila ananassae
Dana\GF17136
Drosophila pseudoobscura pseudoobscura
Dpse\GA11826
Drosophila persimilis
Dper\GL27280
Drosophila willistoni
Dwil\GK12205
Drosophila willistoni
Dwil\GK12204
Drosophila virilis
Dvir\GJ10723
Drosophila mojavensis
Dmoj\GI24446
Drosophila grimshawi
Dgri\GH14070
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150FL4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17026642
Musca domestica
House fly
Mdoa\17026783
Musca domestica
House fly
Mdoa\17009353
Musca domestica
House fly
Mdoa\17025598
Musca domestica
House fly
Mdoa\17025844
Musca domestica
House fly
Mdoa\17027114
Musca domestica
House fly
Mdoa\17026623
Glossina morsitans
Tsetse fly
Gmor\GMOY007339
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_03645
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_03640
Mayetiola destructor
Hessian fly
Mdes\Mdes011129
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL009556
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL015140
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL015135
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL009557
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL009956
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL009555
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL009553
Anopheles darlingi
American malaria mosquito
Adar\ADAC007575
Anopheles darlingi
American malaria mosquito
Adar\ADAC005767
Anopheles darlingi
American malaria mosquito
Adar\ADAC006488
Anopheles gambiae
Malaria mosquito
Agam\AGAP007197
Anopheles gambiae
Malaria mosquito
Agam\AGAP002850
Anopheles gambiae
Malaria mosquito
Agam\AGAP002851
Anopheles gambiae
Malaria mosquito
Agam\AGAP002804
Anopheles gambiae
Malaria mosquito
Agam\AGAP002849
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002746
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013182
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ018326
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ012180
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013180
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0EZQ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA013039
Heliconius melpomene
Postman butterfly
Hmel\HMEL014057
Heliconius melpomene
Postman butterfly
Hmel\HMEL004150
Heliconius melpomene
Postman butterfly
Hmel\HMEL004151
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG012307
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI25260
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI084020
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0EZD )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_222083
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_221856
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) (7)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Npc2a
5 of 10
Npc2b
5 of 10
Npc2c
5 of 10
Npc2e
5 of 10
Npc2f
4 of 10
Npc2g
4 of 10
Npc2h
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 ( 1 )
    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?
    NPC2; NPC intracellular cholesterol transporter 2
    7 of 15
    601015
     
    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
    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.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-49
    Cytogenetic map
    85F8-85F8
    Sequence location
    3R:10,055,356..10,056,083 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    85F8-85F8
    Limits computationally determined from genome sequence between P{lacW}s2681 and P{EP}Fmr1EP3517&P{PZ}tws02414
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-49

    (FlyBase, 2016)

    3-46.6

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (1)
    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 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: Npc2d CG12813

        (Huang et al., 2007)
        Source for database merge of
        Additional comments
        Other Comments
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 23 )
        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 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
        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.
        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 (4)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (26)