FB2020_01, released Feb 12, 2020

Gene: Dmel\Cap-D3

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General Information
Symbol
Dmel\Cap-D3
Species
D. melanogaster
Name
Chromosome associated protein D3
Annotation Symbol
CG31989
Feature Type
protein_coding_gene
FlyBase ID
FBgn0051989
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Snapshot
In progress.Contributions welcome.
Other Summaries
Also Known As

dCap-D3

Key Links
Genomic Location
Cytogenetic map
25E5-25E5
Sequence location
2L:5,525,905..5,535,958 [+]
Recombination map

2-17

RefSeq locus
NT_033779 REGION:5525905..5535958
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 Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
chromatin binding
Predictions / Assertions
chromatin binding; histone binding; methylated histone binding
Summaries
Gene Group (FlyBase)
CONDENSIN II -
In D.mel, the existence of a condensin II complex is disputed as no CAP-G2 subunit or equivalent has been identified. However, the condensin II subunit orthologs have been implicated in various aspects of chromosome organisation. (Adapted from FBrf0191647 and FBrf0225011).
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\Cap-D3 or the JBrowse view of Dmel\Cap-D3 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 5.52

Low-frequency RNA-Seq exon junction(s) not annotated.

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Cap-D3-RA
FBtr0079097
NM_135091
4049
1267
Cap-D3-RB
FBtr0301318
NM_001169416
3960
1267
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
Cap-D3-PA
FBpp0078730
145.2
1267
6.60
NP_608935
AAF52258
Cap-D3-PB
FBpp0290533
145.2
1267
6.60
NP_001162887
ACZ94178
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1267 aa isoforms: Cap-D3-PA, Cap-D3-PB
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\Cap-D3 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 (15 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
chromatin binding
inferred from direct assay
(Schuster et al., 2013)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
chromatin binding
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
histone binding
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
methylated histone binding
inferred from sequence or structural similarity with HGNC:28952
(FlyBase Curators, 2008--)
Biological Process (7 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
chromosome organization
inferred from mutant phenotype
(Hartl et al., 2008)
chromosome separation
inferred from genetic interaction with FLYBASE:Cap-H2; FB:FBgn0037831
(Smith et al., 2013)
male meiosis chromosome segregation
inferred from mutant phenotype
(Hartl et al., 2008)
negative regulation of mitotic recombination
inferred from mutant phenotype
(Schuster et al., 2013)
regulation of DNA double-strand break processing
inferred from mutant phenotype
(Schuster et al., 2013)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
chromosome separation
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
meiotic chromosome condensation
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
mitotic chromosome condensation
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
colocalizes_with chromosome, centromeric region
inferred from direct assay
(Savvidou et al., 2005)
nucleus
inferred from direct assay
(Longworth et al., 2012)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
condensed chromosome, centromeric region
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
condensin complex
inferred from sequence or structural similarity with HGNC:28952
(Ono et al., 2003)
nuclear condensin complex
inferred from biological aspect of ancestor with PANTHER:PTN000368592
(assigned by GO_Central )
(Gaudet et al., 2011)
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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
colocalizes_with chromosome, centromeric region
inferred from direct assay
(Savvidou et al., 2005)
nucleus
inferred from direct assay
(Longworth et al., 2012)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Cap-D3 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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 9 )
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 Cap-D3
Transgenic constructs containing regulatory region of Cap-D3
Deletions and Duplications ( 2 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
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\NCAPD3
5 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
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\Ncapd3
3 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Ncapd3
3 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\ncapd3
2 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\ncapd3
3 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\hcp-6
3 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT4G15890
1 of 9
Yes
Yes
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) ( EOG091901NA )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\Cap-D3
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00001078
Drosophila simulans
Dsim\GD15884
Drosophila sechellia
Dsec\GM18553
Drosophila erecta
Dere\GG25078
Drosophila yakuba
Dyak\GE25461
Drosophila ananassae
Dana\GF15146
Drosophila pseudoobscura pseudoobscura
Dpse\GA16597
Drosophila persimilis
Dper\GL25850
Drosophila willistoni
Dwil\GK15235
Drosophila virilis
Dvir\GJ19577
Drosophila mojavensis
Dmoj\GI17990
Drosophila grimshawi
Dgri\GH10294
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500M6 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17018662
Glossina morsitans
Tsetse fly
Gmor\GMOY003088
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07613
Mayetiola destructor
Hessian fly
Mdes\Mdes009517
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL011548
Anopheles darlingi
American malaria mosquito
Adar\ADAC006101
Anopheles gambiae
Malaria mosquito
Agam\AGAP004751
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002920
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002921
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002922
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00H7 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Apis florea
Little honeybee
Aflo\3223357540
Apis mellifera
Western honey bee
Amel\GB55826
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP13922
Bombus terrestris
Buff-tailed bumblebee
Bter\15215374
Linepithema humile
Argentine ant
Lhum\LH19553
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:002ae7
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG002349
Pediculus humanus
Human body louse
Phum\PHUM022270
Rhodnius prolixus
Kissing bug
Rpro\RPRC001053
Cimex lectularius
Bed bug
Clec\CLEC002500
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI000912
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_11512
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00G9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR000603
Ixodes scapularis
Black-legged tick
Isca\ISCW008216
Stegodyphus mimosarum
African social velvet spider
Smim\KFM81913.1
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_307894
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00PU )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_027171gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ncapd3
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_018926gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ncapd3-2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ncapd2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_010956gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ncapd2-2
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000005863
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000005985
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000025028
Gallus gallus
Domestic chicken
Ggal\NCAPD3
Gallus gallus
Domestic chicken
Ggal\NCAPD2
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Cap-D2
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 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?
    NCAPD3; non-SMC condensin II complex subunit D3
    5 of 15
    609276
      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
      View in Interactions Browser
      Please see the Physical Interaction reports below for full details
      protein-protein
      Physical Interaction
      Assay
      References
      Cap-D3 - Cap-H2
      anti tag coimmunoprecipitation, autoradiography
      (Herzog et al., 2013)
      Cap-D3 - Rbf
      anti tag coimmunoprecipitation, western blot
      (Longworth et al., 2008)
      Cap-D3 - barr
      anti tag coimmunoprecipitation, autoradiography
      (Herzog et al., 2013)
      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
      Cap-D3
      enhanceable
      Cap-H2
      (Hartl et al., 2008)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Cap-H2
      suppressible
      Cap-D3
      (Hartl et al., 2008)
      External Data
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      MIST (genetic) - An integrated Molecular Interaction Database
      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)
      2L
      Recombination map

      2-17

      Cytogenetic map
      25E5-25E5
      Sequence location
      2L:5,525,905..5,535,958 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      25E5-25E5
      Limits computationally determined from genome sequence between P{lacW}vrik05901&P{PZ}cype03771 and P{lacW}Hel25Ek11511
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      2-17

      (FlyBase, 2016)

      2-18.5

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (10)
      Genomic Clones (21)
      cDNA Clones (5)
       

      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
         

        polyclonal

        (Longworth et al., 2012)
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: Cap-D3 CG31989

        (Hartl, 2003.2.28, Ono et al., 2003)
        Source for database merge of

        Source for merge of: CG31989 BcDNA:RE74832

        (FlyBase, 1996-)
        Additional comments

        Source for merge of CG31989 BcDNA:RE74832 was a shared cDNA ( date:030728 ).

        (FlyBase Genome Annotators, 2002-2003, FlyBase, 1996-)
        Other Comments

        Cap-D3 is necessary for normal territory foromation. When it is compromised through mutation, chromatin is seemingly dispersed throughout the nucleus.

        (Hartl et al., 2008)

        Cap-D3 promotes disassembly of polytene structure into chromosomal components.

        (Hartl et al., 2008)

        Homozygous mutants are male sterile and carry polytene chromosomes in their nurse cell nuclei.

        (Hartl et al., 2006)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 43 )
        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
        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
        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
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (13)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (55)