FlyBase Gene Report: Dmel\Cap-D3

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 Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

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

JBrowse GBrowse

Help me choose

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (14 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables chromatin binding

inferred from direct assay

(Schuster et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables histone binding

inferred from biological aspect of ancestor with PANTHER:PTN000368592

(assigned by GO_Central )

(Gaudet et al., 2011)

enables 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

involved_in chromosome organization

inferred from mutant phenotype

(Hartl et al., 2008)

involved_in chromosome separation

inferred from genetic interaction with FLYBASE:Cap-H2; FB:FBgn0037831

(Smith et al., 2013)

involved_in male meiosis chromosome segregation

inferred from mutant phenotype

(Hartl et al., 2008)

involved_in negative regulation of mitotic recombination

inferred from mutant phenotype

(Schuster et al., 2013)

involved_in regulation of DNA double-strand break processing

inferred from mutant phenotype

(Schuster et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in meiotic chromosome condensation

inferred from biological aspect of ancestor with PANTHER:PTN000368592

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in mitotic chromosome condensation

inferred from biological aspect of ancestor with PANTHER:PTN000368592

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (4 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)

located_in nucleus

inferred from direct assay

(Longworth et al., 2012)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in condensed chromosome, centromeric region

inferred from biological aspect of ancestor with PANTHER:PTN000368592

(assigned by GO_Central )

(Gaudet et al., 2011)

part_of condensin complex

inferred from sequence or structural similarity with HGNC:28952

(Ono et al., 2003)

Gene Group (FlyBase)

CONDENSIN II

Protein Family (UniProt)

Protein Signatures (InterPro)

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)

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VMQ4)

If you don't see the viewer to the right, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

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

Nucleotide / Polypeptide Records

UniProt

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.

Cap-D3_1

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 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

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)

located_in 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

View exonic expression by developmental stage for Dmel\Cap-D3

View exonic expression by tissue for Dmel\Cap-D3

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

FBgn0051989

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33778/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0051989

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051989

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0051989

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG31989

Flygut - An atlas of the Drosophila adult midgut

FBgn0051989

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

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

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(2L)Exel6012

(Ryder, 2004.4.26)

Df(2L)Exel7023

(Ryder, 2004.4.26)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

Cap-D3^GD913

viable

Cap-D3^EY00456

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Cap-D3^GD913

viable, with Scer\GAL4^tin.CΔ4

Cap-D3^GD913

viable (with Cap-D3^EY00456)

Cap-D3^GS12862

viable (with Cap-D3^GS12862)

Cap-D3^EY00456

Sterility

Allele

female fertile

Cap-D3^EY00456

female fertile (with Cap-D3^EY00456)

Cap-D3^GS12862

female fertile (with Cap-D3^GS12862)

Cap-D3^EY00456

male fertile

Cap-D3^EY00456

male fertile (with Cap-D3^EY00456)

Cap-D3^GS12862

male fertile (with Cap-D3^GS12862)

Cap-D3^EY00456

male sterile

Cap-D3^EY00456

male sterile (with Df(2L)Exel6023)

Cap-D3^EY00456

Other Phenotypes

Allele

abnormal immune response, with Scer\GAL4^yolk

Cap-D3^GD913

abnormal meiotic cell cycle

Cap-D3^EY00456

some die during pupal stage, with Scer\GAL4^pnr-MD237

Cap-D3^GD913

visible, with Scer\GAL4^pnr-MD237

Cap-D3^GD913

Phenotype manifest in

Allele

embryonic/larval somatic muscle cell, with Scer\GAL4^Mef2.PR

Cap-D3^GD913

polytene chromosome & nurse cell (with Df(2L)Exel7023)

Cap-D3^EY00456

primary spermatocyte in meiotic anaphase I

Cap-D3^EY00456

primary spermatocyte in meiotic prophase I

Cap-D3^EY00456

trichogen cell, with Scer\GAL4^pnr-MD237

Cap-D3^GD913

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\NCAPD3

9 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Ncapd3

7 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Ncapd3

6 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\ncapd3

6 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\ncapd3

6 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\hcp-6

6 of 15

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\AT4G15890

3 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\YCS4

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

2 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?

NCAPD3; non-SMC condensin II complex subunit D3

9 of 15

609276

MICROCEPHALY 22, PRIMARY, AUTOSOMAL RECESSIVE; MCPH22

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

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.

FBgn0051989

MIST (genetic) - An integrated Molecular Interaction Database

Cap-D3

MIST (protein-protein) - An integrated Molecular Interaction Database

Cap-D3

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0051989

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

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}vri^k05901&P{PZ}cype⁰³⁷⁷¹ and P{lacW}Hel25E^k11511

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)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

61979

y¹ v¹; P{TRiP.HMJ23605}attP40

65511

w¹¹¹⁸; PBac{IT.GAL4}Cap-D3^1213-G4

15026

y¹ w^67c23; P{EPgy2}Cap-D3^EY00456

28492

y¹ w^*; P{EP}Cap-D3^G7988 CG31648^G7988

36615

y¹ sc^* v¹ sev²¹; P{TRiP.GL00575}attP2

63489

w¹¹¹⁸; PBac{IT.GAL4}Cap-D3^0720-G4 CG31915^0720-G4/CyO

FlyORF

F001285

M{UAS-Cap-D3.ORF}ZH-86Fb

Kyoto

114531

y^d2 w¹¹¹⁸ P{ey-FLP.N}2; PBac{WH}CG31915^f02191 P{neoFRT}40A/CyO y⁺

VDRC

v29657

w¹¹¹⁸; P{GD913}v29657

v9402

w¹¹¹⁸; P{GD913}v9402/TM3

Genomic Clones (21)

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

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 sequenced

BDGP DGC clones

Other clones

FI21632

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.

FBgn0051989

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

FGM230F05

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051989

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

33778

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 ( 49 )

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.

33778

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9VMQ4

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9VMQ4

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0051989

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0051989

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33778/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0051989

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

Cap-D3_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051989

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0051989

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG31989

Flygut - An atlas of the Drosophila adult midgut

FBgn0051989

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0051989

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

33778

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG31989

MARRVEL_MODEL - MARRVEL (model organism gene)

33778

modMine - A data warehouse for the modENCODE project

FBgn0051989

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0051989

DRSC - Results frm RNAi screens

FBgn0051989

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051989

FlyMine - An integrated database for Drosophila genomics

FBgn0051989

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

Cap-D3

MIST (protein-protein) - An integrated Molecular Interaction Database

Cap-D3

Synonyms and Secondary IDs (13)

Reported As

Symbol Synonym

BcDNA:RE74832

CAP-D2

(Carter and Sjögren, 2012)

CAP-D3

(Jeppsson et al., 2014, Hirano, 2012, Pek and Kai, 2011, Pek and Kai, 2011, Savvidou et al., 2005)

CG14019

CG31989

(Hosono et al., 2015, Schertel et al., 2013, Carter and Sjögren, 2012, Ni et al., 2011.7.19, Perkins et al., 2009, Jiang et al., 2007, Ono et al., 2003)

CG6922

Cap-D3

(Kim et al., 2021, King et al., 2019, Rosin et al., 2018, Clandinin and Owens, 2016-, Klebanow et al., 2016, Nguyen et al., 2015, Nikalayevich and Ohkura, 2015, Wallace et al., 2015, Herzog et al., 2013, Smith et al., 2013, Bauer et al., 2012, Joyce et al., 2012, McKee et al., 2012, Baxley et al., 2011, Hartl et al., 2008, Hartl et al., 2008, Hartl et al., 2008, Jiang et al., 2007)

CapD3

(Smith et al., 2013)

cap-D3

(Buster et al., 2013)

dCAP-D3

(Deutschman et al., 2019, Gordon and Du, 2011)

dCap-D3

(Longworth et al., 2012, Longworth et al., 2008)

Name Synonyms

Chromosome associated protein D3

(Hartl et al., 2006, Wang et al., 2006, Ono et al., 2003)

Chromosome-associated protein D3