FlyBase Gene Report: Dmel\cd

General Information

Symbol

Dmel\cd

Species

D. melanogaster

Name

cardinal

Annotation Symbol

CG6969

Feature Type

protein_coding_gene

FlyBase ID

FBgn0263986

Gene Model Status

Current

Stock Availability

25 publicly available

Gene Summary

cardinal (cd) encodes a phenoxazinone synthetase involved in the kynurenine pathway. It contributes to ommochrome biosynthesis, neuron death and siRNA-mediated gene silencing. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Red Book
Interactive Fly

Also Known As

phenoxazinone synthase, PHS

Key Links

Genomic Location

Cytogenetic map

94C1-94C1

Sequence location

3R:22,694,959..22,697,990 [+]

Recombination map

3-76

RefSeq locus

NT_033777 REGION:22694959..22697990

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (6 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 heme binding

inferred from electronic annotation with InterPro:IPR010255

(InterPro Project Members, 2004-)

enables peroxidase activity

inferred from biological aspect of ancestor with PANTHER:PTN000158755

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR010255

(InterPro Project Members, 2004-)

Biological Process (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in kynurenine metabolic process

inferred from mutant phenotype

(Campesan et al., 2011)

involved_in ommochrome biosynthetic process

inferred from mutant phenotype

(Harris et al., 2011)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in response to oxidative stress

inferred from electronic annotation with InterPro:IPR010255

(InterPro Project Members, 2004-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in lysosome

inferred from direct assay

(Harris et al., 2011)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

HEME PEROXIDASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

HEME PEROXIDASES -: Heme peroxidases are heme enzymes found in bacteria, fungi, plants and animals, which exploit the reduction of hydrogen peroxide to catalyze a number of oxidative reactions, involving a wide variety of organic and inorganic substrates. (Adapted from PMID: 20211593.)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

cd: cardinal

Eye color yellowish vermilion, changing toward wild type with age. Drosopterin content of eyes about 85% normal (Gearhart and MacIntyre, 1970, Anal. Biochem. 37: 21-25). Phenoxazinone synthetase activity about 39% wild type; accumulates 3-hydroxykinurenine (Phillips, Forrest, and Kulkarni, 1973, Genetics 73: 45-56; Sullivan, Grillo, and Kitos, 1974, J. Exp. Zool. 188: 225-34). Ocelli white, showing no effect of age. Accumulates a blue-fluorescent compound termed cardinalic acid (xantherenic acid 8-O-β-O-glucoside) (Ferre, Mensua, and Jacobson, 1985, DIS 61: 71). Eye color autonomous in transplant of larval optic disk into wild type, ca, cn, st, or v larval host (Beadle and Ephrussi, 1936, Genetics 21: 230). Larval Malpighian tubes bright yellow; not distinguishable from wild type. RK2.

cdwo: cardinal-white ocelli

Ocelli colorless. Eye color wild type. Modifies we to a lighter and less yellow tone. cd/cdwo has normal eye color but white ocelli (Jones, 1971, DIS 47: 90). RK2.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\cd 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VCW2)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.53

Gene model reviewed during 5.47

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene

gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cd-RA

FBtr0084303

NM_142824

2619

830

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

UniProt

RefSeq ID

GenBank

cd-PA

FBpp0083696

92.8

830

6.77

Q9VCW2

NP_651081

AAF56043

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

Nucleotide / Polypeptide Records

UniProt

Q9VCW2

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\cd using the Feature Mapper tool.

External Data

Crossreferences

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

cd_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.59

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

day 5 of adulthood & male -- day 7 of adulthood & male

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in lysosome

inferred from direct assay

(Harris et al., 2011)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\cd in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\cd

View exonic expression by tissue for Dmel\cd

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

FBgn0263986

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

42681/tissue=All

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

FBgn0263986

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039005

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

FBgn0263986

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

CG6969

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 23 )

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 cd

Transgenic constructs containing regulatory region of cd

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3R)Exel6192

(Ryder, 2004.4.26)

Ts(YLt;3Lt)D100+Ts(YSt;3Rt)B27

(Jones, 1971)

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

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

cd^GD3115

viable, with Scer\GAL4^Mef2.PR

cd^GD3115

viable, with Scer\GAL4^pnr-MD237

cd^GD3115

viable, with Scer\GAL4^tin.CΔ4

cd^GD3115

Other Phenotypes

Allele

abnormal eye color

visible | recessive

Phenotype manifest in

Allele

eye

cd¹

Malpighian tubule

cd¹

pigment cell

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (21)

Hsap\TPO

4 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

Yes

Hsap\PTGS2

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (15)

Rnor\Epx

4 of 14

Yes

Rnor\Lpo

4 of 14

Yes

Rnor\Tpo

4 of 14

Yes

Rnor\Mpo

3 of 14

Rnor\Ptgs1

2 of 14

Yes

Rnor\Ptgs2

2 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (18)

Mmus\Epx

4 of 14

Yes

Mmus\Mpo

4 of 14

Yes

Mmus\Tpo

4 of 14

Yes

Mmus\Lpo

3 of 14

Mmus\Pxdn

3 of 14

Mmus\Ptgs1

2 of 14

Yes

Mmus\Ptgs2

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (13)

Xtro\btbd6

2 of 13

Yes

Xtro\pxdn

2 of 13

Yes

Xtro\tpo

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (17)

Drer\mpx

4 of 14

Yes

Drer\epx

2 of 14

Drer\ptgs1

2 of 14

Yes

Drer\ptgs2a

2 of 14

Yes

Drer\ptgs2b

2 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Drer\si:ch211-159i8.4

1 of 14

Drer\tpo

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (14)

Cele\skpo-1

6 of 14

Yes

Cele\skpo-2

6 of 14

Yes

5 of 14

5 of 14

5 of 14

4 of 14

4 of 14

4 of 14

3 of 14

3 of 14

3 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (25)

Agam\HPX6

12 of 12

Yes

Agam\AgaP_AGAP004036

4 of 12

Agam\AgaP_AGAP012561

4 of 12

Yes

4 of 12

4 of 12

4 of 12

4 of 12

4 of 12

4 of 12

4 of 12

4 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (12)

Atha\ALPHA DOX2

5 of 13

Yes

Atha\DOX1

5 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:cd. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (14)

CG4009

6 of 13

cysu

6 of 13

Irc

6 of 13

Pxd

6 of 13

Pxt

6 of 13

CG10211

5 of 13

CG42331

5 of 13

Pxn

5 of 13

Duox

2 of 13

Lar

1 of 13

lbk

1 of 13

Nox

1 of 13

Obsc

1 of 13

sls

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

TPO; thyroid peroxidase

model of thyroid dyshormonogenesis 2A

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

cd¹

ameliorates Huntington's disease

modeled by Hsap\HTT^Q93.ex1.UAS

(Campesan et al., 2011)

Disease Associations of Human Orthologs (via DIOPT v9.1 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?

TPO; thyroid peroxidase

4 of 14

606765

THYROID DYSHORMONOGENESIS 2A; TDH2A

thyroid dyshormonogenesis 2A

EPX; eosinophil peroxidase

3 of 14

131399

EOSINOPHIL PEROXIDASE DEFICIENCY; EPXD

3 of 14

3 of 14

Alzheimer's disease 1

PXDN; peroxidasin

3 of 14

605158

ANTERIOR SEGMENT DYSGENESIS 7; ASGD7

anterior segment dysgenesis 7

PXDNL; peroxidasin like

3 of 14

615904

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

MIST Molecular Interaction Search Tool

Summary of Genetic Interactions

esyN Network Diagram

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser View in MIST tool (external link)

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

aos

enhanceable

(Harris et al., 2011)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0263986

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-76

Cytogenetic map

94C1-94C1

Sequence location

3R:22,694,959..22,697,990 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

94C1-94C1

Limits computationally determined from genome sequence between P{lacW}Gclm^L0580 and P{EP}hh^EP3521

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-76

(FlyBase, 2016)

3-78.3

(Comeron et al., 2012)

3-75.7

(Nitasaka et al., 1995, Meyer, 1963, Universita di Pavia, 1952)

Left of (cM)

Right of (cM)

(Plough and Ives, 1934)

Notes

Stocks and Reagents

Stocks (25)

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

Bloomington

3052

cd¹

1892

Df(3R)G1, cd¹/TM3, Sb¹

3357

Df(3R)e-F1, In(3R)C, cd¹/cu¹ H¹ e⁴

1926

sr¹ r-l^K2 cd¹/TM3, Sb¹ Ser¹

67328

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06432}attP40

Kyoto

106560

Df(3R)G1, cd¹/TM3, Sb¹

101666

In(3R)C, cd¹ / Sb¹ H¹

107631

Delta¹ H¹ e^s cd¹/In(3R)P, sprw¹

107600

l(3)93Bd¹ e^LE1 cd¹/TM3, Sb¹ Ser¹

107601

l(3)93Bg¹ e^LE1 cd¹/TM3, Sb¹ Ser¹

107602

Rab11^93Bi e^LE1 cd¹/TM3, Sb¹ Ser¹

VDRC

v6831

w¹¹¹⁸; P{GD3115}v6831/CyO

More stocks available...

Genomic Clones (21)

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

cDNA Clones (1)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

AT03621

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.

FBgn0263986

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Lesions in cd reduces pigmentation in the eye and eliminates pigmentation in the ocelli, tubule and fat body pigmentation remain unaffected.

(Tearle, 1991)

Relationship to Other Genes

Source for database merge of

Source for merge of: cd CG6969

(Harris et al., 2011)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

Name Synonyms

cardinal

(Zhuravlev et al., 2022, Naz and Siddique, 2021, Zhuravlev et al., 2018, Campesan et al., 2011, Harris et al., 2011, Anaka et al., 2008, Lopatina et al., 2008, Savvateeva-Popova et al., 2007)

phenoxazinone synthase

(Zhuravlev et al., 2022, Zhuravlev et al., 2018)

phenoxazinone synthetase

(Navrotskaya et al., 2018)

Secondary FlyBase IDs

FBgn0000272
FBgn0039005

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 26 )

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.

42681

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

BF494857

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.

Q9VCW2

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

Q9VCW2

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.

Q9VCW2

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0263986

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

42681/tissue=All

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

FBgn0263986

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

FBgn0263986

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

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

dme:Dmel_CG6969

MARRVEL_MODEL - MARRVEL (model organism gene)

42681

Linkouts

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

FBgn0263986

DroID - A comprehensive database of gene and protein interactions.

FBgn0263986

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

cd_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039005

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0263986

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

CG6969

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC004579

References (78)

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

-0.59

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