FlyBase Gene Report: Dmel\red

General Information

Symbol

Dmel\red

Species

D. melanogaster

Name

red Malpighian tubules

Annotation Symbol

CG12207

Feature Type

protein_coding_gene

FlyBase ID

FBgn0285913

Gene Model Status

Current

Stock Availability

432 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Red Book
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

88B1-88B3

Sequence location

3R:14,289,071..14,302,276 [+]

Recombination map

3-55

RefSeq locus

NT_033777 REGION:14289071..14302276

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 (0 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

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

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

red: red Malpighian tubules

Malpighian tubes of larva and adult rusty red. Eye color brown, darkening with age. kar2, red flies have orange eyes (Henikoff, 1979, Genetics 93: 105-15); cn; red colorless (Paton and Sullivan, 1975, Genetics 80: s63). Malpighian tubes of v; red and cn; red are colorless and tubes of bw; red are red; therefore, pigment an ommochrome. Eyes contain less drosopterin and isoxanthopterin and more of the other pteridines than normal. Eye color autonomous in red eye disks transplanted into wild-type host. Wild-type Malpighian tubes acquire some red pigment after transplantation into red hosts. RK1.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\red 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 Q961C8)

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

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

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

Gene model reviewed during 5.41

Gene model reviewed during 5.56

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

red-RA

FBtr0082923

NM_169573

2169

343

red-RB

FBtr0082921

NM_142095

2316

366

red-RC

FBtr0082922

NM_169572

1997

366

red-RD

FBtr0309997

NM_001260166

2055

343

red-RE

FBtr0309998

NM_001260167

1927

343

red-RF

FBtr0309999

NM_001260168

2113

366

red-RG

FBtr0344157

NM_001300396

2535

366

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

red-PA

FBpp0082382

37.7

343

7.47

FBpp0082380

40.6

366

7.19

FBpp0082381

40.6

366

7.19

FBpp0301703

37.7

343

7.47

FBpp0301704

37.7

343

7.47

FBpp0301705

40.6

366

7.19

FBpp0310570

40.6

366

7.19

Q961C8

NP_001287325

AHN57324

Polypeptides with Identical Sequences

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

366 aa isoforms: red-PB, red-PC, red-PF, red-PG

343 aa isoforms: red-PA, red-PD, red-PE

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\red using the Feature Mapper tool.

External Data

Crossreferences

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).

1.30

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 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

Malpighian tubule primordium

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic Malpighian tubule

(Fisher et al., 2012)

embryonic/larval midgut

(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

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\red in JBrowse

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

View exonic expression by developmental stage for Dmel\red

View exonic expression by tissue for Dmel\red

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

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

41738/tissue=All

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

FBgn0285913

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0038220

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

FBgn0285913

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

CG12207

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 12 )

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 red

Transgenic constructs containing regulatory region of red

Aberrations (Deficiencies and Duplications) ( 19 )

Inferred from experimentation ( 19 )

Gene duplicated in

Dp(3;2)ry⁺

(Green et al., 1990)

Dp(3;3)E(var)88D11

(Green et al., 1990)

Gene not disrupted in

Df(3R)293γ5

(Landis et al., 1997, Mortin et al., 1992)

Df(3R)293γ7

(Landis et al., 1997)

Df(3R)Exel7321

(Grant et al., 2016)

Df(3R)JY19

(Breen and Harte, 1991)

Df(3R)su(Hw)V

(Mortin et al., 1992, Breen and Harte, 1991)

Inferred from location ( 6 )

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 Scer\GAL4^pnr-MD237

red^GD7528

viable (with Df(3R)BSC487)

red^MB04082

viable (with Df(3R)Exel6267)

red^MB04082

viable | recessive

red^C1

Other Phenotypes

Allele

abnormal eye color

abnormal eye color (with Df(3R)BSC487)

red¹

abnormal eye color (with Df(3R)Exel6267)

red¹

abnormal eye color | recessive

red¹

visible | adult stage

red^unspecified

visible | recessive

red¹

Phenotype manifest in

Allele

eye

red^unspecified

eye (with Df(3R)BSC487)

red¹

eye (with Df(3R)Exel6267)

red¹

Malpighian tubule

red¹

Malpighian tubule (with Df(3R)BSC487)

red¹

Malpighian tubule (with Df(3R)Exel6267)

red¹

pigment cell

red¹

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) (3)

Hsap\LYSMD2

8 of 14

Yes

Hsap\LYSMD1

7 of 14

Yes

Hsap\LYSMD3

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) (2)

Rnor\Lysmd1

7 of 14

Yes

Rnor\Lysmd2

6 of 14

Yes

Mus musculus (laboratory mouse) (2)

Mmus\Lysmd2

8 of 14

Yes

Mmus\Lysmd1

6 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\lysmd2

8 of 13

Yes

Xtro\lysmd1

7 of 13

Yes

Xtro\pttg1ip.1

6 of 13

Yes

Danio rerio (Zebrafish) (3)

Drer\lysmd2

8 of 14

Yes

Drer\lysmd1

6 of 14

Yes

Drer\lysmd4

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\lmd-2

4 of 14

Yes

Cele\lmd-1

1 of 14

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP001430

11 of 12

Yes

Arabidopsis thaliana (thale-cress) (3)

Atha\AT1G55000

1 of 13

Yes

Atha\AT5G08200

1 of 13

Yes

Atha\AT5G23130

1 of 13

Yes

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:red. 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) (2)

CG15471

2 of 13

ima

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 ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

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?

LYSMD2; LysM domain containing 2

8 of 14

LYSMD1; LysM domain containing 1

7 of 14

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

Interaction Browsers

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

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

red - CARPB

experimental knowledge based

(Guruharsha et al., 2011)

red - Chd64

experimental knowledge based

(Guruharsha et al., 2011)

red - Flad1

experimental knowledge based

(Guruharsha et al., 2011)

red - ZnT63C

experimental knowledge based

(Guruharsha et al., 2011)

red - cPges

experimental knowledge based

(Guruharsha et al., 2011)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase 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

red

enhanceable

kar

(Henikoff, 1979)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

kar

enhanceable

red

(Henikoff, 1979)

External Data

Linkouts

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-55

Cytogenetic map

88B1-88B3

Sequence location

3R:14,289,071..14,302,276 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

88B1-88B3

Limits computationally determined from genome sequence between P{lacW}trx^j14A6&P{PZ}trx⁰⁰³⁴⁷ and P{PZ}cv-c⁰⁶⁹⁵¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-55

(FlyBase, 2016)

3-53.1

(Comeron et al., 2012)

3-53.6

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (432)

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

Bloomington

565

red¹

91609

red^K1

1662

red¹ e¹

4431

8980

2382

F002772

M{UAS-red.ORF.3xHA.GW}ZH-86Fb

Kyoto

101730

red¹

106336

Df(3L)Ar11, red¹/TM2, p^p

12207R-1

v104574

v18747

w¹¹¹⁸; P{GD7528}v18747

More stocks available...

Genomic Clones (17)

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

cDNA Clones (87)

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

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

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

Relationship to Other Genes

Source for database merge of

Source for merge of: red CG12207

(Grant et al., 2016)

Additional comments

'CG12207' or 'CG3259' corresponds to the 'red' locus.

(Cook and Cook, 2014.8.7)

FlyBase curator comment: The molecular map shown in Figure 4. of FBrf0054607 indicates that the "red" transcription unit must map between trx and su(Hw). The release 5.19 D.melanogaster genome has two annotations in this region - CG12207 and CG3259, one of which likely corresponds to "red". Molecular mapping of "red" mutations suggest that it is more likely that "red" corresponds to CG12207 rather than "CG3259".

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG12207

(Grant et al., 2016, Ashwal-Fluss et al., 2014, Bonnay et al., 2014, Cook and Cook, 2014.8.7, Sen et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5, Carrera et al., 2008, Maisonhaute et al., 2007)

bw-l

red

(Zhou et al., 2024, Transgenic RNAi Project members, 2017-, Grant et al., 2016, Cook and Cook, 2014.8.7, Mishra et al., 2014)

Name Synonyms

brown-like

red

(Schaeffer, 2018)

red Malpighian tubules

(Grant et al., 2016, Cook and Cook, 2014.8.7)

Secondary FlyBase IDs

FBgn0003228
FBgn0038220

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 47 )

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.

41738

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.

Q961C8

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.

Q961C8

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

41738/tissue=All

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

FBgn0285913

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

FBgn0285913

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

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

dme:Dmel_CG12207

MARRVEL_MODEL - MARRVEL (model organism gene)

41738

Linkouts

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0038220

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0285913

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

CG12207

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

TC009718

References (57)

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

1.30

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