FlyBase Gene Report: Dmel\ro

General Information

Symbol

Dmel\ro

Species

D. melanogaster

Name

rough

Annotation Symbol

CG6348

Feature Type

protein_coding_gene

FlyBase ID

FBgn0003267

Gene Model Status

Current

Stock Availability

82 publicly available

Gene Summary

Required to establish the unique cell identity of photoreceptors R2 and R5 and consequently for ommatidial assembly in the developing eye imaginal disk. Repression of expression in R8 photoreceptor by senseless (sens) is an essential mechanism of R8 cell fate determination. (UniProt, P10181)

Contribute a Gene Snapshot for this gene.

All Summaries

Key Links

Genomic Location

Cytogenetic map

97D4-97D5

Sequence location

3R:26,876,771..26,881,171 [-]

Recombination map

3-92

RefSeq locus

NT_033777 REGION:26876771..26881171

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 (13 terms)

Molecular Function (6 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from direct assay

(Heberlein et al., 1994)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR001356, InterPro:IPR020479

(InterPro Project Members, 2004-)

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000675451

(GO Reference Genome Project, 2011-)

enables DNA-binding transcription factor activity

inferred from electronic annotation with InterPro:IPR046327

(InterPro Project Members, 2004-)

enables RNA polymerase II cis-regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000675451

(GO Reference Genome Project, 2011-)

enables sequence-specific DNA binding

inferred from electronic annotation with InterPro:IPR046327

(InterPro Project Members, 2004-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in establishment of ommatidial planar polarity

inferred from mutant phenotype

(Kimmel et al., 1990)

involved_in positive regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Heberlein et al., 1994)

involved_in R2/R5 cell differentiation

inferred from mutant phenotype

(Heberlein et al., 1994)

involved_in R2/R5 cell fate commitment

inferred from mutant phenotype

(Kimmel et al., 1990)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in regulation of DNA-templated transcription

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000675451

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR046327

(InterPro Project Members, 2004-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Kimmel et al., 1990)

inferred from direct assay

(Heberlein et al., 1994)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000675451

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

HOX-LIKE HOMEOBOX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

HOX-LIKE HOMEOBOX TRANSCRIPTION FACTORS -: HOX-like (HOXL) homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. They encompass transcription factors encoded by the Hox genes of the Antennapedia and the Bithorax gene complexes and genes closely related in sequence. HOXL transcription factors are major regulators of animal development. (Adapted from FBrf0232555).

Protein Function (UniProtKB)

(UniProt, P10181)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

ro: rough

Homozygotes have rough eyes; slightly smaller and narrower than wild type. Approximately normal numbers of facets but arrangement irregular; frequently have fewer and sometimes more than eight retinula cells; some facets missing such that three ommatidial bristles juxtaposed; other facets fused (Stemm-Tegethoff and Dicke, 1974, Theoret. Appl. Genet. 44: 262-65; Ready et al.). Fiber pathways through lamina and into medulla in considerable disarray; optic chiasma between the two replaced by parallel fibers; laminar cartridge and medullar columns deranged, ventral epithelial nuclear row absent; medulla displaced from normal position and rotated anteriorly. Mosaic studies demonstrate that phenotype is eye autonomous; i.e., the genotype of the eye dictates that of the underlying nervous elements. Expression, as determined by in situ hybridization found in the eye-antenna imaginal disk, especially in the region of the morphogenetic furrow, as well as in a specific area of the brain. No evidence of embryonic expression (Saint, Kalionis, Lockett, and Elizur, 1988, Nature (London) 334: 151-54). RK1.

Summary (Interactive Fly)

transcription factor - homeodomain - plays a critical role in restriction of the number of photoreceptor precursors in the specification of R8 photoreceptors - a bistable loop between senseless and rough locks in R8 fate

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\ro 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 P10181)

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 5.48

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

ro-RA

FBtr0085090

NM_079797

1169

350

ro-RB

FBtr0085091

NM_170294

1241

350

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

ro-PA

FBpp0084460

39.4

350

9.72

FBpp0084461

39.4

350

9.72

P10181

NP_733173

AAN14093

Polypeptides with Identical Sequences

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

350 aa isoforms: ro-PA, ro-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

P10181

Mapped Features

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

External Data

Crossreferences

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

ro_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).

-0.33

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 | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic/larval posterior spiracle

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

third instar larval stage

mystery cell

(Freeman et al., 1992)

wandering third instar larval stage

eye disc morphogenetic furrow

• nucleus

(Kimmel et al., 1990)

photoreceptor cell R8

• nucleus

(Kimmel et al., 1990)

mystery cell

• nucleus

(Kimmel et al., 1990)

wandering third instar larval stage -- pupal stage P7

photoreceptor cell R2

• nucleus

(Kimmel et al., 1990)

photoreceptor cell R3

• nucleus

(Kimmel et al., 1990)

photoreceptor cell R4

• nucleus

(Kimmel et al., 1990)

photoreceptor cell R5

• nucleus

(Kimmel et al., 1990)

Additional Descriptive Data

In addition to the wild type staining in receptor cells R2, R3, R4, and R5, additional staining is observed in the position of the mystery cell in the rho^hs.sev line.

(Freeman et al., 1992)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Kimmel et al., 1990)

inferred from direct assay

(Heberlein et al., 1994)

Expression Deduced from Reporters

Reporter: P{ro.lacZ-tau.G}

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

photoreceptor cell R2

(Poeck et al., 2001)

photoreceptor cell R3

(Poeck et al., 2001)

photoreceptor cell R4

(Poeck et al., 2001)

photoreceptor cell R5

(Poeck et al., 2001)

third instar larval stage

photoreceptor cell R4

(Ruan et al., 2013, Garrity et al., 1999)

photoreceptor cell R5

(Ruan et al., 2013, Garrity et al., 1999)

photoreceptor cell R3

(Ruan et al., 2013, Garrity et al., 1999)

photoreceptor cell R2

(Ruan et al., 2013, Garrity et al., 1999)

pupal stage P6

photoreceptor R2 precursor cell

(Kulkarni et al., 2016)

photoreceptor R5 precursor cell

(Kulkarni et al., 2016)

adult stage

eyelet photoreceptor cell

(Malpel et al., 2002)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\ro in JBrowse

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

View exonic expression by developmental stage for Dmel\ro

View exonic expression by tissue for Dmel\ro

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

FBgn0003267

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

43234/tissue=All

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

FBgn0003267

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003267

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

FBgn0003267

Flygut - An atlas of the Drosophila adult midgut

FBgn0003267

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 46 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 30 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of ro

Transgenic constructs containing regulatory region of ro

Aberrations (Deficiencies and Duplications) ( 23 )

Inferred from experimentation ( 23 )

Gene duplicated in

Dp(3;1)Dr-RXT11

(Jurgens and Weigel, 1988)

Dp(3;1)H135

Gene not duplicated in

Dp(3;1)R87

Ts(YSt;3Rt)B226

(Jurgens and Weigel, 1988)

Ts(YSt;3Rt)J116

(Jurgens and Weigel, 1988)

Gene not disrupted in

Df(3R)Espl3

(Cook and Carpenter, 2002)

Df(3R)ME61

(Cook and Carpenter, 2002)

Df(3R)Tl-X

(Cook and Carpenter, 2002)

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

lethal | heat sensitive

ro^hs.PB

lethal | recessive

ro^X13

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

ro^GD1520

lethal - all die during larval stage, with Scer\GAL4^Mef2.PR

ro^GD1520

viable

Other Phenotypes

Allele

abnormal planar polarity | recessive

ro¹

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

ro^GD1520

visible

visible | dominant

ro^DOM

visible | heat sensitive

visible | recessive

wild-type

Phenotype manifest in

Allele

cone cell

eye

eye, with Scer\GAL4^lz-gal4

ro^UAS.cFa

eye | heat sensitive

ro^hs.PB

eye disc morphogenetic furrow

ro^DOM

eye photoreceptor cell

eye photoreceptor cell, with ro^H3

ro^w

eye photoreceptor cell, with ro^w

ro^H3

lens

macrochaeta

ommatidium

ommatidium, with ro^H3

ro^w

ommatidium, with ro^w

ro^H3

ommatidium | heat sensitive

ro^hs.PB

photoreceptor cell R1 | ectopic

photoreceptor cell R2 | ectopic

photoreceptor cell R2 | precursor

ro¹

photoreceptor cell R3 | ectopic

photoreceptor cell R3 | ectopic | precursor

ro¹

photoreceptor cell R4 | ectopic

photoreceptor cell R4 | ectopic | precursor

ro¹

photoreceptor cell R5 | ectopic

photoreceptor cell R5 | precursor

ro¹

photoreceptor cell R6 | ectopic

photoreceptor cell R7

photoreceptor cell R7 | cell autonomous | somatic clone

ro^hs.sev1

photoreceptor cell R8 | ectopic

ro^x63

photoreceptor cell R8 | increased number

ro^x63

primary pigment cell

retina

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) (95)

Hsap\HOXA2

3 of 14

Yes

Hsap\HOXA4

3 of 14

Yes

Hsap\HOXA6

3 of 14

Yes

Hsap\HOXA7

3 of 14

Yes

Hsap\HOXB1

3 of 14

Yes

Hsap\HOXB2

3 of 14

Yes

Hsap\HOXB6

3 of 14

Yes

Hsap\HOXB7

3 of 14

Yes

Hsap\HOXB8

3 of 14

Yes

Hsap\HOXC8

3 of 14

Yes

Hsap\HOXD1

3 of 14

Yes

Hsap\HOXD8

3 of 14

Yes

Hsap\MNX1

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\DUX4L7

1 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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Hsap\LOC112268164

1 of 14

Yes

Hsap\NANOGP1

1 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

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) (69)

Rnor\Hoxb1

3 of 14

Yes

Rnor\Hoxd3

3 of 14

Yes

Rnor\Mnx1

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 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

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

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (72)

Mmus\Hoxa1

3 of 14

Yes

Mmus\Hoxa2

3 of 14

Yes

Mmus\Hoxa4

3 of 14

Yes

Mmus\Hoxb1

3 of 14

Yes

Mmus\Mnx1

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 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

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (97)

Xtro\LOC101731251

3 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 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

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

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

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

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

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

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

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

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (89)

Drer\hoxa2b

3 of 14

Yes

Drer\hoxb1a

3 of 14

Yes

Drer\hoxb2a

3 of 14

Yes

Drer\mnx1

3 of 14

Yes

Drer\mnx2a

3 of 14

Yes

Drer\mnx2b

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

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

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

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

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

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

Caenorhabditis elegans (Nematode, roundworm) (33)

Cele\ceh-12

3 of 14

Yes

Cele\ceh-63

3 of 14

Yes

Cele\lin-39

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

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

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

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (39)

Agam\AgaP_AGAP002372

5 of 12

Yes

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 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

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 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) (29)

Atha\HB51

4 of 13

Yes

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\YHP1

1 of 13

Yes

Scer\YOX1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\phx1

2 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:ro. 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) (78)

abd-A

5 of 13

ftz

5 of 13

lab

5 of 13

Scr

5 of 13

zen2

5 of 13

Antp

4 of 13

bcd

4 of 13

Dfd

4 of 13

exex

4 of 13

ind

4 of 13

zen

4 of 13

Abd-B

3 of 13

btn

3 of 13

CG34031

3 of 13

Ubx

3 of 13

unpg

3 of 13

2 of 13

B-H1

2 of 13

B-H2

2 of 13

bsh

2 of 13

C15

2 of 13

cad

2 of 13

CG11294

2 of 13

CG18599

2 of 13

Dbx

2 of 13

Dll

2 of 13

ems

2 of 13

eve

2 of 13

gsb

2 of 13

hbn

2 of 13

inv

2 of 13

lbe

2 of 13

lms

2 of 13

OdsH

2 of 13

Pph13

2 of 13

prd

2 of 13

scro

2 of 13

tin

2 of 13

unc-4

2 of 13

1 of 13

Awh

1 of 13

bap

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

Gsc

1 of 13

H2.0

1 of 13

HGTX

1 of 13

HHEX

1 of 13

Hmx

1 of 13

lbl

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

otp

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

tup

1 of 13

vnd

1 of 13

1 of 13

1 of 13

1 of 13

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

MNX1; motor neuron and pancreas homeobox 1

model of Currarino syndrome

IEA

(FlyBase, 2019-)

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?

HOXA2; homeobox A2

3 of 14

604685

MICROTIA, HEARING IMPAIRMENT, AND CLEFT PALATE

3 of 14

3 of 14

3 of 14

3 of 14

FACIAL PARESIS, HEREDITARY CONGENITAL, 3; HCFP3

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

MNX1; motor neuron and pancreas homeobox 1

3 of 14

142994

CURRARINO SYNDROME

Currarino syndrome

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

ro - Irbp18

two hybrid array

(Shokri et al., 2019)

ro - Rel

two hybrid array

(Shokri et al., 2019)

ro - drm

two hybrid array

(Shokri et al., 2019)

ro - foxo

two hybrid array

(Shokri et al., 2019)

ro - sage

two hybrid array

(Shokri et al., 2019)

ro - tio

two hybrid array

(Shokri et al., 2019)

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

suppressible

amos

(Chanut et al., 2002, Heberlein et al., 1993)

suppressible

ato

(Chanut et al., 2000)

enhanceable

ato

(Chanut et al., 2000)

enhanceable

Delta

(Chanut et al., 2000)

suppressible

Dfd::ro

(Lockett et al., 1993)

enhanceable

E(ro^DOM)50

(Chanut et al., 2000)

enhanceable

E(ro^DOM)1065

(Chanut et al., 2000)

enhanceable

E(ro^DOM)1777

(Chanut et al., 2000)

enhanceable

E(ro^DOM)1801

(Chanut et al., 2000)

enhanceable

E(ro^DOM)2051

(Chanut et al., 2000)

enhanceable

E(ro^DOM)2409

(Chanut et al., 2000)

enhanceable

E(ro^DOM)3222

(Chanut et al., 2000)

enhanceable

(Chanut et al., 2000)

suppressible

gro

(Chanut et al., 2000)

suppressible

(Chanut et al., 2000)

suppressible

(Chanut et al., 2000)

enhanceable

(Chanut et al., 2000)

suppressible

lilli

(Pepple et al., 2007)

suppressible

osa

(Chanut et al., 2000, Treisman et al., 1997)

suppressible

ptc

(Chanut et al., 2000)

enhanceable

ptc

(Chanut et al., 2000)

suppressible

Su(ro^DOM)345

(Chanut et al., 2000)

suppressible

Su(ro^DOM)519

(Chanut et al., 2000)

suppressible

Su(ro^DOM)923

(Chanut et al., 2000)

suppressible

Su(ro^DOM)1480

(Chanut et al., 2000)

suppressible

Su(ro^DOM)1993

(Chanut et al., 2000)

suppressible

Su(ro^DOM)2014

(Chanut et al., 2000)

suppressible

Su(ro^DOM)3023

(Chanut et al., 2000)

enhanceable

(Treisman et al., 1997)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

ato

enhanceable

(White and Jarman, 2000)

sens

suppressible

(Frankfort et al., 2001)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

68125

DroID - A comprehensive database of gene and protein interactions.

FBgn0003267

MIST (genetic) - An integrated Molecular Interaction Database

43234

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

43234

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-92

Cytogenetic map

97D4-97D5

Sequence location

3R:26,876,771..26,881,171 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

97D4-97D5

Limits computationally determined from genome sequence between P{lacW}His2Av^L1602 and P{PZ}sda⁰³⁸⁸⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

97D2-97D3

(determined by in situ hybridisation)

(Ranz et al., 2001)

97D3-97D5

(determined by in situ hybridisation)

(Saint et al., 1988)

97D5-97D7

(determined by in situ hybridisation)

(Tomlinson et al., 1988)

Experimentally Determined Recombination Data

Location

3-92

(FlyBase, 2016)

3-89.3

(Comeron et al., 2012)

3-91.1

Left of (cM)

Right of (cM)

Margin

(Whittle, 1977)

Notes

Maps adjacent to l(3)97Db.

(Knibb et al., 1993)

Stocks and Reagents

Stocks (82)

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

Bloomington

6201

ro^64c

5770

P{sevroI}1/CyO; ry⁵⁰⁶

496

e⁴ wo¹ ro¹

47255

w¹¹¹⁸; P{GMR94D11-GAL4}attP2

28671

y¹ v¹; P{TRiP.JF03086}attP2

92382

y¹ w^*; PBac{ro-GFP.FPTB}VK00037

1713

ss¹ e⁴ ro¹/TM3, Sb¹

6335

w^*; P{neoFRT}82B ro^x63/TM6B, Tb¹

Kyoto

105984

ro¹

107569

ant¹/CyO; ro¹

VDRC

v11792

w¹¹¹⁸; P{GD1520}v11792/TM3

v318012

PBac{fTRG00027.sfGFP-TVPTBF}VK00033

More stocks available...

Genomic Clones (16)

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

IP01518

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.

FBgn0003267

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0003267

Antibody Information

Laboratory Generated Antibodies

monoclonal

(Kimmel et al., 1990)

polyclonal

(Kimmel et al., 1990)

Commercially Available Antibodies

Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research

ro-62C2A8_anti-rough

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

ro^DOM affects morphogenetic furrow progression by interfering with hh signalling and preventing implementation of furrow-specific cell fates.

(Chanut et al., 2000)

ro expression in and around the morphogenetic furrow of the developing eye is regulated by hh.

(Dominguez, 1999)

Spred is positively regulated by ro and gl.

(DeMille et al., 1996)

ro is a retina-specific negative regulator required for proper resolution of ato expression and proneural migration. ro acts in conjunction with the more ubiquitously used N regulatory pathway.

(Dokucu et al., 1996)

The R8 fate in the developing eye is likely to be decided by the balance of the transcription factors encoded by ato and ro. The ato and ro products act as positive and negative factors, respectively, of such R8-specific genes as boss.

(Dokucu et al., 1995)

Alleles of S and of ro have been identified in a screen for abnormal numbers of R8 cells.

(Spencer et al., 1995)

A 5.8kb genomic fragment contains all the information required for normal ro expression and function. Important cis-regulatory sequences are located both in the 5' promoter region (between -940 and -340, coordinates from FBrf0047664) and a tissue-specific enhancer is located in the first intron. Amino acids located in the C-terminal region of the homeodomain play an important role in binding site recognition.

(Heberlein et al., 1994)

Mutagenesis of the ro locus demonstrates the ro gene product is required for the correct patterning of the developing eye.

(Knibb et al., 1993)

ro and gl gene products are required for B and B-H2 gene expression in R1 and R6.

(Higashijima et al., 1992)

ro function is required during the early steps of ommatidial assembly. No R2 or R5 cells are present in ro^- ommatidia as all existing out photoreceptors require svp⁺ function for their development.

(Heberlein et al., 1991)

Mutations in ro affect early ommatidia development.

(van Vactor et al., 1991)

Expression of ro in the presumptive R7 cell transforms the cell into an R1-6 type photoreceptor. The transformation is cell autonomous and depends on the presence of the sev gene. In wild type, ro may function autonomously in the specification of R2/5 photoreceptor identity but by itself may not initiate neural development.

(Basler et al., 1990)

Adult eyes are rough with irregular facet size and shape. Ommatidia irregular size and shape. The abnormal ro phenotype is due to a developmental defect: pattern formation defect.

(Renfranz and Benzer, 1989)

Analysis of somatic mosaics suggests that the or gene function is required only in photoreceptors R2 and R5.

(Tomlinson et al., 1988)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG6348

(Perkins et al., 2009)

DROROUGH

(Kennington et al., 2006)

(Chen and Desplan, 2020, Majot and Bidwai, 2017, Quan et al., 2016, Nfonsam et al., 2012, Bhattacharya and Baker, 2011, Aerts et al., 2010, Fan et al., 2010, Almudi et al., 2009, O'Keefe et al., 2009, McNeill et al., 2008)

Name Synonyms

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 39 )

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.

43234

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.

P10181

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P10181

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.

P10181

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0003267

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

43234/tissue=All

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

FBgn0003267

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

FBgn0003267

FlyMine - An integrated database for Drosophila genomics

FBgn0003267

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

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

dme:Dmel_CG6348

MARRVEL_MODEL - MARRVEL (model organism gene)

43234

Linkouts

BioGRID - A database of protein and genetic interactions.

68125

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

FBgn0003267

DroID - A comprehensive database of gene and protein interactions.

FBgn0003267

DRSC - Results frm RNAi screens

FBgn0003267

Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research

ro-62C2A8_anti-rough

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

ro_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003267

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0003267

Flygut - An atlas of the Drosophila adult midgut

FBgn0003267

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

TC030553

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

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

43234

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

43234

References (237)

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

-0.33

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