FlyBase Gene Report: Dmel\retn

FB2024_03 , released June 25, 2024

FB2024_03 , released June 25, 2024

Gene: Dmel\retn

General Information

Symbol

Dmel\retn

Species

D. melanogaster

Name

retained

Annotation Symbol

CG5403

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004795

Gene Model Status

Stock Availability

26 publicly available

Gene Summary

Transcription factor which is a downstream target of gcm and repo. Directly or indirectly activates the transcription of locos and pros, which are essential for the development of some glial cells. Plays an essential role in defining the cell shape and migration characteristics of longitudinal glia that enable them to establish a normal axon scaffold. (UniProt, Q24573)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

dri, dead ringer, l(2)02535, Dead Ringer/Retain

Key Links

Genomic Location

Cytogenetic map

Sequence location

2R:23,632,610..23,654,820 [+]

Recombination map

2-104

RefSeq locus

NT_033778 REGION:23632610..23654820

Sequence

Get Decorated FASTA

Genomic Maps

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (17 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables DNA binding

inferred from direct assay

(Gregory et al., 1996)

inferred from direct assay

(Iwahara et al., 2002)

enables DNA-binding transcription factor binding

inferred from physical interaction with FLYBASE:gro; FB:FBgn0001139

(Valentine et al., 1998)

enables transcription cis-regulatory region binding

inferred from direct assay

(Valentine et al., 1998)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR001606, InterPro:IPR036431

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000394188

(GO Reference Genome Project, 2011-)

Biological Process (13 terms)

Terms Based on Experimental Evidence (11 terms)

CV Term

Evidence

References

involved_in anterior/posterior pattern specification

inferred from mutant phenotype

(Shandala et al., 1999)

involved_in axon guidance

inferred from mutant phenotype

(Ditch et al., 2005)

involved_in dendrite morphogenesis

inferred from mutant phenotype

(Iyer et al., 2013)

involved_in embryonic pattern specification

inferred from mutant phenotype

(Shandala et al., 1999)

involved_in gliogenesis

inferred from mutant phenotype

(Shandala et al., 2003)

involved_in male courtship behavior

inferred from mutant phenotype

(Ditch et al., 2005)

involved_in muscle organ development

inferred from mutant phenotype

(Shandala et al., 1999)

involved_in negative regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Valentine et al., 1998)

involved_in oogenesis

inferred from high throughput mutant phenotype

(Schupbach and Wieschaus, 1991)

involved_in positive regulation of DNA-templated transcription

inferred from mutant phenotype

(Shandala et al., 2003)

involved_in regulation of female receptivity

inferred from mutant phenotype

(Ditch et al., 2005)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

involved_in negative regulation of transcription by RNA polymerase II

non-traceable author statement

(Courey and Jia, 2001)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000394188

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR045147

(InterPro Project Members, 2004-)

involved_in salivary gland development

non-traceable author statement

(Abrams et al., 2003)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Shandala et al., 2002, Shandala et al., 1999, Valentine et al., 1998, Gregory et al., 1996)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000394188

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

A-T RICH INTERACTION DOMAIN TRANSCRIPTION FACTORS

Protein Family (UniProt)

-

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

A-T RICH INTERACTION DOMAIN TRANSCRIPTION FACTORS -: The A-T Rich Interaction Domain (ARID) transcription factors are sequence specific DNA-binding proteins that regulate transcription. The ARID-domain containing proteins contact DNA through the variant helix-turn-helix motif and hairpin structure. (Adapted from FBrf0146923 and FBrf0112110).

Protein Function (UniProtKB)

Transcription factor which is a downstream target of gcm and repo. Directly or indirectly activates the transcription of locos and pros, which are essential for the development of some glial cells. Plays an essential role in defining the cell shape and migration characteristics of longitudinal glia that enable them to establish a normal axon scaffold.

(UniProt, Q24573)

Summary (Interactive Fly)

transcription factor - ARID domain protein - required for proper patterning of the abdomen - necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors.

Interactive Fly

Gene Model and Products

Number of Transcripts

5

Number of Unique Polypeptides

5

Please see the JBrowse view of Dmel\retn 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 Q24573)

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

PDB - An information portal to biological macromolecular structures

1C20
1KQQ

Comments on Gene Model

Gene model reviewed during 5.50

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

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0072072

4291

906

FBtr0072073

4306

911

FBtr0340029

4142

904

FBtr0340030

3051

635

FBtr0340031

3535

654

Additional Transcript Data and Comments

Reported size (kB)

3.696 (compiled cDNA)

(Gregory et al., 1996)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

FBpp0071981

96.8

906

6.13

FBpp0071982

97.4

911

6.20

FBpp0309043

96.5

904

6.17

FBpp0309044

69.6

635

5.98

FBpp0309045

71.6

654

6.03

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

901 (aa)

(Gregory et al., 1996)

Comments

External Data

Crossreferences

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

PDB - An information portal to biological macromolecular structures

1C20
1KQQ

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

Mapped Features

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

External Data

Crossreferences

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

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).

-0.40

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 1 -- 4

organism | ubiquitous

Comment: reference states <2 hr AEL

(Gregory et al., 1996)

embryonic stage 4 -- 6

central brain anlage in statu nascendi

(Fisher et al., 2012)

Comment: rapidly degraded

(Fisher et al., 2012)

organism | gap expression pattern

(Fisher et al., 2012)

antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)

dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)

visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)

embryonic stage 5 -- 6

organism | 40-60% egg length

Comment: reference states 2-3 hr AEL

(Gregory et al., 1996)

embryonic stage 5 -- 7

organism | 0-30% egg length

Comment: 0-25% egg length

(Gregory et al., 1996)

organism | 70-100% egg length

Comment: 75-100% egg length

(Gregory et al., 1996)

embryonic stage 6 -- 10

Comment: reference states 3-5 hr AEL

(Gregory et al., 1996)

embryonic stage 7 -- 8

antennal anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

central brain anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

dorsal ectoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

amnioserosa primordium

(Fisher et al., 2012)

(Fisher et al., 2012)

embryonic stage 11 -- 12

(Fisher et al., 2012)

(Fisher et al., 2012)

stomatogastric nervous system primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

(Fisher et al., 2012)

embryonic hypopharynx

(Fisher et al., 2012)

embryonic/larval muscle system

(Fisher et al., 2012)

dorsal pharyngeal muscle cell

(Fisher et al., 2012)

embryonic stomatogastric nervous system

(Fisher et al., 2012)

embryonic stage 15 -- 16

embryonic/larval posterior midgut

(Gregory et al., 1996)

(Gregory et al., 1996)

embryonic/larval salivary gland duct

(Gregory et al., 1996)

embryonic/larval anterior midgut

(Gregory et al., 1996)

embryonic/larval hindgut

(Gregory et al., 1996)

pharyngeal muscle cell

(Gregory et al., 1996)

Additional Descriptive Data

dri transcripts are expressed in a dynamic pattern during embryogenesis. They are distributed throughout the embryo during syncytial cleavage stages and at cellularization, are distributed in broad bands at the termini and in the center of the embryo. At germ band extension, the transcripts are found predominantly in the mesoderm and at later stages, are detected in the pharyngeal muscles, the amnioserosa, and in a distinct row of cells in the hindgut. They are also observed in the ring gland, in the clypeolabrum, in a ring of cells around the hindgut-midgut junction, and in several cells in each brain lobe. Ventrally, expression is observed in the salivary ducts, in a ring of cells at the foregut-midgut junction and in a repeated pattern in the CNS.

(Gregory et al., 1996)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

presumptive embryonic salivary gland

(Haberman et al., 2003)

embryonic stage 1 -- 4

organism | ubiquitous

Comment: reference states <2 hr AEL

(Gregory et al., 1996)

embryonic stage 3 -- 4

• nucleus

(Shandala et al., 1999)

embryonic stage 4 -- 6

organism | 40-60% egg length

Comment: reference states 2-3 hr AEL

(Gregory et al., 1996)

embryonic stage 5 -- 6

organism | 0-30% egg length

Comment: reference states 2-3 hr AEL; 0-25% egg length

(Gregory et al., 1996)

organism | 70-100% egg length

Comment: reference specifies 75-100% egg length

(Gregory et al., 1996)

embryonic stage 6 -- 10

Comment: reference states 3-5 hr AEL

(Gregory et al., 1996)

embryonic stage 13 -- 14

large intestine primordium

(Iwaki et al., 2001)

embryonic/larval brain | posterior

(Shandala et al., 2002)

epithelium of wing disc

(Shandala et al., 2002)

adult stage | female

• nucleus

(Shandala et al., 1999)

• nucleus

(Shandala et al., 1999)

• nucleus

(Shandala et al., 1999)

Additional Descriptive Data

dri protein is expressed in a dynamic pattern during embryogenesis. It is distributed evenly in syncytial nuclei and in contrast to the RNA is also uniformly distributed in late blastoderm embryos. At germ band extension, dri protein is found predominantly in the mesoderm. At later stages, protein is detected in the pharyngeal muscles, the amnioserosa, and in a distinct row of cells in the hindgut. It is also observed in the ring gland, clypeolabrum, a ring of cells around the hindgut-midgut junction, and several cells in each brain lobe. Ventrally, expression is observed in the salivary ducts, a ring of cells at the foregut-midgut junction and in a repeated pattern in the CNS.

(Gregory et al., 1996)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Shandala et al., 2002, Shandala et al., 1999, Valentine et al., 1998, Gregory et al., 1996)

Expression Deduced from Reporters

Reporter: P{GMR9F04-GAL4}

Stage

Tissue/Position (including subcellular localization)

Reference

third instar larval stage

prothoracic gland

(Vallejo et al., 2015)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\retn in JBrowse

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

View exonic expression by developmental stage for Dmel\retn

View exonic expression by tissue for Dmel\retn

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

FBgn0004795

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

45976/tissue=All

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

FBgn0004795

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004795

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

FBgn0004795

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

CG5403

Flygut - An atlas of the Drosophila adult midgut

FBgn0004795

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\retn

Stages(s) 1-3
Stages(s) 4-6
Stages(s) 7-8
Stages(s) 13-16

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 24 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of retn

Transgenic constructs containing regulatory region of retn

Aberrations (Deficiencies and Duplications) ( 9 )

Inferred from experimentation ( 9 )

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

lethal, with Scer\GAL4^retn-GAL4

retn^δH5.UAS

lethal | recessive

lethal - all die during embryonic stage | partially | recessive | rescuable maternal effect

lethal - all die during embryonic stage | recessive

partially lethal (with retn¹)

partially lethal (with retn²)

partially lethal (with retn^89.GAL4)

retn^z2-428

partially lethal (with retn^RU50)

partially lethal (with retn^z2-428)

partially lethal - majority die

retn⁰²⁵³⁵

Sterility

Allele

female semi-fertile

retn^z2-428

Other Phenotypes

Allele

abnormal behavior | female

retn^z2-428

abnormal courtship behavior | female (with retn²)

abnormal courtship behavior | female (with retn⁰⁵⁰⁹⁶)

retn^z2-428

abnormal courtship behavior | female (with retn^RU50)

abnormal courtship behavior | female (with retn^z2-428)

abnormal mitotic cell cycle | germline clone

retn^unspecified

abnormal neuroanatomy, with Scer\GAL4^MZ1580

retn^UAS.cSa

abnormal neuroanatomy, with Scer\GAL4^ppk.1.9

abnormal neuroanatomy (with retn¹)

retn²

abnormal neuroanatomy (with retn²)

retn¹

abnormal neuroanatomy | somatic clone | third instar larval stage

some die during embryonic stage | recessive

some die during embryonic stage | recessive | rescuable maternal effect

visible, with Scer\GAL4^71B

retn^δH5.UAS

visible, with Scer\GAL4^71B, retn¹

retn^δH5.UAS

visible, with Scer\GAL4^71B, retn^δH5.UAS

retn¹

visible, with Scer\GAL4^Bx-MS1096

retn^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

abdominal anterior ventral multidendritic neuron vdaa, with Scer\GAL4^ppk.1.9

adult mushroom body

retn^RO44

adult mushroom body (with retn^89.GAL4)

retn^z2-428

adult mushroom body (with retn⁰⁵⁰⁹⁶)

retn^z2-428

adult mushroom body (with retn^z2-428)

adult mushroom body beta-lobe

retn^RO44

adult mushroom body beta-lobe (with retn^89.GAL4)

retn^z2-428

adult mushroom body beta-lobe (with retn⁰⁵⁰⁹⁶)

retn^z2-428

adult mushroom body beta-lobe (with retn^z2-428)

axon, with Scer\GAL4^MZ1580

retn^UAS.cSa

campaniform sensillum, with Scer\GAL4^71B

retn^δH5.UAS

campaniform sensillum, with Scer\GAL4^71B, retn¹

retn^δH5.UAS

campaniform sensillum, with Scer\GAL4^71B, retn^δH5.UAS

retn¹

cephalopharyngeal skeleton | germline clone

egg | germline clone

embryo | dorsal closure stage | germline clone

embryo | embryonic stage 4 | germline clone

embryo | extended germ band stage | germline clone

embryonic/larval glial cell, with Scer\GAL4^MZ1580

retn^UAS.cSa

embryonic/larval hindgut | embryonic stage

embryonic/larval pericardial cell | germline clone

embryonic/larval somatic muscle cell

embryonic hindgut

retn^unspecified

embryonic hindgut, with Scer\GAL4^byn-Gal4

retn^UAS.cSa

embryonic longitudinal glial cell (with retn¹)

retn²

embryonic longitudinal glial cell (with retn²)

retn¹

embryonic segment | germline clone

gnathal ganglion | somatic clone

retn^89.GAL4

hypostomal sclerite | germline clone

larval dorsal multidendritic neuron ddaC, with Scer\GAL4^ppk.1.9

larval longitudinal connective (with retn¹)

retn²

larval longitudinal connective (with retn²)

retn¹

lateral process of cephalopharyngeal skeleton | germline clone

neuron | somatic clone

pharyngeal muscle cell | germline clone

photoreceptor cell R1 | somatic clone

retn^89.GAL4

photoreceptor cell R2 | somatic clone

retn^89.GAL4

photoreceptor cell R3 | somatic clone

retn^89.GAL4

photoreceptor cell R4 | somatic clone

retn^89.GAL4

photoreceptor cell R5 | somatic clone

retn^89.GAL4

photoreceptor cell R6 | somatic clone

retn^89.GAL4

somatic muscle cell | germline clone

wing, with Scer\GAL4^Bx-MS1096

retn^{UAS.ORF.GW.Tag:HA}

wing sensillum, with Scer\GAL4^71B

retn^δH5.UAS

wing sensillum, with Scer\GAL4^71B, retn¹

retn^δH5.UAS

wing sensillum, with Scer\GAL4^71B, retn^δH5.UAS

retn¹

wing vein, with Scer\GAL4^71B

retn^δH5.UAS

wing vein, with Scer\GAL4^71B, retn¹

retn^δH5.UAS

wing vein, with Scer\GAL4^71B, retn^δH5.UAS

retn¹

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) (15)

10 of 14

Yes

Yes

8 of 14

No

Yes

7 of 14

No

Yes

2 of 14

No

No

2 of 14

No

No

2 of 14

No

No

2 of 14

No

No

2 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (13)

10 of 14

Yes

Yes

8 of 14

No

Yes

7 of 14

No

Yes

2 of 14

No

No

2 of 14

No

No

2 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Mus musculus (laboratory mouse) (15)

10 of 14

Yes

Yes

8 of 14

No

Yes

8 of 14

No

Yes

2 of 14

No

No

2 of 14

No

No

2 of 14

No

No

2 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Xenopus tropicalis (Western clawed frog) (10)

6 of 13

Yes

Yes

4 of 13

No

Yes

3 of 13

No

Yes

2 of 13

No

Yes

1 of 13

No

No

1 of 13

No

No

1 of 13

No

Yes

1 of 13

No

No

Xtro\LOC100492975

1 of 13

No

No

1 of 13

No

No

Danio rerio (Zebrafish) (17)

9 of 14

Yes

Yes

7 of 14

No

Yes

6 of 14

No

Yes

2 of 14

No

No

2 of 14

No

No

2 of 14

No

Yes

2 of 14

No

Yes

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

Yes

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

Yes

Caenorhabditis elegans (Nematode, roundworm) (4)

9 of 14

Yes

Yes

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Anopheles gambiae (African malaria mosquito) (6)

Agam\AgaP_AGAP005156

9 of 12

Yes

Yes

Agam\AgaP_AGAP012313

2 of 12

No

Yes

Agam\AgaP_AGAP001786

1 of 12

No

No

Agam\AgaP_AGAP004854

1 of 12

No

No

Agam\AgaP_AGAP006990

1 of 12

No

No

Agam\AgaP_AGAP007503

1 of 12

No

No

Arabidopsis thaliana (thale-cress) (8)

5 of 13

Yes

Yes

5 of 13

Yes

Yes

5 of 13

Yes

Yes

4 of 13

No

Yes

2 of 13

No

Yes

2 of 13

No

Yes

1 of 13

No

No

1 of 13

No

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

2 of 13

Yes

No

1 of 13

No

No

Schizosaccharomyces pombe (Fission yeast) (2)

2 of 12

Yes

No

1 of 12

No

No

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:retn. 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) (5)

2 of 13

2 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 ( 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?

ARID3A; AT-rich interaction domain 3A

10 of 14

ARID3C; AT-rich interaction domain 3C

8 of 14

ARID3B; AT-rich interaction domain 3B

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

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

On

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

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other 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

far western blotting, autoradiography

(Shandala et al., 2002)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

retn - Ssb-c31a

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

two hybrid array

(Shokri et al., 2019)

Summary of Genetic Interactions

esyN Network Diagram

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

esyN Network Key:

Suppression

Enhancement

Other 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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Rebay et al., 2000)

suppressible

(Wilk et al., 2004)

enhanceable

(Rebay et al., 2000)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

70031

DroID - A comprehensive database of gene and protein interactions.

FBgn0004795

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

45976

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

2R

Recombination map

2-104

Cytogenetic map

Sequence location

2R:23,632,610..23,654,820 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

59F5-59F5

Limits computationally determined from genome sequence between P{PZ}apt⁰³⁰⁴¹ and P{EP}egl^EP938

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

59F2-59F4

(Gregory, 1996.6.27)

59F3-59F4

(determined by in situ hybridisation)

(Spradling et al., 1999)

59F3-59F4

(Beaton, 1997.12.27)

59F1-59F4

59F3--4

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

2-104

(FlyBase, 2016)

2-108.8

(Comeron et al., 2012)

2-

(Gregory, 1996.6.27)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (26)

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

40734

w¹¹¹⁸; P{GMR9F03-GAL4}attP2

41330

w¹¹¹⁸; P{GMR9F12-GAL4}attP2

47433

w¹¹¹⁸; P{GMR9F06-GAL4}attP2

89611

w¹¹¹⁸; P{R9F06-p65.AD}JK22C

75712

w¹¹¹⁸; P{R9F03-p65.AD}attP40

68624

w¹¹¹⁸; P{R9F06-GAL4.DBD}attP2

73455

w¹¹¹⁸; P{VT021450-p65.AD}attP40

73776

w¹¹¹⁸; P{VT021450-GAL4.DBD}attP2

52608

w¹¹¹⁸; P{R9F06-P-lexA::p65}attP40

14858

P{VT021450-GAL4}attP2

16324

PBac{R9F06-lexA::p65}VK00022

v100579

P{KK108289}VIE-260B

More stocks available...

Genomic Clones (19)

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

cDNA Clones (97)

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.

FBgn0004795

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004795

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Shandala et al., 1999, Gregory et al., 1996)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

retn is required for positioning of the longitudinal glia in the embryonic central nervous system.

(Shandala et al., 2003)

retn is essential for anterior-posterior patterning and for muscle development in the embryo.

(Shandala et al., 1999)

Identification: Enhancer trap expression pattern survey for loci expressed in the ring gland.

(Harvie et al., 1998)

retn has been cloned and sequenced, and its expression pattern has been analysed.

(Gregory et al., 1996)

Identified in a screen for clones which bind an en homeodomain binding site.

(Gregory et al., 1995)

Mutations at the retn locus cause defects in midoogenesis.

(Schupbach and Wieschaus, 1991)

Relationship to Other Genes

Source for database merge of

Source for merge of: dri l(2)02535

(Shandala et al., 1999)

Source for merge of: retn BcDNA:LD35748

(Ditch et al., 2001, FlyBase, 1996-)

Additional comments

Source for merge of retn BcDNA:LD35748 was a shared cDNA ( date:030728 ).

(Ditch et al., 2001, FlyBase, 1996-)

cDNA sequence of "l(2)02535" is in large parts identical to "dri" sequence.

(Gerisch and Korge, 1997)

Nomenclature History

Source for database identify of

Source for identity of: dri CG5403

(Zhang, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (18)

Reported As

Symbol Synonym

2535

(Harvie et al., 1998)

BcDNA:LD35748

CG5403

(National Institute of Genetics Fly Stocks, 2022-, Yuan et al., 2015, Ni et al., 2011.7.19, Keleman et al., 2009.8.5, Perkins et al., 2009.3.31, Berger et al., 2008, Qin et al., 2005)

DRI

(Yuasa and Hiromi, 2007, Yuasa and Hiromi, 2004, Iwahara et al., 2002, Bradley and Andrew, 2001)

Dead Ringer/Retain

(Yuasa and Hiromi, 2005)

Dri

(Loganathan et al., 2021, Sun et al., 2015, Stathopoulos and Levine, 2004, Stathopoulos and Levine, 2002, Iwaki et al., 2001, Dallas et al., 2000)

EHMT

(Kleefstra et al., 2012)

EY2-10

(Rebay et al., 2000)

Retn

(O'Sullivan et al., 2013)

dri

(Altenhein et al., 2016, Kerr et al., 2014, Berger et al., 2008, Chandrasekaran and Beckendorf, 2005, Luschnig et al., 2004, Schnorrer and Dickson, 2004, Abrams et al., 2003, Freeman et al., 2003, Haberman et al., 2003, Johansen et al., 2003, Johansen et al., 2003, Michaut et al., 2003, Shandala et al., 2003, Shandala et al., 2003, Iwaki and Lengyel, 2002, Lengyel and Iwaki, 2002, Shandala et al., 2002, Berger et al., 2001, Bradley et al., 2001, Ditch et al., 2001, Nepveu, 2001, Sibbons et al., 2001, Andrew et al., 2000, Chen and Courey, 2000, Hader et al., 2000, Kortschak et al., 2000, Riechmann et al., 2000, Iwahara and Clubb, 1999, Mannervik et al., 1999, Shandala et al., 1999, Valentine et al., 1998, Gerisch and Korge, 1997, Treisman et al., 1997, Gregory et al., 1996, Gregory et al., 1995)

l(2)02535

(Spradling et al., 1999, Beaton, 1997.12.27, Gerisch and Korge, 1997, Meister and Braun, 1995.10, BDGP Project Members, 1994-1999)

retn

(Pelletier et al., 2023, Ding et al., 2022, Hurtado et al., 2022, Saha et al., 2022, Lepesant et al., 2020, Shokri et al., 2019, Yang et al., 2019, Gene Disruption Project members, 2018-, Stegeman et al., 2018, Karaiskos et al., 2017, Transgenic RNAi Project members, 2017-, Altenhein et al., 2016, Clandinin and Owens, 2016-, Naval-Sánchez et al., 2015, Schertel et al., 2015, Ugrankar et al., 2015, Ashwal-Fluss et al., 2014, Kerr et al., 2014, Toshima et al., 2014, Aleksic et al., 2013, Iyer et al., 2013, Naval-Sánchez et al., 2013, Nfonsam et al., 2012, Ruaud et al., 2010, Christensen et al., 2009.5.6, Southall and Brand, 2009, Christensen et al., 2008.12.28, Christensen et al., 2008.12.28, Christensen et al., 2008.12.28, Sandmann et al., 2007, Shirangi et al., 2006, Qin et al., 2005, Shandala et al., 2002)

retn/dri

(Ditch et al., 2002)

Name Synonyms

Dead Ringer/Retain

(Yuasa and Hiromi, 2007)

Dead ringer

(Iwahara et al., 2005)

Retained

(Pawar et al., 2011, Nie et al., 2009)

dead ringer

(Abrams et al., 2003, Shandala et al., 2002, Bradley et al., 2001, Courey and Jia, 2001, Kortschak et al., 2000, Gregory, 1996.6.27, Gregory et al., 1995)

dead-ringer

(Berger et al., 2008)

retained

(Ruaud et al., 2010, Shirangi et al., 2006, Qin et al., 2005, Shandala et al., 2002)

Secondary FlyBase IDs

FBgn0010517
FBgn0014151
FBgn0063144

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 58 )

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.

45976

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.

Q24573

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

Q24573

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.

Q24573

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004795

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

45976/tissue=All

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

FBgn0004795

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

FBgn0004795

FlyMine - An integrated database for Drosophila genomics

FBgn0004795

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

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

dme:Dmel_CG5403

MARRVEL_MODEL - MARRVEL (model organism gene)

45976

PDB - An information portal to biological macromolecular structures

1C20
1KQQ

Linkouts

BioGRID - A database of protein and genetic interactions.

70031

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

FBgn0004795

DroID - A comprehensive database of gene and protein interactions.

FBgn0004795

DRSC - Results frm RNAi screens

FBgn0004795

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004795

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004795

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

CG5403

Flygut - An atlas of the Drosophila adult midgut

FBgn0004795

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

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

Interactive Fly

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

45976

References (136)