FlyBase Gene Report: Dmel\okr

General Information

Symbol

Dmel\okr

Species

D. melanogaster

Name

okra

Annotation Symbol

CG3736

Feature Type

protein_coding_gene

FlyBase ID

FBgn0002989

Gene Model Status

Current

Stock Availability

9 publicly available

Gene Summary

okra (okr) encodes a helicase involved in homologous DNA repair. It functions in meiotic recombination. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

rad54, DmRAD54

Key Links

Genomic Location

Cytogenetic map

23C4-23C4

Sequence location

2L:2,989,594..2,992,759 [-]

Recombination map

2-8

RefSeq locus

NT_033779 REGION:2989594..2992759

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (18 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR000330

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables ATP-dependent chromatin remodeler activity

inferred from electronic annotation with InterPro:IPR000330

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables DNA translocase activity

inferred from biological aspect of ancestor with PANTHER:PTN001650063

(assigned by GO_Central )

(Gaudet et al., 2011)

enables hydrolase activity, acting on acid anhydrides

inferred from electronic annotation with InterPro:IPR013967

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (13 terms)

Terms Based on Experimental Evidence (11 terms)

CV Term

Evidence

References

involved_in chromatin remodeling

inferred from mutant phenotype

(assigned by UniProt )

(Alexiadis et al., 2004)

involved_in DNA synthesis involved in double-strand break repair via homologous recombination

inferred from mutant phenotype

(assigned by UniProt )

(Ghabrial et al., 1998)

involved_in dorsal appendage formation

inferred from high throughput mutant phenotype

(Schupbach and Wieschaus, 1991)

involved_in double-strand break repair via homologous recombination

inferred from mutant phenotype

(assigned by UniProt )

(Alexiadis et al., 2004)

involved_in double-strand break repair via synthesis-dependent strand annealing

inferred from mutant phenotype

(Wei and Rong, 2007)

involved_in double-strand break repair

inferred from mutant phenotype

(Joyce and McKim, 2009, Kooistra et al., 1997)

involved_in meiotic DNA repair synthesis

inferred from mutant phenotype

(assigned by UniProt )

(Ghabrial et al., 1998)

involved_in oocyte fate determination

inferred from mutant phenotype

(Joyce and McKim, 2009)

involved_in oogenesis

inferred from genetic interaction with FLYBASE:p53; FB:FBgn0039044

(Lu et al., 2010)

inferred from high throughput mutant phenotype

(Schupbach and Wieschaus, 1991)

involved_in reciprocal meiotic recombination

inferred from mutant phenotype

(Joyce and McKim, 2009)

involved_in response to ionizing radiation

inferred from mutant phenotype

(assigned by UniProt )

(Kooistra et al., 1997)

inferred from mutant phenotype

(Gorski et al., 2003)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in double-strand break repair via synthesis-dependent strand annealing

inferred from biological aspect of ancestor with PANTHER:PTN001650063

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in intracellular mRNA localization

traceable author statement

(Cooperstock and Lipshitz, 1997)

involved_in reciprocal meiotic recombination

inferred from biological aspect of ancestor with PANTHER:PTN001650063

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of translation

traceable author statement

(Cooperstock and Lipshitz, 1997)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(assigned by UniProt )

(Ghabrial et al., 1998)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN001650063

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

SNF2-LIKE CHROMATIN REMODELERS

Protein Family (UniProt)

Belongs to the SNF2/RAD54 helicase family. (O76460)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

okra (okr) encodes a helicase involved in homologous DNA repair. It functions in meiotic recombination. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

SNF2-LIKE CHROMATIN REMODELERS -: Snf2-like chromatin remodelers are a family of helicase-like proteins that direct energy derived from ATP hydrolysis into the mechanical remodelling of chromatin structure. They are so-called due to the presence of a domain homologous to the helicase-like ATPase domain of the S. cerevisiae Snf2 protein. This domain, the Snf2 domain, consists of two tandem RecA-like folds and contains seven conserved helicase-related sequence motifs that classify it as part of the helicase superfamily 2 (SF2). However, Snf2 proteins are not bona fide helicases, lacking the ability to separate nucleic acid strands. Instead, Snf2 proteins are DNA translocases that apply an ATP-dependent torsional strain to DNA, which provides the necessary force to remodel nucleosomes or in some cases other DNA-protein complexes. (Adapted from PMID:21862382.)

Protein Function (UniProtKB)

Involved in mitotic DNA repair and meiotic recombination. Functions in the recombinational DNA repair pathway. Essential for interhomolog gene conversion (GC), but may have a less important role in intersister GC than spn-A/Rad51. In the presence of DNA, spn-A/Rad51 enhances the ATPase activity of okr/Rad54.

(UniProt, O76460)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

okr: okra (T. Schupbach)

Female sterile; homozygous females lay eggs which are of variable shapes; in the most extreme cases, the eggs are longer than normal, more pointed at the posterior end, and lack dorsal appendages, resembling eggs produced by the dominant female-sterile mutation Fs(2)D.

Summary (Interactive Fly)

DNA helicase involved in DNA repair - required for meiosis - the Drosophila homolog of the yeast DNA-repair protein Rad54

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\okr for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry O76460)

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

Model Confidence:

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

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

Comments on Gene Model

Gene model reviewed during 5.45

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

okr-RA

FBtr0077673

NM_057313

2878

784

Additional Transcript Data and Comments

Reported size (kB)

4.5, 2.7, 1.6 (northern blot)

(Ghabrial et al., 1998)

3 (northern blot)

(Kooistra et al., 1997)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

okr-PA

FBpp0077357

89.5

784

8.56

NP_476661

AAF51168

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)

784 (aa)

(Ghabrial et al., 1998, Kooistra et al., 1997)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts (via N-terminus) with spn-A/Rad51.

(UniProt, O76460)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

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

External Data

Crossreferences

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

okr_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

oogenesis

(Ghabrial et al., 1998)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- pupal stage

(Kooistra et al., 1997)

oogenesis & adult stage | female

ovary

(Kooistra et al., 1997)

Additional Descriptive Data

okr transcripts are widely distributed at all stages of oogenesis.

(Ghabrial et al., 1998)

okr transcripts are detected throughout development on northern blots. In adults, they are specifically expressed in the female ovary.

(Kooistra et al., 1997)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(assigned by UniProt )

(Ghabrial et al., 1998)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\okr in GBrowse 2

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

View exonic expression by developmental stage for Dmel\okr

View exonic expression by tissue for Dmel\okr

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

FBgn0002989

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

33507/tissue=All

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

FBgn0002989

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002989

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

FBgn0002989

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

CG3736

Flygut - An atlas of the Drosophila adult midgut

FBgn0002989

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 ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of okr

Transgenic constructs containing regulatory region of okr

Aberrations (Deficiencies and Duplications) ( 5 )

Inferred from experimentation ( 5 )

Gene disrupted in

Df(2L)AS8

(Ferro, 2002.12)

Df(2L)Exel7014

(Ryder, 2004.4.26)

Df(2L)JS17

(Ghabrial et al., 1998, Eeken et al., 1997, Kooistra et al., 1997)

Gene not disrupted in

Df(2L)C144

(Ghabrial et al., 1998)

Df(2L)JS7

(Ghabrial et al., 1998)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

viable

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

okr^GD4181

viable, with Scer\GAL4^Mef2.PR

okr^GD4181

viable, with Scer\GAL4^pnr-MD237

okr^GD4181

viable, with Scer\GAL4^tin.CΔ4

okr^GD4181

viable (with okr^17-11)

okr^A19-10

viable (with okr^A19-10)

okr^17-11

Sterility

Allele

female semi-fertile

female sterile

female sterile (with okr^AA)

okr^RU

female sterile (with okr^RU)

okr^AA

female sterile | recessive

okr^17-11

fertile

okr⁷⁸²

male fertile

okr^17-11

sterile

okr^WS

Other Phenotypes

Allele

abnormal DNA repair

okr^RU

abnormal DNA repair (with okr^AA)

okr^RU

abnormal DNA repair (with okr^RU)

okr^AA

abnormal meiotic cell cycle

okr⁷⁸²

abnormal meiotic cell cycle (with okr^AA)

okr^RU

abnormal meiotic cell cycle (with okr^RU)

okr^AA

chemical sensitive

chemical sensitive (with okr^AA)

okr^RU

chemical sensitive (with okr^RU)

okr^AA

chemical sensitive | maternal effect

okr^17-11

chemical sensitive | recessive

radiation sensitive

radiation sensitive (with okr^AA)

okr^RU

radiation sensitive (with okr^RU)

okr^AA

radiation sensitive | embryonic stage | rescuable maternal effect (with Df(2L)JS17)

okr⁷⁸²

radiation sensitive | maternal effect

okr^17-11

radiation sensitive | recessive

wild-type

okr^+t4.7

Phenotype manifest in

Allele

dorsal appendage

dorsal appendage (with okr^AA)

okr^RU

dorsal appendage (with okr^RU)

okr^AA

egg

okr^AA

egg chorion (with okr^AA)

okr^RU

egg chorion (with okr^RU)

okr^AA

egg chorion | maternal effect

okr^RU

egg chorion | maternal effect (with okr^AA)

okr^RU

egg chorion | maternal effect (with okr^RU)

okr^AA

eye disc | conditional

okr^17-11

follicle cell

okr^AB

karyosome

okr^unspecified

karyosome (with okr^AA)

okr^RU

karyosome (with okr^RU)

okr^AA

metaphase & condensed nuclear chromosome | conditional qualifier

okr^17-11

micropyle

okr^AB

nucleus

okr^AA

oocyte

okr^AA

presumptive oocyte

okr^WS

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\RAD54L

15 of 15

Yes

Hsap\RAD54B

4 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Rad54l

15 of 15

Yes

Mmus\Rad54b

3 of 15

Yes

Rattus norvegicus (Norway rat) (3)

Rnor\Rad54l

9 of 13

Yes

Rnor\Rad54b

6 of 13

Yes

Rnor\Fsbp

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\rad54l

9 of 12

Yes

Xtro\rad54b

3 of 12

Yes

Xtro\LOC101732000

1 of 12

Yes

Danio rerio (Zebrafish) (2)

Drer\rad54l

10 of 15

Yes

Drer\rad54b

4 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\rad-54

15 of 15

Yes

Cele\Y116A8C.13

3 of 15

Yes

Arabidopsis thaliana (thale-cress) (3)

Atha\RAD54

9 of 9

Yes

Atha\ATRX

1 of 9

Atha\BRM

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\RAD54

14 of 15

Yes

Scer\RDH54

4 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\rhp54

11 of 12

Yes

Spom\rdh54

2 of 12

Yes

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (17)

Gene Symbol

Score

Source

Alignment

brm

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

dom

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

kis

1 of 10

lds

1 of 10

Marcal1

1 of 10

Mi-2

1 of 10

XNP

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

cancer, epithelial, compromised apoptosis and DNA repair defects

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

okr^KK107487

model of cancer

CEA with BacA\p35^UAS.cHa

(Dekanty et al., 2015)

Potential Models Based on Orthology ( 4 )

Human Ortholog

Disease

Evidence

References

RAD54L; RAD54 like

model of breast cancer

IEA

(FlyBase, 2019-)

model of non-Hodgkin lymphoma

IEA

(FlyBase, 2019-)

RAD54B; RAD54 homolog B

model of colorectal cancer

IEA

(FlyBase, 2019-)

model of non-Hodgkin lymphoma

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 2 )

Allele

Disease

Interaction

References

okr^RU

ameliorates Bloom syndrome

modeled by Blm^D2, Blm^N1

(Lafave et al., 2014)

okr^KK107487

model of cancer

is ameliorated by bsk^K53R.UAS

(Dekanty et al., 2015)

Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

RAD54L; RAD54 like

15 of 15

603615

RAD54B; RAD54 homolog B

4 of 15

604289

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

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

okr

enhanceable

Blm

(Kooistra et al., 1999)

okr

suppressible

Brca2

(Klovstad et al., 2008)

okr

suppressible

bsk

(Dekanty et al., 2015)

okr

enhanceable

c(2)M

(Bhagat et al., 2004)

okr

suppressible

c(3)G

(Ghabrial and Schupbach, 1999)

okr

enhanceable

DNAlig4

(Gorski et al., 2003)

okr

suppressible

Hus1-like

(Abdu et al., 2007)

okr

suppressible

lok

(Abdu et al., 2002)

okr

suppressible

mei-41

(Ghabrial and Schupbach, 1999)

okr

suppressible

mei-P22

(Ghabrial and Schupbach, 1999)

okr

suppressible

mei-W68

(Barbosa et al., 2007, Ghabrial and Schupbach, 1999)

suppressible

(Lu et al., 2010)

suppressible

(Joyce and McKim, 2009)

okr

suppressible

trem

(Lake et al., 2011)

okr

suppressible

vilya

(Lake et al., 2015)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Blm

enhanceable

okr

(Kooistra et al., 1999)

DNAlig4

enhanceable

okr

(Gorski et al., 2003)

External Data

Subunit Structure (UniProtKB)

Interacts (via N-terminus) with spn-A/Rad51.

(UniProt, O76460 )

Linkouts

BioGRID - A database of protein and genetic interactions.

59726

DroID - A comprehensive database of gene and protein interactions.

FBgn0002989

MIST (genetic) - An integrated Molecular Interaction Database

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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Homologous recombination

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-8

Cytogenetic map

23C4-23C4

Sequence location

2L:2,989,594..2,992,759 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

23C4-23C4

Limits computationally determined from genome sequence between P{PZ}lilli⁰⁰⁶³² and P{PZ}toc⁰¹³⁶¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

23C1-23E6

(Pastink, 1996.12.20)

23C-23C

(Ghabrial, 1998.5.28)

23D-23E

(determined by in situ hybridisation)

(Kooistra et al., 1997)

23D-23D

(determined by in situ hybridisation)

(Eeken et al., 1997)

Experimentally Determined Recombination Data

Location

2-8

(FlyBase, 2016)

2-6.6

(Comeron et al., 2012)

2-5.6

(Ghabrial et al., 1998)

(Pastink, 1996.12.20)

2-1

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

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

Bloomington

31047

y¹ v¹; P{TRiP.JF01494}attP2

31329

y¹ v¹; P{TRiP.JF01286}attP2

8524

okr^17-11 cn¹ bw¹/CyO

8525

okr^A19-10 cn¹ bw¹/CyO

5098

okr^RU cn¹ bw¹/CyO, l(2)DTS513¹

33707

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00585}attP2

Kyoto

108040

okr^RU cn¹ bw¹/CyO, l(2)DTS513¹

VDRC

v104323

P{KK107487}VIE-260B

v30472

w¹¹¹⁸; P{GD4181}v30472/TM3

Genomic Clones (13)

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

cDNA Clones (27)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

LD35220

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.

FBgn0002989

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0002989

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

33507

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Additional comments

Other Comments

Gene is involved in post-replication recombination repair.

(de Buendia, 1998)

Characterisation of mutants implies okr is crucial in repair and recombination.

(Kooistra et al., 1997)

Mutant phenotype is consistent with a defect in the repair of double-stranded breaks.

(Kooistra et al., 1997)

Mutations at the okr locus cause defects in midoogenesis.

(Schupbach and Wieschaus, 1991)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 48 )

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.

33507

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.

O76460

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

O76460

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.

O76460

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0002989

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

FBgn0002989

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

33507/tissue=All

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

FBgn0002989

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

okr_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002989

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

FBgn0002989

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

CG3736

Flygut - An atlas of the Drosophila adult midgut

FBgn0002989

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

33507

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

TC030720

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

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

Dmel_CG3736

MARRVEL_MODEL - MARRVEL (model organism gene)

33507

modMine - A data warehouse for the modENCODE project

FBgn0002989

Linkouts

BioGRID - A database of protein and genetic interactions.

59726

DroID - A comprehensive database of gene and protein interactions.

FBgn0002989

DRSC - Results frm RNAi screens

FBgn0002989

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0002989

FlyMine - An integrated database for Drosophila genomics

FBgn0002989

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

Interactive Fly

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Homologous recombination

MIST (genetic) - An integrated Molecular Interaction Database

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

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

CG3736

(Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Schneiderman et al., 2009, Ni et al., 2008, Spellman and Rubin, 2002)

DhR54

(de Buendia, 1998)

DmRAD54

(Kooistra et al., 1999, Kooistra et al., 1998, Eeken et al., 1997, Kooistra et al., 1997)

DmRad54

(Eeken et al., 1999, Pastink and Lohman, 1999)

Dmrad54

(Abdu et al., 2007)

OKR

(Ellis et al., 2015)

Okr

(Nagel et al., 2012)

RAD54

(Vijg, 2002, Pastink et al., 2001, Pastink, 1996.12.20)

RAD54L

(Somma et al., 2008)

Rad54

(Bozas et al., 2009, Bozas and Carroll, 2006, Holmes et al., 2006, Alexiadis et al., 2004, Gorski et al., 2003, Jang et al., 2003, Alexiadis and Kadonaga, 2002)

Ras54

(Wei and Rong, 2007)

okra

(Richardson and Portela, 2018, Clemente-Ruiz et al., 2016, Kim et al., 2015, Barclay et al., 2014, Lake et al., 2013, Abdu et al., 2007, Hochwagen, 2006, Holmes et al., 2006)

rad54

(Bhargava et al., 2020, Wylie et al., 2014, Iijima et al., 2010, Lu et al., 2010, Klovstad et al., 2008, Siddique et al., 2008, Johnson-Schlitz et al., 2007, Moskalev et al., 2006, Romeijn et al., 2005, Jaklevic and Su, 2002)

Name Synonyms

Okra

(Landmann et al., 2020, Pedersen et al., 2008)

okra

(Chakravarti et al., 2022, Lake et al., 2019, Schüpbach, 2019, Lake et al., 2015, Collins et al., 2014, Lake et al., 2011, Lu et al., 2010, Joyce and McKim, 2009, Klovstad et al., 2008, McDaniel et al., 2008, Somma et al., 2008, Vázquez et al., 2008, Ghabrial, 1998.6.2)

Secondary FlyBase IDs

FBgn0017554

Datasets (8)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (8)

Result

Result Type

Title

scRNAseq_2020_Cattenoz_NI_seq_clustering

cell clustering analysis

Clustering analysis of hemocytes from non-infested third instar larvae

scRNAseq_2020_Cattenoz_WI_seq_clustering

cell clustering analysis

Clustering analysis of hemocytes from wasp-infested third instar larvae

scRNAseq_2020_Cho_NI72LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying

scRNAseq_2020_Cho_NI96LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying

scRNAseq_2020_Cho_WI96LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI96HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying

References (140)

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