FlyBase Gene Report: Dmel\CG5543

General Information

Symbol

Dmel\CG5543

Species

D. melanogaster

Name

Annotation Symbol

CG5543

Feature Type

protein_coding_gene

FlyBase ID

FBgn0034908

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

60A2-60A2

Sequence location

2R:23,809,236..23,811,398 [+]

Recombination map

2-105

RefSeq locus

NT_033778 REGION:23809236..23811398

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 (2 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000410770

(GO Reference Genome Project, 2011-)

is_active_in site of double-strand break

inferred from biological aspect of ancestor with PANTHER:PTN000410770

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the WD repeat GAD-1 family. (Q9W1J3)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\CG5543 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 Q9W1J3)

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 5.52

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

CG5543-RA

FBtr0072124

NM_137988

2163

655

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

CG5543-PA

FBpp0072033

73.6

655

7.00

Q9W1J3

NP_611832

AAF47065

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\CG5543 using the Feature Mapper tool.

External Data

Crossreferences

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

CG5543_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

(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)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

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

spermatozoon

(Dorus et al., 2006)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\CG5543 in JBrowse

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

View exonic expression by developmental stage for Dmel\CG5543

View exonic expression by tissue for Dmel\CG5543

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

FBgn0034908

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

37768/tissue=All

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

FBgn0034908

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0034908

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

FBgn0034908

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

CG5543

Flygut - An atlas of the Drosophila adult midgut

FBgn0034908

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of CG5543

Transgenic constructs containing regulatory region of CG5543

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 9 )

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^insc-Mz1407

CG5543^GD11687

lethal | pupal stage, with Scer\GAL4^pnr-MD237

CG5543^GD11687

partially lethal - majority die | pupal stage, with Scer\GAL4^pnr-MD237

CG5543^GD11687

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

CG5543^GD11687

viable, with Scer\GAL4^tin.CΔ4

CG5543^GD11687

Other Phenotypes

Allele

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

CG5543^GD11687

Phenotype manifest in

Allele

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

CG5543^GD11687

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

CG5543^GD11687

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) (17)

Hsap\WDR70

14 of 14

Yes

Hsap\APAF1

1 of 14

Hsap\DDB2

1 of 14

Yes

Hsap\ERCC8

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

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (11)

Rnor\Wdr70

14 of 14

Yes

Rnor\Ddb2

1 of 14

Yes

Rnor\Ercc8

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

Yes

Mus musculus (laboratory mouse) (11)

Mmus\Wdr70

13 of 14

Yes

Mmus\Ddb2

1 of 14

Yes

Mmus\Ercc8

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

Yes

Xenopus tropicalis (Western clawed frog) (14)

Xtro\wdr70

10 of 13

Yes

Xtro\ddb2

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

Danio rerio (Zebrafish) (13)

Drer\wdr70

2 of 14

Yes

Drer\daw1

1 of 14

Drer\ddb2

1 of 14

Yes

Drer\ercc8

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

Yes

Caenorhabditis elegans (Nematode, roundworm) (12)

Cele\gad-1

14 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

Anopheles gambiae (African malaria mosquito) (15)

Agam\AgaP_AGAP008233

7 of 12

Yes

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) (15)

Atha\AT2G20330

13 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\DRS1

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (4)

Scer\CMR1

1 of 13

Yes

Scer\PAN2

1 of 13

Yes

Scer\TAF5

1 of 13

Yes

Scer\UTP7

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\SPAC343.17c

10 of 12

Yes

Spom\pop3

1 of 12

Spom\taf73

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:CG5543. 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) (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

wds

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?

WDR70; WD repeat domain 70

14 of 14

617233

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

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0034908

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

mRNA Splicing - Major Pathway

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

Q9W1J3

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-105

Cytogenetic map

60A2-60A2

Sequence location

2R:23,809,236..23,811,398 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

60A2-60A2

Limits computationally determined from genome sequence between P{EP}egl^EP938 and P{lacW}eIF6^k13214

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-105

(FlyBase, 2016)

2-109.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

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

Bloomington

62333

y¹ v¹; P{TRiP.HMJ23690}attP40

NIG-Fly

5543R-4

P{NIG.5543R}4

HMJ23690

y¹ v¹; P{TRiP.HMJ23690}attP40/CyO

2RG-1075

y² VhaAC39-1^cho-1 v¹; P{U6-CG5543.NIG.sgRNA}attP40/CyO

VDRC

v106320

P{KK109031}VIE-260B

v27454

w¹¹¹⁸; P{GD11687}v27454

Genomic Clones (25)

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

cDNA Clones (48)

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.

FBgn0034908

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0034908

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Area matching Drosophila ESTs AA441247 and AA820771.

(Davies, 2001.3.15)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG5543 anon-WO0118547.181

(FlyBase, 1996-)

Additional comments

FlyBase curator comment: the insertion in the "f04855" Exelixis line (PBac{WH}Nxt1^f04855) was originally assigned to the CG5543 gene in FBrf0179797, resulting in the "CG5543^f04855" (FBal0161270) allele. However, FBrf0184340 shows that the insertion is actually within Nxt1.

(Bloomington Drosophila Stock Center, 2004.11.6)

Source for merge of CG5543 anon-WO0118547.181 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (2)

Reported As

Symbol Synonym

CG5543

(National Institute of Genetics Fly Stocks, 2022-, Singh et al., 2020, Hosono et al., 2015, Luck et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5, Perkins et al., 2009, Buszczak et al., 2007, Dorus et al., 2006)

anon-WO0118547.181

Name Synonyms

Secondary FlyBase IDs

FBgn0062187

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.

37768

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.

Q9W1J3

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

Q9W1J3

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.

Q9W1J3

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0034908

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

37768/tissue=All

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

FBgn0034908

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

FBgn0034908

FlyMine - An integrated database for Drosophila genomics

FBgn0034908

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

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

dme:Dmel_CG5543

MARRVEL_MODEL - MARRVEL (model organism gene)

37768

Linkouts

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

FBgn0034908

DroID - A comprehensive database of gene and protein interactions.

FBgn0034908

DRSC - Results frm RNAi screens

FBgn0034908

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

CG5543_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0034908

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0034908

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

CG5543

Flygut - An atlas of the Drosophila adult midgut

FBgn0034908

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

TC002358

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

mRNA Splicing - Major Pathway

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

Q9W1J3

References (30)

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

0.33

Report Sections