FB2020_05, released Oct 14, 2020

Gene: Dmel\CG5543

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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
3 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
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
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
regulation of DNA double-strand break processing
inferred from biological aspect of ancestor with PANTHER:PTN000410770
(assigned by GO_Central )
(Gaudet et al., 2011)
regulation of histone H2B conserved C-terminal lysine ubiquitination
inferred from biological aspect of ancestor with PANTHER:PTN000410770
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000410770
(assigned by GO_Central )
(Gaudet et al., 2011)
site of double-strand break
inferred from biological aspect of ancestor with PANTHER:PTN000410770
(assigned by GO_Central )
(Gaudet et al., 2011)
Protein Family (UniProt)
Belongs to the WD repeat GAD-1 family. (Q9W1J3)
Protein Signatures (InterPro)
Summaries
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

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
Comments on Gene Model

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
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
RefSeq ID
GenBank
CG5543-PA
FBpp0072033
73.6
655
7.00
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.
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)
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

GBrowse - Visual display of RNA-Seq signals

View Dmel\CG5543 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of CG5543
Transgenic constructs containing regulatory region of CG5543
Deletions and Duplications ( 0 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\WDR70
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Wdr70
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Wdr70
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\wdr70
13 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\wdr70
3 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\gad-1
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\AT2G20330
9 of 9
Yes
Yes
Atha\LUG
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\CRN1
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPAC343.17c
10 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919046J )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00002168
Drosophila simulans
Dsim\GD11798
Drosophila sechellia
Dsec\GM16049
Drosophila erecta
Dere\GG22888
Drosophila yakuba
Dyak\GE14326
Drosophila ananassae
Dana\GF12507
Drosophila pseudoobscura pseudoobscura
Dpse\GA18958
Drosophila persimilis
Dper\GL11034
Drosophila willistoni
Dwil\GK22197
Drosophila virilis
Dvir\GJ20568
Drosophila mojavensis
Dmoj\GI20836
Drosophila grimshawi
Dgri\GH20751
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091502C7 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17022783
Glossina morsitans
Tsetse fly
Gmor\GMOY009341
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_09361
Mayetiola destructor
Hessian fly
Mdes\Mdes011951
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL001729
Anopheles darlingi
American malaria mosquito
Adar\ADAC000567
Anopheles gambiae
Malaria mosquito
Agam\AGAP008233
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ019404
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0395 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA009144
Danaus plexippus
Monarch butterfly
Dple\DPOGS213337-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL014499
Apis florea
Little honeybee
Aflo\2151263668
Apis mellifera
Western honey bee
Amel\LOC410205
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP19705
Bombus terrestris
Buff-tailed bumblebee
Bter\15206118
Linepithema humile
Argentine ant
Lhum\LH15135
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:00257f
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG023761
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_09973
Tribolium castaneum
Red flour beetle
Tcas\TC002358
Pediculus humanus
Human body louse
Phum\PHUM516260
Rhodnius prolixus
Kissing bug
Rpro\RPRC013538
Cimex lectularius
Bed bug
Clec\CLEC009098
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI005619
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_07914
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0364 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR004346
Ixodes scapularis
Black-legged tick
Isca\ISCW022682
Stegodyphus mimosarum
African social velvet spider
Smim\KFM73740.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur04g03840
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G043W )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Wdr70
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Wdr70_1
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000007272
Gallus gallus
Domestic chicken
Ggal\WDR70
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 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?
    WDR70; WD repeat domain 70
    14 of 15
    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
        esyN Network Diagram
        Interactions Browser
        Summary of Genetic Interactions
        esyN Network Diagram
        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.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        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}eglEP938 and P{lacW}eIF6k13214
        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 (3)
        Genomic Clones (25)
        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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

        cDNA clones, fully sequenced
        BDGP DGC clones
        Other clones
          Drosophila Genomics Resource Center cDNA clones

          For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

          cDNA Clones, End Sequenced (ESTs)
          BDGP DGC clones
          Other clones
          RNAi and Array Information
          Linkouts
          DRSC - Results frm RNAi screens
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          Antibody Information
          Laboratory Generated Antibodies
           
          Commercially Available Antibodies
           
          Other Information
          Relationship to Other Genes
          Source for database identify of
          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}Nxt1f04855) was originally assigned to the CG5543 gene in FBrf0179797, resulting in the "CG5543f04855" (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-)
          Other Comments

          Area matching Drosophila ESTs AA441247 and AA820771.

          (Davies, 2001.3.15)
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 36 )
          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.
          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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
          Other crossreferences
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          modMine - A data warehouse for the modENCODE project
          SignaLink - A signaling pathway resource with multi-layered regulatory networks.
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyMine - An integrated database for Drosophila genomics
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          Synonyms and Secondary IDs (2)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (27)