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Gene Dmel\CG42458

General Information
Symbol	Dmel\CG42458	Species	D. melanogaster
Name		Annotation symbol	CG42458
Feature type	protein_coding_gene	FlyBase ID	FBgn0259935
Gene Model Status	Current	Stock availability	6 publicly available
Also Known As	CG18656
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	66A1-66A1	Sequence location	3L:7,416,927..7,447,719 [+]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents Beta	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	This gene is referred to in FlyBase by the symbol Dmel\CG42458 (FBgn0259935). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: mRNA binding. The biological processes in which it is involved are not known. 6 alleles are reported. The phenotype of these alleles is annotated with: mesothoracic tergum. It has one annotated transcript and one annotated polypeptide. Protein features are: Nucleotide-binding, alpha-beta plait; RNA recognition motif domain; Zinc finger, C2H2; Zinc finger, C2H2-like. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages. Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. Gene sequence location is 3L:7416927..7447719.
User Contributed Data
	Beta version, feedback welcome
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 66A1-66A1   Limits computationally determined from genome sequence between P{PZ}l(3)0721708223&P{EP}Rac2EP3118 and P{lacW}Nmtj1C7 66A1
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\CG42458 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene model reviewed during 5.45 Low-frequency RNA-seq exon junction(s) not annotated. Gene split based on BLASTX data Gene split based on EST data Gene merge based on EST/cDNA data and conservation of additional coding exon across Drosophila species.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) CG42458-RA FBtr0300248  NM_206288   3633   711
Additional Transcript Data & 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 protein CG42458-PA   FBpp0289481   76.9   711   7.64     NP_996010   AAS65066
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • RNA recognition motif domain (IPR000504) Nucleotide-binding, alpha-beta plait (IPR012677) Zinc finger, C2H2 (IPR007087) Zinc finger, C2H2-like (IPR015880)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014296 AAS65066   BI563972   BI568923   BI568924   BI588816   BI589640   BI609697   BI611907   BT058070   BX030038   BX043468   CO186743   CO262348   CO278962   CO290819   CO291095   CO291310   CO300864   CO308895   CO326657   CO342843   CO342847   CX309521   CX309522   EC203816   EC204254   EC210123   EC211578   EC219434   EC230887   EC231002   EC242460   FE527461   FE527561
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q7KU81
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
[an error occurred while processing this directive] FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
[an error occurred while processing this directive]
modENCODE Development RNA-Seq
[an error occurred while processing this directive] modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
[an error occurred while processing this directive]
modENCODE Treatments RNA-Seq
[an error occurred while processing this directive]
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_14 mE1_20_mRNA_expression_cluster_13
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0259935 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG33277-RA;CG33279-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele partially lethal - majority die | pupal stage, with Scer\GAL4pnr-MD237 CG42458GD16040 viable, with Scer\GAL4pnr-MD237 CG42458GD16041 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 CG42458GD16040 Phenotype manifest in Allele chaeta | supernumerary, with Scer\GAL4pnr-MD237 CG42458GD16040 mesothoracic tergum, with Scer\GAL4pnr-MD237 CG42458GD16040
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of CG42458 Class Mutagen Stocks Known lesion CG42458MI06870 1 --
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of CG42458 Class Mutagen Stocks Known lesion CG42458GD16040 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes CG42458GD16041 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes CG42458HMJ02071 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes CG42458KK106121 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes CG42458KK113285 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{KK106121} NA P{KK113285} NA P{TRiP.HMJ02071} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions Mi{MIC}CG33278MI06870 NA
Gene Ontology: Function, Process & Cellular Component ( 3 unique terms )
	There is no information supporting a biological process term for this gene. (Based on a review of available data before: 2006)
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 3 terms )
Molecular Function
CV term Evidence References
mRNA binding inferred from sequence or structural similarity (Lasko, 2000) inferred from sequence or structural similarity with InterPro:IPR000504 (FlyBase Genome Annotators, 2004) nucleotide binding inferred from electronic annotation with InterPro:IPR012677 (FlyBase Curators et al., 2004-) zinc ion binding inferred from electronic annotation with InterPro:IPR007087, InterPro:IPR015880 (FlyBase Curators et al., 2004-)
Biological Process ( 0 terms)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions CG42458 allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0259935 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 2768945
Orthologs
OrthoDB Orthologs (51) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6ZS9PS Dipteran inclusive ortholog search EOG6PCB2H Insect inclusive ortholog search EOG6K3JSX Arthropod inclusive ortholog search EOG67D7ZP Metazoa inclusive ortholog search EOG6RNQ5B
Orthologs in Drosophila Species (EOG6ZS9PS)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\CG42458     Drosophila simulans   Dsim\GD14016 Y   Drosophila sechellia   Dsec\GM14843 Y   Drosophila erecta   Dere\GG14426 Y   Drosophila yakuba   Dyak\GE21617 Y   Drosophila ananassae   Dana\GF10644 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA23671 Y   Drosophila persimilis   Dper\GL26440 Y   Drosophila willistoni   Dwil\GK17383 Y   Drosophila virilis   Dvir\GJ13002 Y   Drosophila mojavensis   Dmoj\GI12860 Y   Drosophila grimshawi   Dgri\GH14884 Y   Drosophila grimshawi   Dgri\GH17232
Orthologs in non-Drosophila Dipterans (EOG6PCB2H)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ010811
Orthologs in non-Dipteran Insects (EOG6K3JSX)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB43701   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG021398   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH13536   Atta cephalotes Leafcutter ant  Acep\ACEP11768   Atta cephalotes Leafcutter ant  Acep\ACEP11769   Camponotus floridanus Florida carpenter ant  Cflo\CFLO20119   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL14143   Linepithema humile Argentine ant  Lhum\LH22925   Pogonomyrmex barbatus Red harvester ant  Pbar\PB25003   Solenopsis invicta Red fire ant  Sinv\SINV17296   Acyrthosiphon pisum Pea aphid  Apim\ACYPI21068   Pediculus humanus Human body louse  Phum\PHUM564010
Orthologs in non-Insect Arthropods (EOG67D7ZP)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Ixodes scapularis Deer tick  Isca\ISCW016264
Orthologs in non-Arthropod Metazoa (EOG6RNQ5B)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_005434gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_005433gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_021801gn   Danio rerio Zebrafish  Drer\CR384099.1   Danio rerio Zebrafish  Drer\zgc:55733   Danio rerio Zebrafish  Drer\ENSDARG00000053810   Danio rerio Zebrafish  Drer\raly   Xenopus tropicalis Western clawed frog  Xtro\ralyl   Xenopus tropicalis Western clawed frog  Xtro\hnrnpc   Xenopus tropicalis Western clawed frog  Xtro\raly   Gallus gallus Domestic chicken  Ggal\RALYL   Gallus gallus Domestic chicken  Ggal\RALY   Mus musculus House mouse  Mmus\Hnrnpc   Mus musculus House mouse  Mmus\Raly   Mus musculus House mouse  Mmus\ENSMUSG00000039717   Rattus norvegicus Norway rat  Rnor\ENSRNOG00000042602   Rattus norvegicus Norway rat  Rnor\Ralyl   Rattus norvegicus Norway rat  Rnor\Raly   Rattus norvegicus Norway rat  Rnor\ENSRNOG00000028224   Rattus norvegicus Norway rat  Rnor\Hnrpc   Homo sapiens Human  Hsap\HNRNPC   Homo sapiens Human  Hsap\HNRNPCL1   Homo sapiens Human  Hsap\RALYL   Homo sapiens Human  Hsap\RALY
Human Orthologs (4)
Gene OMIM HGNC Hsap\HNRNPC     Hsap\HNRNPCL1     Hsap\RALYL     Hsap\RALY
AAA Orthologs (21) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD14016 Drosophila simulans Dsim\GD14018 Drosophila sechellia Dsec\GM14843 Drosophila sechellia Dsec\GM14845 Drosophila erecta Dere\GG14426 Drosophila erecta Dere\GG14430 Drosophila yakuba Dyak\GE21617 Drosophila yakuba Dyak\GE21619 Drosophila ananassae Dana\GF10644 Drosophila pseudoobscura pseudoobscura Dpse\GA23671 Drosophila pseudoobscura pseudoobscura Dpse\GA23673 Drosophila persimilis Dper\GL26440 Drosophila persimilis Dper\GL26462 Drosophila willistoni Dwil\GK17383 Drosophila willistoni Dwil\GK17384 Drosophila virilis Dvir\GJ13002 Drosophila virilis Dvir\GJ13004 Drosophila mojavensis Dmoj\GI12860 Drosophila mojavensis Dmoj\GI12862 Drosophila grimshawi Dgri\GH14884 Drosophila grimshawi Dgri\GH14885
Stocks & Reagents
Stocks Listed in FlyBase ( 6 )
Bloomington	42506 y1 v1; P{TRiP.HMJ02071}attP40 42443 y1 w*; Mi{MIC}CG33278MI06870 CG42458MI06870
VDRC	v106608 P{KK106121}VIE-260B v108072 P{KK113285}VIE-260B v47828 w1118; P{GD16040}v47828 v46453 w1118; P{GD16041}v46453/TM3
Genomic Clones ( 1 )
	BACR09E21 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
Other clones	MIP04025
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RH03111 RH14517 RH18368 RH30252 RH34933
Other clones	19484 58203 156558 165626 AM02285 CK01.97A.F6 CK01.98C.H1 CK01.100D.G5 DMG3-chr3L.6129.pred.a EK022701 EK075242 EK076122 EK077527 EK085127 EK132442 EK179546 EK259614 EP04407 EP15612 EP15616 RH01185
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0259935 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 2768945
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: CG33277 CG33279 (FlyBase Genome Annotators, 2008)
Additional comments	Annotations CG33277 and CG33279 merged as CG42458 in release r5.11 of the genome annotation. (FlyBase Genome Annotators, 2008) Release 3.2 annotations CG33277 and CG33279 correspond to distinct parts of the release 2 annotation CG18656 which were not annotated on the genome in release 3.1. Release 3.2 annotation CG33278, which also corresponds to a distinct part of the release 2 annotation CG18656, was annotated on the genome in release 3.1, where it was labelled "CG18656". (FlyBase Genome Annotators, 2004)
Other Comments
	RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells. (Boutros et al., 2004)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_206288 RefSeq (Proteins) • NP_996010 DDBJ / EMBL / GenBank • AAS65066 CX309521 CX309522 Entrez Gene - A searchable database of RefSeq genes. • 2768945 UniProtKB/TrEMBL • Q7KU81
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • RNA recognition motif domain (IPR000504) Nucleotide-binding, alpha-beta plait (IPR012677) Zinc finger, C2H2 (IPR007087) Zinc finger, C2H2-like (IPR015880)
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0259935 DRSC - Results from RNAi screens. • FBgn0259935 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0259935 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG33277-RA;CG33279-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0259935 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 2768945 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 2768945 modMine - Data generated by the modENCODE project. • FBgn0259935
Synonyms & Secondary IDs ( 6 )
Reported As
Symbol Synonym	CG18656 (Boutros et al., 2004, ) cg18656 (Lasko, 2000) CG33277 (Keleman et al., 2009.8.5) CG33279 (Keleman et al., 2009.8.5) CG42458 (FlyBase Genome Annotators, 2008, Luo et al., 2011, Ni et al., 2010.12.1) unnamed (Yandell et al., 2005)
Name Synonym	CG33277   CG33279
Secondary FlyBase IDs
	FBgn0035784 FBgn0053277 FBgn0053279
References ( 18 )
Research paper	Luo et al., 2011, Development 138(13): 2761--2771 Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development. [FBrf0213878] Yandell et al., 2005, Proc. Natl. Acad. Sci. U.S.A. 102(5): 1566--1571 A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. [FBrf0183655] Lasko, 2000, J. Cell Biol. 150(2): F51--F56 The Drosophila melanogaster genome: translation factors and RNA binding proteins. [FBrf0129923]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 33. Fuzzy Cluster Members. [FBrf0213980] The modENCODE Consortium, 2010, Science 330(6012): DataS14: Gene co-expression clusters. [FBrf0213979] Mummery-Widmer et al., 2009, Nature 458(7241): Supplementary Table 2 - Genome-wide bristle screen results. [FBrf0214518] Yandell et al., 2005, Proc. Natl. Acad. Sci. U.S.A.: Validation of gene predictions in Drosophila melanogaster. Supplementary information for Yandell et al., 2005, Proc. Natl. Acad. Sci. USA 102(5): 1566--1571. [FBrf0183657] Boutros et al., 2004, Science 303(5659): Supporting Online Material: Figures S1 to S8; Tables S1 to S6. [FBrf0174218]
Personal communication to FlyBase	Bellen, 2012.11.5, set1011.xml set1011.xml [FBrf0219886] Ni et al., 2010.12.1, A genome-scale shRNA resource for transgenic RNAi in Drosophila. A genome-scale shRNA resource for transgenic RNAi in Drosophila. [FBrf0212437] Keleman et al., 2009.8.5, RNAi-phiC31 construct and insertion data submitted by the Vienna Drosophila RNAi Center RNAi-phiC31 construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0208510] Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327] FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
FlyBase analysis	FlyBase Genome Annotators, 2008, Changes affecting gene model number or type in release 5.11 of the annotated D.melanogaster genome. Changes affecting gene model number or type in release 5.11 of the annotated D.melanogaster genome. [FBrf0205039] FlyBase Genome Annotators, 2004, Changes affecting gene model number or type in release 3.2 of the annotated D.melanogaster genome. Changes affecting gene model number or type in release 3.2 of the annotated D.melanogaster genome. [FBrf0166453] FlyBase Curators, 2002-, Use of the ND evidence code for Gene Ontology (GO) terms in FlyBase. Use of the ND evidence code for Gene Ontology (GO) terms in FlyBase. [FBrf0159398]
Curated genome annotation	FamiliarityBreedsContempt, 1999.11, [Automatic annotations performed at the Celera Jamboreee.] [Automatic annotations performed at the Celera Jamboreee.] [FBrf0126705] Guan, 1999.11, [Annotations performed at the Celera Jamboreee.] [Annotations performed at the Celera Jamboreee.] [FBrf0126671]