Gene Dmel\CG6015

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General Information

Symbol

Dmel\CG6015

Species

D. melanogaster

Name

CG6015

Annotation symbol

CG6015

Feature type

protein_coding_gene

FlyBase ID

FBgn0038927

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

94A1-94A1

Sequence location

3R:17,857,865..17,860,116 [-]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

This gene is referred to in FlyBase by the symbol CG6015 (FBgn0038927). It has the cytological map location 94A1. Its sequence location is 3R:17857865..17860116. Its molecular function is described as RNA splicing factor activity, transesterification mechanism. It is involved in the biological process nuclear mRNA splicing, via spliceosome. 2 alleles are reported. The phenotypes of these alleles are annotated with: embryonic peripheral nervous system; longitudinal connective; ventral nerve cord commissure; ventral nerve cord. It has one annotated transcript and one annotated polypeptide.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

94A1-94A1

Limits computationally determined from genome sequence between P{PZ}tsl⁰⁰⁶¹⁷ and P{lacW}how^j5B5&P{EP}EP738

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

Left of (cM)

Right of (cM)

Notes

Molecular Map Data

Gene Order (in direction of increasing cytology)

References

Gene Order (overall orientation not stated)

References

Gene Model & Products

Please see the GBrowse view of Dmel\CG6015 for information on other features

Comments on Gene Model

EST data suggest additional 5' exon(s)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

CG6015-RA

FBtr0084183

NM_142748

2127

576

Additional Transcript Data & Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

CG6015-PA

FBpp0083581

65.4

576

7.37

NP_651005

AAF55949

Additional Polypeptide Data & Comments

Reported size (kD)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0038927

Crossreferences

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

•

WD40 repeat (IPR001680)

WD40 repeat-like (IPR011046)

WD40/YVTN repeat-like (IPR015943)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Q9VD52

Maps to

Does NOT map to

Identified with

(BDGP Project Members, 2000-)

Mapped Features & Mutations

Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here

Type

Symbol & Location

Additional Notes

References

External Data

Linkouts

DEDB - Drosophila exon database: splicing graphs

•

10287

Crossreferences

Expression Data

FlyBase-Curated Data

Transcript and
Protein data

Please see the FlyBase Gene Expression Report for details of gene expression from the literature.

Summary of Transcript Expression

Stage

Tissue/Position

Reference

Marker for

Subcellular Localization

CV Term

Summary of Polypeptide Expression

Stage

Tissue/Position

Reference

Marker for

Subcellular Localization

CV Term

Microarray Data

Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)

Untitled Document detailed view

AI134057

External Data & Images

Linkouts

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

•

FBgn0038927

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0038927

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0038927

Alleles & Phenotypes

Summary of Allele Phenotypes

Other Phenotypes

Allele

neuroanatomy defective

CG6015^dsRNA.cIa

Phenotype manifest in

Allele

embryonic peripheral nervous system

CG6015^dsRNA.cIa

ventral midline neuron & axon

CG6015^dsRNA.cIa

longitudinal connective

CG6015^dsRNA.cIa

ventral nerve cord commissure

CG6015^dsRNA.cIa

ventral nerve cord

CG6015^dsRNA.cIa

Classical Alleles ( 0 )

For All Classical Alleles Show

Allele of CG6015	Class	Mutagen	Stocks	Known lesion

Alleles Carried on Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Allele of CG6015	Class	Mutagen	Stocks	Known lesion
CG6015^GD9910		in vitro construct \| RNAi in vitro construct \| regulatory fusion	1	Yes
CG6015^dsRNA.cIa		in vitro construct \| RNAi	0	Yes

Aneuploid Aberrations

Useful deficiency

Df(3R)e-N19

Useful duplication

Dp(3;3)M95A⁺13

Disrupted in

Df(3R)Exel6188

(Ryder, 2004.4.26)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD9910}

Insertions

Type of insertions

Name

Expression data

Related Comments

Please look at the allele reports for the complete phenotype data

Gene Ontology: Function, Process & Cellular Component ( 3 )

Molecular Function

CV term

Evidence

References

RNA splicing factor activity, transesterification mechanism

inferred from sequence or structural similarity with SGD_LOCUS:CDC40; SGD:S0002772

(Mount and Salz, 2000)

Biological Process

CV term

Evidence

References

nuclear mRNA splicing, via spliceosome

inferred from sequence or structural similarity with EMBL:AF038392

(FlyBase, 1992-)

inferred from sequence or structural similarity with SGD_LOCUS:CDC40; SGD:S0002772 AND inferred from sequence or structural similarity with protein_id:AAC39730

(Mount and Salz, 2000)

Cellular Component

CV term

Evidence

References

spliceosome

inferred from sequence or structural similarity with EMBL:AF038392

(FlyBase, 1992-)

inferred from sequence or structural similarity with SGD_LOCUS:CDC40; SGD:S0002772 AND inferred from sequence or structural similarity with protein_id:AAC39730

(Mount and Salz, 2000)

Sequence Ontology: Class of Gene

protein_coding_gene

nuclear_gene

Interactions & Pathways

Summary of Genetic Interactions

Interacts with

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

CG6015 allele

Gene

References

External Data

Linkouts

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

67554

Orthologs

Genome-wide drosophilid orthologs

Dana\GF16948

Dere\GG12541

Dgri\GH19818

Dmoj\GI22293

Dper\GL23513

Dpse\GA19297

Dsec\GM23670

Dsim\GD18480

Dvir\GJ24085

Dwil\GK13002

Dyak\GE24061

Curated drosophilid orthologs

Dpse\GA19297

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000021381
Anopheles gambiae (Ensembl)
ENSBTAP00000000526
Bos taurus (Ensembl)
ENSCAFP00000005771
Canis familiaris (Ensembl)
ENSCINP00000019657
Ciona intestinalis (Ensembl)
NEWSINFRUP00000134988
Takifugu rubripes (Ensembl)
ENSGALP00000024253
Gallus gallus (Ensembl)
ENSP00000304370
Homo sapiens (Ensembl)
ENSMMUP00000010716
Macaca mulatta (Ensembl)
ENSMODP00000022372
Monodelphis domestica (Ensembl)
ENSPTRP00000031586
Pan troglodytes (Ensembl)
ENSRNOP00000000709
Rattus norvegicus (Ensembl)
GSTENP00023042001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000046098
Xenopus tropicalis (Ensembl)
Q84MU4
Oryza sativa (Gramene)
AT1G10580.1
Arabidopsis thaliana (Arabidopsis)
WBGene00039392
Caenorhabditis briggsae (Wormbase)
WBGene00018625
Caenorhabditis elegans (Wormbase)
ZDB-CDNA-050116-3
Danio rerio (Zfin)
ZDB-GENE-050116-3
Danio rerio (Zfin)
DDB0188449
Dictyostelium discoideum (Dictybase)
MGI:1918963
Mus musculus (Informatics)
YDR364C
Saccharomyces cerevisiae (Yeastgenome)
SPBC6B1.10
Schizosaccharomyces pombe (Sanger)

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 1 )

VDRC

v41708

w¹¹¹⁸; P{GD9910}v41708

Genomic Clones ( 2 )

cDNA Clones ( 25 )

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

LD21931

Other clones

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Affy Oligo

Linkouts

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0038927

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0038927

Antibody Information

Other Information

Discoverer

Etymology

Identification

Position Effect Variegation Data

Relationship to Other Genes

Source for database identity of

Source for database merge of

Additional comments

FlyBase curator comment: the insertion in the "f06954" Exelixis line (PBac{WH}BG4^f06954) was originally assigned to the CG6015 gene in FBrf0179797, resulting in the "CG6015^f06954" (FBal0161206) allele. However, FBrf0184340 shows that the insertion is actually within both BG4 and pit (nested genes).

(Bloomington Drosophila Stock Center, 2004.11.6)

Comments About Role

Comments About Molecular Function

Other Comments

Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells.

(Nybakken et al., 2005)

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•

NM_142748

RefSeq (Proteins)

•

NP_651005

DDBJ / EMBL / GenBank

•

UniProtKB/TrEMBL

•

Q9VD52

Other Crossreferences

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

•

WD40 repeat (IPR001680)

WD40 repeat-like (IPR011046)

WD40/YVTN repeat-like (IPR015943)

Linkouts

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

67554

DEDB - Drosophila exon database: splicing graphs

•

10287

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0038927

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

•

FBgn0038927

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0038927

FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans

•

FBgn0038927

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0038927

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0038927

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000021381
Anopheles gambiae (Ensembl)
ENSBTAP00000000526
Bos taurus (Ensembl)
ENSCAFP00000005771
Canis familiaris (Ensembl)
ENSCINP00000019657
Ciona intestinalis (Ensembl)
NEWSINFRUP00000134988
Takifugu rubripes (Ensembl)
ENSGALP00000024253
Gallus gallus (Ensembl)
ENSP00000304370
Homo sapiens (Ensembl)
ENSMMUP00000010716
Macaca mulatta (Ensembl)
ENSMODP00000022372
Monodelphis domestica (Ensembl)
ENSPTRP00000031586
Pan troglodytes (Ensembl)
ENSRNOP00000000709
Rattus norvegicus (Ensembl)
GSTENP00023042001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000046098
Xenopus tropicalis (Ensembl)
Q84MU4
Oryza sativa (Gramene)
AT1G10580.1
Arabidopsis thaliana (Arabidopsis)
WBGene00039392
Caenorhabditis briggsae (Wormbase)
WBGene00018625
Caenorhabditis elegans (Wormbase)
ZDB-CDNA-050116-3
Danio rerio (Zfin)
ZDB-GENE-050116-3
Danio rerio (Zfin)
DDB0188449
Dictyostelium discoideum (Dictybase)
MGI:1918963
Mus musculus (Informatics)
YDR364C
Saccharomyces cerevisiae (Yeastgenome)
SPBC6B1.10
Schizosaccharomyces pombe (Sanger)

PANTHER - Protein classification by function, families, and pathways

•

FBgn0038927

University of Chicago Dev. Expression

•

FBgn0038927

Synonyms & Secondary IDs ( 1 )

Reported As

Symbol Synonym

CG6015

(Nybakken et al., 2005)

Name Synonym

CG6015

Secondary FlyBase IDs

References ( 10 )

Research paper

Nybakken et al., 2005, Nature Genetics 37(12): 1323--1332: A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. [FBrf0191274]
Ivanov et al., 2004, Proc. Natl. Acad. Sci. USA 101(46): 16216--16221: Genes required for Drosophila nervous system development identified by RNA interference. [FBrf0180653]
Mount and Salz, 2000, J. Cell Biol. 150(2): F37--F43: Pre-messenger RNA processing factors in the Drosophila genome. [FBrf0129982]

Personal communication to FlyBase

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]
Bloomington Drosophila Stock Center, 2004.11.6, Exelixis insertion alleles that are not in FlyBase.: Exelixis insertion alleles that are not in FlyBase. [FBrf0179797]
Ryder, 2004.4.26, Exelixis CG deletion data.: Exelixis CG deletion data. [FBrf0184335]

FlyBase analysis

FlyBase, 1992-, FlyBase curation: FlyBase curation. [FBrf0105495]

Computer file

BDGP Project Members, 2000-, Berkeley Drosophila Genome Project.: Berkeley Drosophila Genome Project. [FBrf0125078]

Automatic genome annotation

FamiliarityBreedsContempt, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126705]

Curated genome annotation

Gelbart, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126667]