Gene Dmel\CG42863

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General Information

Symbol

Dmel\CG42863

Species

D. melanogaster

Name

Annotation symbol

CG42863

Feature type

protein_coding_gene

FlyBase ID

FBgn0262110

Gene Model Status

Current

Stock availability

4 publicly available

Also Known As

CG5691

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

62B11-62B12

Sequence location

3L:1,950,306..1,964,178 [-]

Genomic Maps

Select View:

modENCODE GBrowse

Summary Information

Automatically generated summary

See sections below for more information

This gene is referred to in FlyBase by the symbol Dmel\CG42863 (FBgn0262110). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. Based on sequence similarity, it is predicted to be involved in the biological process: lysosome organization; lysosomal transport. 5 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: BEACH domain; PH-BEACH domain; WD40 repeat; WD40 repeat 2; WD40 repeat, conserved site; WD40 repeat, subgroup; WD40 repeat-like-containing domain; WD40-repeat-containing domain; WD40/YVTN repeat-like-containing domain. Gene sequence location is 3L:1950306..1964178.

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.

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FB2012_01

Sequence features

BKN23203

HFA08208

HFA08570

BKN21413

FB2011_10

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

62B11-62B12

Limits computationally determined from genome sequence between P{PZ}dlt⁰⁴²⁷⁶ and P{PZ}sls^rL182

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\CG42863 for information on other features

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

Comments on Gene Model

Gene merge based on RNA-Seq data.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

CG42863-RB

FBtr0304060

NM_139424

11334

3535

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

CG42863-PB

FBpp0293022

399.8

3535

6.91

NP_647681

AAF47598

Additional Polypeptide Data & Comments

Reported size (kDa)

Comments

External Data

Linkouts

Crossreferences

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

•

PH-BEACH domain (IPR023362)

BEACH domain (IPR000409)

WD40 repeat (IPR001680)

WD40 repeat-like-containing domain (IPR011046)

WD40-repeat-containing domain (IPR017986)

WD40/YVTN repeat-like-containing domain (IPR015943)

WD40 repeat, conserved site (IPR019775)

WD40 repeat, subgroup (IPR019781)

WD40 repeat 2 (IPR019782)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

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

Notes

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Notes

High-Throughput Expression Data

Untitled Document detailed view

See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.

modENCODE Temporal Expression Data (Graveley et al., 2011)
FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)

Expression Clusters

A cluster of genes with similar mRNA expression dynamics across development.

(The modENCODE Consortium, 2010)

mE2_34_mRNA_expression_cluster_27

External Data & Images

Linkouts

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

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

CG42863^GD7392

viable, with Scer\GAL4^pnr-MD237

CG42863^GD11736

Phenotype manifest in

Allele

Classical Alleles ( 1 )

For All Classical Alleles Show

Allele of CG42863	Class	Mutagen	Stocks	Known lesion
CG42863^MI02196			1	--

Alleles Carried on Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Allele of CG42863	Mutagen	Stocks	Known lesion
CG42863^GD11736	in vitro construct - RNAi in vitro construct - regulatory fusion	1	Yes
CG42863^GD7392	in vitro construct - RNAi in vitro construct - regulatory fusion	1	Yes
CG42863^KK101362	in vitro construct - RNAi in vitro construct - regulatory fusion	1	Yes
CG42863^KK103011	in vitro construct - RNAi in vitro construct - regulatory fusion	0	Yes

Aneuploid Aberrations

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{KK103011}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

Mi{MIC}CG42863^MI02196

Gene Ontology: Function, Process & Cellular Component ( 2 unique terms )

Terms Based on Experimental Evidence ( 0 terms )

Terms Based on Predictions or Assertions ( 2 terms )

Molecular Function ( 0 terms)

Biological Process

CV term

Evidence

References

lysosomal transport

inferred from sequence or structural similarity with UniProtKB:P97412

(FlyBase, 1992-)

lysosome organization

inferred from sequence or structural similarity with EMBL:AF114785

(FlyBase, 1992-)

Cellular Component ( 0 terms)

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Interactions & Pathways

Summary of Physical Interactions

Protein-protein

Interacting group

Assay

References

Summary of Genetic Interactions

Interacts with

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

CG42863 allele

Gene

References

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

•

FBgn0262110

InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.

•

38259

Orthologs

Genome-wide drosophilid orthologs

Dana\GF24944

Dana\GF24945

Dere\GG14542

Dere\GG14543

Dgri\GH16500

Dgri\GH16501

Dmoj\GI12177

Dmoj\GI12178

Dper\GL24810

Dper\GL24811

Dpse\GA11214

Dpse\GA19060

Dsec\Acp26Aa

Dsec\Acp26Ab

Dsim\GD13421

Dsim\GD13422

Dvir\GJ13451

Dvir\GJ13452

Dwil\GK12610

Dwil\GK12611

Dyak\GE20896

Dyak\GE20897

Curated drosophilid orthologs

Dmir\CG11814

(Thornton, 2005.12.20)

Dpse\GA11214

Dpse\GA19060

Linkouts

Stocks & Reagents

Stocks Listed in FlyBase ( 4 )

Bloomington

33174

y¹ w^*; Mi{MIC}CG42863^MI02196

VDRC

v105417

P{KK101362}VIE-260B

v38567

w¹¹¹⁸ P{GD7392}v38567

v28653

w¹¹¹⁸; P{GD11736}v28653

Genomic Clones ( 1 )

BACR16A03

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

cDNA Clones ( 26 )

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

MIP12294

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Linkouts

DRSC - Results from RNAi screens.

•

FBgn0262110

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

•

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: CG11814 CG5691

(FlyBase Genome Annotators, 2010)

Additional comments

Annotations CG11814 and CG5691 merged as CG42863 in release 5.30 of the genome annotation.

(FlyBase Genome Annotators, 2010)

Other Comments

Identified in an RNAi screen for host factors that alter infection of SL2 cells by L.monocytogenes.

(Agaisse et al., 2005)

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•

NM_139424

RefSeq (Proteins)

•

NP_647681

DDBJ / EMBL / GenBank

•

Entrez Gene - A searchable database of RefSeq genes.

•

UniProtKB/TrEMBL

•

Other Crossreferences

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

•

PH-BEACH domain (IPR023362)

BEACH domain (IPR000409)

WD40 repeat (IPR001680)

WD40 repeat-like-containing domain (IPR011046)

WD40-repeat-containing domain (IPR017986)

WD40/YVTN repeat-like-containing domain (IPR015943)

WD40 repeat, conserved site (IPR019775)

WD40 repeat, subgroup (IPR019781)

WD40 repeat 2 (IPR019782)

Linkouts

DroID - A comprehensive database of gene and protein interactions.

•

FBgn0262110

DRSC - Results from RNAi screens.

•

FBgn0262110

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

•

FBgn0262110

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

•

InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.

•

38259

modMine - Data generated by the modENCODE project.

•

FBgn0262110

Synonyms & Secondary IDs ( 3 )

Reported As

Symbol Synonym

CG5691

(Barmina et al., 2005, Keleman et al., 2009.8.5)

CG11814

(Keleman et al., 2009.8.5)

CG42863

(FlyBase Genome Annotators, 2010)

Name Synonym

Secondary FlyBase IDs

FBgn0035296
FBgn0035297

References ( 16 )

Research paper

Blanco et al., 2010, BMC Dev. Biol. 10: 94: Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs. [FBrf0211812]
Agaisse et al., 2005, Science 309(5738): 1248--1251: Genome-wide RNAi screen for host factors required for intracellular bacterial infection. [FBrf0188315]
Barmina et al., 2005, Dev. Biol. 288(2): 528--544: Sex- and segment-specific modulation of gene expression profiles in Drosophila. [FBrf0190088]
Gonzalez-Aguero et al., 2005, Gene 345(2): 213--224: Identification of genes expressed during Drosophila melanogaster gastrulation by using subtractive hybridization. [FBrf0187577]

Supplementary material

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]
Giot et al., 2003, Science 302(5651):: Tables S1 to S7. [FBrf0166452]
Kraut et al., 2001, Curr. Biol. 11(6):: A gain-of-function screen for genes controlling motor axon guidance and synaptogenesis in Drosophila. [FBrf0135968]

Personal communication to FlyBase

Bellen, 2010.12.6, BDGP_2010_1209.GDP.xml: BDGP_2010_1209.GDP.xml [FBrf0212438]
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 analysis

FlyBase Genome Annotators, 2010, Changes affecting gene model number or type in release 5.30 of the annotated D.melanogaster genome.: Changes affecting gene model number or type in release 5.30 of the annotated D.melanogaster genome. [FBrf0210979]
FlyBase, 1992-, FlyBase curation: FlyBase curation. [FBrf0105495]

Computer file

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

DNA/RNA sequence record

Thornton, 2005.12.20, GenBank/EMBL/DDBJ: DQ334074: Drosophila miranda CG11814 gene, partial cds. [FBrf0197683]

Curated genome annotation

Kodira, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126678]