Gene Dmel\CG4328

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General Information

Symbol

Dmel\CG4328

Species

D. melanogaster

Name

Annotation symbol

CG4328

Feature type

protein_coding_gene

FlyBase ID

FBgn0036274

Gene Model Status

Current

Stock availability

3 publicly available

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

69A5-69A5

Sequence location

3L:12,284,056..12,289,121 [-]

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\CG4328 (FBgn0036274). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: sequence-specific DNA binding transcription factor activity. There is experimental evidence that it is involved in the biological process: dendrite morphogenesis; phagocytosis, engulfment. 2 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: Homeobox; Homeobox, conserved site; Homeodomain-like; Homeodomain-related; Zinc finger, LIM-type. 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 18-24 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult central nervous system. Comments on Affy2 ProbeSet: ProbeSet 1633414_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of CG4328. Gene sequence location is 3L:12284056..12289121.

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

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FB2011_10

FB2012_01

Sequence features

HFA10410

BKN30729

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

69A5-69A5

Limits computationally determined from genome sequence between P{PZ}l(3)05088⁰⁵⁰⁸⁸ and P{PZ}l(3)06924⁰⁶⁹²⁴

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\CG4328 for information on other features

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

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

CG4328-RB

FBtr0301071

NM_140310

1866

544

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

CG4328-PB

FBpp0290293

59.6

544

7.93

NP_648567

AAF49932

Additional Polypeptide Data & Comments

Reported size (kDa)

Comments

External Data

Linkouts

Crossreferences

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

•

Homeobox (IPR001356)

Zinc finger, LIM-type (IPR001781)

Homeodomain-like (IPR009057)

Homeodomain-related (IPR012287)

Homeobox, conserved site (IPR017970)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Q9VTW3

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.

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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_29

External Data & Images

Linkouts

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

•

FBgn0036274

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

CG4328-RA

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

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

CG4328^GD4287

Other Phenotypes

Allele

body color defective, with Scer\GAL4^pnr-MD237

CG4328^GD4287

Phenotype manifest in

Allele

mesothoracic tergum, with Scer\GAL4^pnr-MD237

CG4328^GD4287

Classical Alleles ( 0 )

For All Classical Alleles Show

Allele of CG4328	Class	Mutagen	Stocks	Known lesion

Alleles Carried on Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Allele of CG4328	Class	Mutagen	Stocks	Known lesion
CG4328^GD4287		in vitro construct - RNAi in vitro construct - regulatory fusion	2	Yes
CG4328^JF02314		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{GD4287}

P{TRiP.JF02314}

Insertions

Type of insertions

Name

Expression data

Gene Ontology: Function, Process & Cellular Component ( 7 unique terms )

Terms Based on Experimental Evidence ( 2 terms )

Molecular Function ( 0 terms)

Biological Process

CV term

Evidence

References

dendrite morphogenesis

inferred from mutant phenotype

(Parrish et al., 2006)

phagocytosis, engulfment

inferred from mutant phenotype

(Stroschein-Stevenson et al., 2006)

Cellular Component ( 0 terms)

Terms Based on Predictions or Assertions ( 5 terms )

Molecular Function

CV term

Evidence

References

sequence-specific DNA binding

inferred from electronic annotation with InterPro:IPR001356, InterPro:IPR017970

(FlyBase Curators et al., 2004-)

sequence-specific DNA binding transcription factor activity

inferred from sequence or structural similarity with EMBL:AF078166

(FlyBase, 1992-)

zinc ion binding

inferred from electronic annotation with InterPro:IPR001781

(FlyBase Curators et al., 2004-)

Biological Process

CV term

Evidence

References

regulation of transcription, DNA-dependent

inferred from electronic annotation with InterPro:IPR001356, InterPro:IPR012287, InterPro:IPR017970

(FlyBase Curators et al., 2004-)

Cellular Component

CV term

Evidence

References

nucleus

inferred from sequence or structural similarity with EMBL:AF078166

(FlyBase, 1992-)

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

CG4328 allele

Gene

References

External Data

Linkouts

BioGRID - A database of protein and genetic interactions

•

64758

DroID - A comprehensive database of gene and protein interactions.

•

FBgn0036274

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

•

39405

Orthologs

Genome-wide drosophilid orthologs

Dana\GF24989

Dere\GG13839

Dgri\GH16074

Dmoj\GI12337

Dper\GL25001

Dpse\GA18112

Dsec\GM24666

Dsim\GD12730

Dvir\GJ12228

Dwil\GK12807

Dyak\GE20130

Curated drosophilid orthologs

Dpse\GA18112

Linkouts

OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs.

•

Stocks & Reagents

Stocks Listed in FlyBase ( 3 )

Bloomington

27987

y¹ v¹; P{TRiP.JF02314}attP2

VDRC

v30516

w¹¹¹⁸; P{GD4287}v30516

v30517

w¹¹¹⁸; P{GD4287}v30517

Genomic Clones ( 1 )

BACR48J05

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

cDNA Clones ( 3 )

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

IP01440

Other clones

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Linkouts

DRSC - Results from RNAi screens.

•

FBgn0036274

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

•

39405

Antibody Information

Other Information

Discoverer

Etymology

Identification

Relationship to Other Genes

Source for database identity of

Source for database merge of

Additional comments

Other Comments

dsRNA has been made from templates generated with primers directed against this gene. RNAi of CG4328 results in inappropriate anterior arborization of ddaE neurons. These neurons also show anterior or even ventral displacement of ddaD concomitant with anterior arborization of ddaE as well as displacement of ddaE arbors concomitant with misrouting of ddaD. RNAi also causes other general defects in dendrite morphogenesis.

(Parrish et al., 2006)

S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

(Stroschein-Stevenson et al., 2006)

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_140310

RefSeq (Proteins)

•

NP_648567

DDBJ / EMBL / GenBank

•

AAF49932

Entrez Gene - A searchable database of RefSeq genes.

•

39405

UniProtKB/TrEMBL

•

Q9VTW3

Other Crossreferences

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

•

Homeobox (IPR001356)

Zinc finger, LIM-type (IPR001781)

Homeodomain-like (IPR009057)

Homeodomain-related (IPR012287)

Homeobox, conserved site (IPR017970)

Linkouts

BioGRID - A database of protein and genetic interactions

•

64758

DroID - A comprehensive database of gene and protein interactions.

•

FBgn0036274

DRSC - Results from RNAi screens.

•

FBgn0036274

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

•

FBgn0036274

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

CG4328-RA

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

•

FBgn0036274

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

•

39405

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

•

39405

modMine - Data generated by the modENCODE project.

•

FBgn0036274

OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs.

•

Synonyms & Secondary IDs ( 1 )

Reported As

Symbol Synonym

CG4328

(Hoskins et al., 2005, Parrish et al., 2006, Roignant et al., 2010, Stroschein-Stevenson et al., 2006, Perkins et al., 2009)

Name Synonym

Secondary FlyBase IDs

References ( 15 )

Research paper

Roignant et al., 2010, Development 137(2): 273--281: The transcriptional co-factor Chip acts with LIM-homeodomain proteins to set the boundary of the eye field in Drosophila. [FBrf0209594]
Parrish et al., 2006, Genes Dev. 20(7): 820--835: Genome-wide analyses identify transcription factors required for proper morphogenesis of Drosophila sensory neuron dendrites. [FBrf0190556]
Stroschein-Stevenson et al., 2006, PLoS Biol. 4(1): 87--99: Identification of Drosophila gene products required for phagocytosis of Candida albicans. [FBrf0191376]
Hoskins et al., 2005, Nucleic Acids Res. 33(21): e185: Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). [FBrf0191341]
Popovici et al., 2001, FEBS Lett. 491(3): 237--242: Homeobox gene clusters and the human paralogy map. [FBrf0135227]

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]
Boutros et al., 2004, Science 303(5659):: Supporting Online Material: Figures S1 to S8; Tables S1 to S6. [FBrf0174218]
Giot et al., 2003, Science 302(5651):: Tables S1 to S7. [FBrf0166452]

Personal communication to FlyBase

Perkins et al., 2009, Update to TRiP stock collection.: Update to TRiP stock collection. [FBrf0208864]
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, 1992-, FlyBase curation: FlyBase curation. [FBrf0105495]

Automatic genome annotation

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

Curated genome annotation

Lei, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126680]