Gene Dmel\qkr58E-1

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General Information

Symbol

Dmel\qkr58E-1

Species

D. melanogaster

Name

quaking related 58E-1

Annotation symbol

CG3613

Feature type

protein_coding_gene

FlyBase ID

FBgn0022986

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

58D8-58D8

Sequence location

2R:18,300,413..18,303,047 [-]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene quaking related 58E-1 is referred to in FlyBase by the symbol qkr58E-1 (CG3613, FBgn0022986). It has the cytological map location 58D8. Its sequence location is 2R:18300413..18303047. Its molecular function is described as: mRNA binding; RNA binding. The biological processes in which it is involved are not known. 2 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

58D8-58D8

Limits computationally determined from genome sequence between P{lacW}l(2)k13211^k13211&P{EP}EP827 and P{PZ}l(2)rG270^rG270

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

58E-58E

(Fyrberg, 1997.12.16)

58E-58E

(determined by in situ hybridisation)

(Fyrberg et al., 1998)

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\qkr58E-1 for information on other features

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

qkr58E-1-RA

FBtr0071843

NM_079085

1625

396

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

qkr58E-1-PA

FBpp0071754

45.4

396

9.41

NP_523809

AAF46844

Additional Polypeptide Data & Comments

Reported size (kD)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0022986

Crossreferences

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

•

K Homology (IPR004087)

K Homology, type 1 (IPR004088)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

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

•

1324

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

AI107920

External Data & Images

Linkouts

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

•

FBgn0022986

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

•

FBgn0022986

Alleles & Phenotypes

Summary of Allele Phenotypes

Phenotype manifest in

Allele

Classical Alleles ( 1 )

For All Classical Alleles Show

Allele of qkr58E-1	Class	Mutagen	Stocks	Known lesion
qkr58E-1^EP2103		P-element activity	2	Yes

Alleles Carried on Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Allele of qkr58E-1	Class	Mutagen	Stocks	Known lesion
qkr58E-1^GD11161		in vitro construct \| RNAi in vitro construct \| regulatory fusion	2	Yes

Aneuploid Aberrations

Useful deficiency

Df(2R)02311

Useful duplication

Dp(2;2)l-32

Disrupted in

Df(2R)Exel7173

(Ryder, 2004.4.26)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD11161}

Insertions

Type of insertions

Name

Expression data

insertion of mobile activating element

P{EP}qkr58E-1^EP2103

Related Comments

Please look at the allele reports for the complete phenotype data

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

Molecular Function

CV term

Evidence

References

RNA binding

inferred from electronic annotation with InterPro:IPR004087, InterPro:IPR004088

(FlyBase Curators et al., 2004-)

mRNA binding

non-traceable author statement

(Fyrberg, 1997.12.16)

Biological Process

CV term

Evidence

References

Cellular Component

CV term

Evidence

References

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

qkr58E-1 allele

Gene

References

External Data

Linkouts

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

•

63177

Orthologs

Genome-wide drosophilid orthologs

Dana\GF13021

Dere\GG20696

Dgri\GH20534

Dmoj\GI18980

Dper\GL16924

Dpse\GA17559

Dsec\GM15641

Dsim\GD25130

Dvir\GJ19941

Dwil\GK20824

Dyak\GE11680

Curated drosophilid orthologs

Dpse\GA17559

Linkouts

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 4 )

Szeged

P{EP}qkr58E-1^EP2103

VDRC

v26332

w¹¹¹⁸; P{GD11161}v26332

v26333

w¹¹¹⁸; P{GD11161}v26333/TM3

Bloomington

17023

w¹¹¹⁸; P{EP}qkr58E-1^EP2103 qkr58E-2^EP2103

Genomic Clones ( 2 )

cDNA Clones ( 16 )

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

GH05812

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

•

FBgn0022986

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

•

FBgn0022986

Antibody Information

Other Information

Discoverer

Etymology

Identification

Position Effect Variegation Data

Relationship to Other Genes

Source for database identity of

Source for identity of: qkr58E-1 CG3613

(Milshina, 1999.11)

Source for database merge of

Additional comments

Comments About Role

Comments About Molecular Function

Other Comments

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•

NM_079085

RefSeq (Proteins)

•

NP_523809

DDBJ / EMBL / GenBank

•

UniProtKB/TrEMBL

•

Other Crossreferences

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

•

K Homology (IPR004087)

K Homology, type 1 (IPR004088)

Linkouts

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

•

63177

DEDB - Drosophila exon database: splicing graphs

•

1324

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

•

FBgn0022986

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

•

FBgn0022986

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

•

FBgn0022986

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

•

FBgn0022986

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

•

FBgn0022986

PANTHER - Protein classification by function, families, and pathways

•

FBgn0022986

University of Chicago Dev. Expression

•

FBgn0022986

Synonyms & Secondary IDs ( 6 )

Reported As

Symbol Synonym

CG3613

(Kraut et al., 2001, Kraut et al., 2001, )

qkr-58-E

(Mutsuddi et al., 2004)

qkr58E-1

qrk58E-1

Name Synonym

KH-domain

(Kraut et al., 2001, Kraut et al., 2001)

quaking related 58E-1

Secondary FlyBase IDs

References ( 18 )

Research paper

Mutsuddi et al., 2004, Curr. Biol. 14(4): 302--308: The spinocerebellar ataxia 8 noncoding RNA causes neurodegeneration and associates with staufen in Drosophila. [FBrf0174476]
Orian et al., 2003, Genes Dev. 17(9): 1101--1114: Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. [FBrf0158942]
Kraut et al., 2001, Curr. Biol. 11(6): 417--430: A gain-of-function screen for genes controlling motor axon guidance and synaptogenesis in Drosophila. [FBrf0135708]
Lasko, 2000, J. Cell Biol. 150(2): F51--F56: The Drosophila melanogaster genome: translation factors and RNA binding proteins. [FBrf0129923]
Fyrberg et al., 1998, Biochem. Genet. 36(1-2): 51--64: A family of Drosophila genes encoding quaking-related maxi-KH domains. [FBrf0102312]

Supplementary material

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

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]
Ryder, 2004.4.26, Exelixis CG deletion data.: Exelixis CG deletion data. [FBrf0184335]

FlyBase analysis

FlyBase, 1996-, FlyBase inference based on genome sequence analysis.: FlyBase inference based on genome sequence analysis. [FBrf0104946]
FlyBase, 1992-, FlyBase curation: FlyBase curation. [FBrf0105495]

Curated genome annotation

Guan, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126671]
Milshina, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126686]

DNA/RNA sequence record

Fyrberg, 1997.12.16, GenBank/EMBL/DDBJ: AF038584: Drosophila melanogaster QKR58E-1 (qkr58E-1) mRNA, complete cds. [FBrf0115108]

Computer file

Gene Disruption Project members, 2001-, [title not yet available]: [title not yet available] [FBrf0132177]
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]