Gene Dmel\Rfx

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General Information

Symbol

Dmel\Rfx

Species

D. melanogaster

Name

Rfx

Annotation symbol

CG6312

Feature type

protein_coding_gene

FlyBase ID

FBgn0020379

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

86B1-86B2

Sequence location

3R:6,188,233..6,203,790 [-]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

This gene is referred to in FlyBase by the symbol Rfx (CG6312, FBgn0020379). It has the cytological map location 86B1-86B2. Its sequence location is 3R:6188233..6203790. Its molecular function is described as: RNA polymerase II transcription factor activity; DNA binding. It is involved in the biological processes: nervous system development; dendrite morphogenesis; regulation of transcription; regulation of transcription, DNA-dependent. 8 alleles are reported. The phenotypes of these alleles are annotated with: macrochaeta; antenna; abdominal lateral pentascolopidial chordotonal organ lch5. It has 2 annotated transcripts and 2 annotated polypeptides.

External Summaries

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

86B1-86B2

Limits computationally determined from genome sequence between P{PZ}jumu⁰⁶⁴³⁹&P{lacW}l(3)j8B6^j8B6 and P{PZ}hth⁰⁵⁷⁴⁵

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

86A-86B

(determined by in situ hybridisation)

(Durand et al., 2000)

Experimentally Determined Recombination Data

Location

(Durand and Couble, 1997)

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

Overall orientation not stated: CG17100? Rfx+

(Durand et al., 2000)

Gene Model & Products

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

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

Rfx-RA

FBtr0082238

NM_141742

3943

897

Rfx-RB

FBtr0112895

NM_001104268

4489

1079

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

Rfx-PA

FBpp0081716

98.0

897

4.72

NP_649999

AAF54526

Rfx-PB

FBpp0111808

117.4

1079

6.14

NP_001097738

ABW08636

Additional Polypeptide Data & Comments

Reported size (kD)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0020379

Crossreferences

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

•

DNA-binding RFX (IPR003150)

Winged helix repressor DNA-binding (IPR011991)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Maps to

(Durand et al., 2000)

Does NOT map to

Identified with

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

point mutation

Rfx[253]
3R:6,190,957..6,190,957

evidence=experimental
na_change=C6190957T
pr_change=S435F|Rfx-PA
reported_na_change=C1899T
reported_pr_change=S435F

(Dubruille et al., 2002)

External Data

Linkouts

DEDB - Drosophila exon database: splicing graphs

•

8906

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

External Data & Images

Linkouts

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

•

FBgn0020379

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0020379

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

•

FBgn0020379

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

viable

Rfx^c02503

lethal | larval stage | recessive

Other Phenotypes

Allele

olfaction defective | larval stage

Rfx⁴⁹

olfaction defective | larval stage (with Rfx⁴⁹)

Rfx²⁵³

olfaction defective | larval stage (with Rfx²⁵³)

Rfx⁴⁹

taste defective | larval stage (with Rfx⁴⁹)

Rfx²⁵³

taste defective | larval stage (with Rfx²⁵³)

Rfx⁴⁹

uncoordinated | adult stage (with Df(3R)S143702)

Rfx²⁵³

uncoordinated | adult stage (with Rfx⁴⁹)

Rfx²⁵³

uncoordinated | adult stage (with Rfx²⁵³)

Rfx⁴⁹

neurophysiology defective (with Rfx⁴⁹)

Rfx²⁵³

neurophysiology defective (with Rfx²⁵³)

Rfx⁴⁹

Sterility

Allele

fertile

Rfx^c02503

Phenotype manifest in

Allele

macrochaeta (with Rfx⁴⁹)

Rfx²⁵³

antenna (with Rfx⁴⁹)

Rfx²⁵³

Johnston's organ & scolopidium (with Rfx⁴⁹)

Rfx²⁵³

Johnston's organ & scolopidial cilium (with Rfx⁴⁹)

Rfx²⁵³

Johnston's organ & scolopale (with Rfx⁴⁹)

Rfx²⁵³

sensillum campaniformium & wing sensillum & dendrite (with Rfx⁴⁹)

Rfx²⁵³

sensillum campaniformium & wing sensillum (with Rfx⁴⁹)

Rfx²⁵³

chordotonal organ & leg sensillum (with Df(3R)S143702)

Rfx²⁵³

chordotonal organ & leg sensillum & scolopidial cilium (with Df(3R)S143702)

Rfx²⁵³

macrochaeta (with Rfx²⁵³)

Rfx⁴⁹

antenna (with Rfx²⁵³)

Rfx⁴⁹

Johnston's organ & scolopidium (with Rfx²⁵³)

Rfx⁴⁹

Johnston's organ & scolopidial cilium (with Rfx²⁵³)

Rfx⁴⁹

Johnston's organ & scolopale (with Rfx²⁵³)

Rfx⁴⁹

sensillum campaniformium & wing sensillum & dendrite (with Rfx²⁵³)

Rfx⁴⁹

sensillum campaniformium & wing sensillum (with Rfx²⁵³)

Rfx⁴⁹

abdominal lateral pentascolopidial chordotonal organ lch5

Rfx⁴⁹

abdominal lateral pentascolopidial chordotonal organ lch5 & dendrite

Rfx⁴⁹

abdominal lateral pentascolopidial chordotonal organ lch5 & scolopidial cilium

Rfx⁴⁹

Classical Alleles ( 6 )

For All Classical Alleles Show

Allele of Rfx	Mutagen	Stocks	Known lesion
Rfx²⁵³	ethyl methanesulfonate	0	--
Rfx⁴⁹	Δ2-3	0	Yes
Rfx^MB03617		1	--
Rfx^c01250	piggyBac transposase	1	--
Rfx^c02503	piggyBac transposase	2	--
Rfx^unspecified		0	--

Alleles Carried on Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Allele of Rfx	Class	Mutagen	Stocks	Known lesion
Rfx^GD4148		in vitro construct \| RNAi in vitro construct \| regulatory fusion	1	Yes
Rfx^Scer\UAS.cDa		in vitro construct \| regulatory fusion	0	Yes

Aneuploid Aberrations

Useful deficiency

Df(3R)by77

Useful duplication

Dp(3;3)M86D⁺2

Disrupted in

Df(3R)Exel6157

(Ryder, 2004.4.26)

Df(3R)Rfx⁴⁹

(Dubruille et al., 2002)

Df(3R)S143702

(Dubruille et al., 2002)

Df(3R)hth

(Dubruille et al., 2002)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD4148}

P{UAS-Rfx.D}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

PBac{PB}Rfx^c01250

PBac{PB}Rfx^c02503

P{?lArB}Rfx⁴⁹

insertion of enhancer trap binary system

Mi{ET1}Rfx^MB03617

Related Comments

Please look at the allele reports for the complete phenotype data

Rfx mutants show defects in chemosensory and mechanosensory behaviours. They have abnormal function and structure of neuronal cilia.

(Dubruille et al., 2002)

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

Molecular Function

CV term

Evidence

References

DNA binding

inferred from electronic annotation with InterPro:IPR003150

(FlyBase Curators et al., 2004-)

RNA polymerase II transcription factor activity

non-traceable author statement

(Durand, 1999.2.16)

Biological Process

CV term

Evidence

References

dendrite morphogenesis

traceable author statement

(Gao and Bogert, 2003)

nervous system development

inferred from mutant phenotype

(Dubruille et al., 2002)

regulation of transcription

traceable author statement

(Gao and Bogert, 2003)

regulation of transcription, DNA-dependent

inferred from electronic annotation with InterPro:IPR003150

(FlyBase Curators et al., 2004-)

Cellular Component

CV term

Evidence

References

nucleus

non-traceable author statement

(Durand, 1999.2.16)

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

Rfx allele

Gene

References

External Data

Linkouts

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

•

66413

Drosophila PIMRider - The Drosophila Protein Interaction map

•

522515

Orthologs

Genome-wide drosophilid orthologs

Dana\GF17463

Dere\GG17288

Dgri\GH18452

Dmoj\GI24030

Dper\GL23834

Dpse\GA19507

Dsec\GM26172

Dvir\GJ23659

Dwil\GK11555

Dyak\GE24689

Curated drosophilid orthologs

Dpse\GA19507

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000002747
Anopheles gambiae (Ensembl)
ENSBTAP00000023488
Bos taurus (Ensembl)
ENSCAFP00000003031
Canis familiaris (Ensembl)
ENSCINP00000018686
Ciona intestinalis (Ensembl)
NEWSINFRUP00000171051
Takifugu rubripes (Ensembl)
ENSGALP00000016529
Gallus gallus (Ensembl)
ENSP00000265775
Homo sapiens (Ensembl)
ENSMMUP00000001093
Macaca mulatta (Ensembl)
ENSMODP00000019237
Monodelphis domestica (Ensembl)
ENSPTRP00000018049
Pan troglodytes (Ensembl)
ENSRNOP00000019515
Rattus norvegicus (Ensembl)
GSTENP00004934001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000012250
Xenopus tropicalis (Ensembl)
WBGene00024204
Caenorhabditis briggsae (Wormbase)
WBGene00000914
Caenorhabditis elegans (Wormbase)
ZDB-CDNA-050227-4
Danio rerio (Zfin)
ZDB-GENE-050227-4
Danio rerio (Zfin)
MGI:106582
Mus musculus (Informatics)

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 5 )

v10416

w¹¹¹⁸; P{GD4148}v10416

Bloomington

10923

w¹¹¹⁸; PBac{PB}Rfx^c02503

23634

w¹¹¹⁸; Mi{ET1}Rfx^MB03617

Genomic Clones ( 1 )

BACR03L12

cDNA Clones ( 5 )

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