Gene Dmel\rod

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General Information

Symbol

Dmel\rod

Species

D. melanogaster

Name

rough deal

Annotation symbol

CG1569

Feature type

protein_coding_gene

FlyBase ID

FBgn0003268

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

3-105.1

Cytogenetic map

100C6-100C7

Sequence location

3R:27,406,394..27,413,861 [+]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene rough deal is referred to in FlyBase by the symbol rod (CG1569, FBgn0003268). It has the cytological map location 100C6-100C7. Its sequence location is 3R:27406394..27413861. Its molecular function is unknown. It is involved in the biological processes: mitotic cell cycle spindle assembly checkpoint; mitotic sister chromatid segregation. 19 alleles are reported. The phenotypes of these alleles are annotated with: mitotic anaphase; nuclear chromosome; eye; anterior fascicle; spermatocyte; meiotic cell cycle. It has one annotated transcript and one annotated polypeptide.

Phenotypic Description from the Red Book (Lindsley & Zimm 1992)

Gene/Allele symbols may differ from current usage

rod: rough deal

Mutants show mitotic abnormalities in larval neuroblasts; there is a high frequency of both aneuploid cells and abnormal anaphase figures, with lagging chromatids, anaphase bridges, and stretched chromatid arms. Abnormal chromosome behavior also occurs in the second meiotic anaphase in male meiosis, although motile sperm are produced. All surviving homozygous females and 90% of surviving homozygous males are sterile and have roughened eyes, sparse abdominal bristles, and notched wings.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

100C6-100C7

Limits computationally determined from genome sequence between P{EP}pygo^EP1076 and P{PZ}ttk⁰²⁶⁶⁷&P{lacW}ttk^j6C7

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

100C5-100C5

(Aguliera, 1998.12.16)

100C-100D

(determined by in situ hybridisation)

(Karess and Glover, 1989)

Experimentally Determined Recombination Data

Location

3-105.1

Left of (cM)

Right of (cM)

Notes

Molecular Map Data

Gene Order (in direction of increasing cytology)

References

In direction of increasing cytology: pygo- rod+

(Scaerou et al., 1999)

Gene Order (overall orientation not stated)

References

Gene Model & Products

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

Comments on Gene Model

Predicted protein sequences differs from that of Accession Q96695. The difference is likely due to a frame shift mutation in either the reference sequence or the reported sequence Q96695.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

rod-RA

FBtr0085795

NM_057357

6653

2089

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

rod-PA

FBpp0085156

239.7

2089

6.07

NP_476705

AAF57162

Additional Polypeptide Data & Comments

Reported size (kD)

2098 (aa); 200 (kD observed); 240 (kD predicted)

(Scaerou et al., 1999)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0003268

Crossreferences

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Maps to

FBcl0298204

(FlyBase, 1992-)

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

deletion

rod[X-1]
3R:27,406,054..27,410,625

comment=nucleotides 538-5109 of GB:AF114152 deleted
evidence=experimental

(Scaerou et al., 1999)

deletion

rod[X-5]-1
3R:27,409,301..27,409,312

comment=One of three lesions associated with this mutation; 12 bp deletion.
evidence=experimental

(Scaerou et al., 1999)

deletion

rod[X-5]-2
3R:27,409,532..27,409,720

comment=One of three lesions associated with this mutation; 189 bp deletion.
evidence=experimental

(Scaerou et al., 1999)

External Data

Linkouts

DEDB - Drosophila exon database: splicing graphs

•

11481

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

larval stage | third instar

neuroblast <of> larval brain

(Scaerou et al., 1999)

larval stage

larval brain

(Scaerou et al., 1999)

adult stage, spermatogenesis

spermatocyte

(Scaerou et al., 1999)

Marker for

Subcellular Localization

CV Term

kinetochore

(Scaerou et al., 1999)

External Data & Images

Linkouts

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

•

FBgn0003268

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0003268

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

•

FBgn0003268

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

viable

rod^EY04576

viable | reduced

semi-viable

rod^X-2

lethal | recessive

rod^X-1

lethal | larval stage | recessive

rod^H4.8

Other Phenotypes

Allele

wild-type

rod^+tC3L9

visible, with Scer\GAL4^ey.PH

rod^EP3408

mitotic cell cycle defective

Sterility

Allele

fertile

rod^EY04576

Phenotype manifest in

Allele

spermatocyte

rod¹¹⁰⁰

meiotic cell cycle

rod¹¹⁰⁰

eye, with Scer\GAL4^ey.PH

rod^EP3408

anterior fascicle, with Scer\GAL4^elav-C155

rod^EP3408

nuclear chromosome & mitotic anaphase

rod^H4.8

chromatin & mitotic anaphase

rod^H4.8

chromatin & mitotic telophase

rod^H4.8

mitotic anaphase

nuclear chromosome

Classical Alleles ( 15 )

For All Classical Alleles Show

Allele of rod	Mutagen	Stocks	Known lesion
rod¹¹⁰⁰	ethyl methanesulfonate	0	Yes
rod^29D	PM hybrid dysgenesis	0	Yes
rod^EP3408	P-element activity	1	--
rod^EY04576	P-element activity	1	--
rod^H4.8	PM hybrid dysgenesis	0	Yes
rod^RP153	PM hybrid dysgenesis	0	Yes
rod^X-1	X ray	0	Yes
rod^X-2	X ray	0	--
rod^X-3	X ray	0	--
rod^X-4	X ray	0	--
rod^X-5	X ray	0	Yes
rod^X-6	X ray	0	--
rod^f00967	piggyBac transposase	1	--
rod^pygo9	Δ2-3	0	Yes
rod^unspecified		0	--

Alleles Carried on Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Allele of rod	Mutagen	Stocks	Known lesion
rod^+tC3L9	in vitro construct \| genomic fragment	0	Yes
rod^GD8768	in vitro construct \| RNAi in vitro construct \| regulatory fusion	1	Yes
rod^{T:Avic\GFP-EGFP}	in vitro construct \| coding region fusion	0	Yes
rod^{T:Disc\RFP-mRFP}	in vitro construct \| coding region fusion	0	Yes

Aneuploid Aberrations

Useful deficiency

Df(3R)R113

Useful duplication

Dp(3;3)516

Disrupted in

Df(3R)A113

(Schejter and Wieschaus, 1993)

Df(3R)E(sina)9

(Wisotzkey et al., 1998)

Df(3R)P4.1

(Scaerou et al., 1999)

Not disrupted in

Df(3R)E40

(Wisotzkey et al., 1998)

Df(3R)Kpn-A

(Wisotzkey et al., 1998)

Duplicated in

Dp(3;1)48

(Schejter and Wieschaus, 1993)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD8768}

characterization construct

P{rod-GFP.B}

P{rod.RFP}

P{rod^+tC3L9}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

insertion of mobile activating element

P{EPgy2}rod^EY04576

P{EP}rod^EP3408

Related Comments

Please look at the allele reports for the complete phenotype data

Mutations in rod result in mitotic segregational failure due to delayed or incomplete release of sister chromatids.

(Karess et al., 1990)

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

Molecular Function

CV term

Evidence

References

Biological Process

CV term

Evidence

References

mitotic cell cycle spindle assembly checkpoint

non-traceable author statement

(Gonzalez and Bornens, 2000)

traceable author statement

(Lee and Orr-Weaver, 2003)

mitotic sister chromatid segregation

inferred from mutant phenotype

(Scaerou et al., 2001)

Cellular Component

CV term

Evidence

References

cytoplasm

inferred from direct assay

(Buffin et al., 2005)

kinetochore

inferred from direct assay

(Scaerou et al., 1999)

inferred from direct assay

(Basto et al., 2004)

inferred from direct assay

(Buffin et al., 2005)

inferred from direct assay

(Scaerou et al., 2001)

inferred from direct assay

(Griffis et al., 2007)

kinetochore microtubule

inferred from direct assay

(Scaerou et al., 1999)

inferred from direct assay

(Basto et al., 2004)

inferred from direct assay

(Buffin et al., 2005)

non-traceable author statement

(Gonzalez and Bornens, 2000)

inferred from direct assay

(Scaerou et al., 2001)

outer kinetochore of condensed chromosome

non-traceable author statement

(Blower and Karpen, 2001)

spindle

inferred from direct assay

(Griffis et al., 2007)

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

rod allele

Gene

References

unspecified

External Data

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

•

68562

Orthologs

Genome-wide drosophilid orthologs

Dana\GF22970

Dere\GG11814

Dgri\GH18637

Dmoj\GI23397

Dper\GL23634

Dpse\GA13892

Dsec\GM16431

Dvir\GJ23087

Dwil\GK11720

Dyak\GE10947

Curated drosophilid orthologs

Dpse\GA13892

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000009150
Anopheles gambiae (Ensembl)
ENSBTAP00000029648
Bos taurus (Ensembl)
ENSCAFP00000011596
Canis familiaris (Ensembl)
NEWSINFRUP00000150722
Takifugu rubripes (Ensembl)
ENSGALP00000007179
Gallus gallus (Ensembl)
ENSP00000328236
Homo sapiens (Ensembl)
ENSMODP00000015395
Monodelphis domestica (Ensembl)
ENSRNOP00000050210
Rattus norvegicus (Ensembl)
GSTENP00029432001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000017034
Xenopus tropicalis (Ensembl)
ZDB-GENE-050208-92
Danio rerio (Zfin)

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 4 )

v19152

w¹¹¹⁸; P{GD8768}v19152

Bloomington

19842

y¹ w^67c23; P{EPgy2}rod^EY04576

Genomic Clones ( 2 )

cDNA Clones ( 11 )

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

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

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FBgn0003268

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

•

FBgn0003268

Antibody Information

polyclonal

(Scaerou et al., 1999)

Other Information

Discoverer

Etymology

Identification

Position Effect Variegation Data

Relationship to Other Genes

Source for database identity of

Source for identity of: rod CG1569

(Zhao, 1999.11)

Source for database merge of

Source for merge of: rod EP3408 Source for merge of rod EP3408 was that EP3408 insertion is within rod (and in the right orientation) (date:040519).

(FlyBase, 1996-)

Additional comments

FlyBase curator comment: "EP3408" overexpression phenotype stated to be due to its effect on pygo but orientation of the P{EP} element suggests otherwise.

(Singh et al., 2005)

Comments About Role

Comments About Molecular Function

Other Comments

dsRNA has been synthesised against this gene and transfected into S2 cells.

(Griffis et al., 2007)

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•