FlyBase Gene Report: Dmel\ca

RAB GUANINE NUCLEOTIDE EXCHANGE FACTORS - OTHER -: RabGEFs are Guanine Nucleotide Exchange Factors (GEFs) for Rab family GTPases. The 'RAB GUANINE NUCLEOTIDE EXCHANGE FACTORS - OTHER' gene group contains RabGEF genes whose products have been shown to act as RabGEFs or have homology to RabGEFs in other species but do not fall into the main RabGEF subgroups.

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

ca: claret

Eye color ruby. With cn, eye color is deep reddish yellow; with bw, translucent brownish yellow (Mainx, 1938, Z. Indukt. Abstamm. Vererbungsl. 75: 256-76). Larval Malpighian tubes colorless (Beadle, 1937, Genetics 22: 587-611). Eye color autonomous when larval optic disk from ca is transplanted into wild type or v. Wild-type disk in ca not entirely autonomous (Beadle and Ephrussi, 1936, Genetics 21: 230); ca flies produce less v+ substance than wild type (Clancy, 1942, Genetics 27: 417-40). Uptake of radio-labeled kynurenine by larval Malpighian tubules greatly reduced; uptake by developing eyes nearly normal (Sullivan and Sullivan, 1975, Biochem. Genet. 13: 603-13). Presence of 4-0-glucosyl-N-acetyldopamine, possibly a detoxification product of dopamine, reported by Okubo (1958, Med. J. Osaka Univ. 9: 327-37). Slightly narrow body and pointed wing. RK1.

cav: claret-variegated

cav/ca slightly variegated. Can be confused with wild type. cav/cand1 females produce normal progeny. Homozygous lethal. RK3A.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\ca or the JBrowse view of Dmel\ca for information on other features

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

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Comments on Gene Model

Gene model reviewed during 5.55

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.49

Gene model reviewed during 5.57

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

ca-RA

FBtr0085484

NM_170430

7026

1961

ca-RC

FBtr0346613

NM_001300664

6398

1961

Additional Transcript Data and 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

ca-PA

FBpp0084850

217.9

1961

5.48

NP_733309

AAF56945

ca-PC

FBpp0312193

217.9

1961

5.48

NP_001287593

AHN57592

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1961 aa isoforms: ca-PA, ca-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\ca using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

ca_1

Linkouts

Gene Ontology (9 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

Rab GTPase binding

inferred from physical interaction with FLYBASE:Rab32; FB:FBgn0002567

(Ma et al., 2004)

Rab guanyl-nucleotide exchange factor activity

inferred from physical interaction with FLYBASE:Rab32; FB:FBgn0002567

(Ma et al., 2004)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (7 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

eye pigment granule organization

inferred from mutant phenotype

(Ma et al., 2004)

negative regulation of gene silencing by RNA

inferred from mutant phenotype

(Harris et al., 2011)

ommochrome biosynthetic process

inferred from mutant phenotype

(Tearle, 1991)

regulation of autophagy

inferred from mutant phenotype

(Wang et al., 2012)

regulation of lipid storage

inferred from mutant phenotype

(Wang et al., 2012)

regulation of Rab protein signal transduction

inferred from direct assay

(Ma et al., 2004)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

eye pigment precursor transport

traceable author statement

(Reaume et al., 1991)

Cellular Component (0 terms)

There is no information supporting a Cellular Component term for this gene. (Based on a review of available data on: 2015-08-06 )

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\ca in GBrowse 2

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\ca

View exonic expression by tissue for Dmel\ca

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

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

FBgn0000247

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG31037-RA

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG31037

Flygut - An atlas of the Drosophila adult midgut

FBgn0000247

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 59 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 8 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of ca

Transgenic constructs containing regulatory region of ca

Deletions and Duplications ( 48 )

Duplicated in

Dp(3;1)B152

(Frisardi and MacIntyre, 1984)

(Harris, 1977)

(Frisardi and MacIntyre, 1984)

Ts(Y;3Rt)Kpn⁺

Ts(YSt;3Rt)B226

(Jurgens and Weigel, 1988)

Ts(YSt;3Rt)J116

(Jurgens and Weigel, 1988)

Disrupted in

Df(3R)BSC547

(Christensen et al., 2008.6.11)

Df(3R)ca^nd1

(Yamamoto et al., 1989)

Df(3R)ca^nd5

(Yamamoto et al., 1989)

Df(3R)ca^nd6

(Yamamoto et al., 1989)

Df(3R)ca^nd7

(Yamamoto et al., 1989)

Df(3R)ca^nd8

(Yamamoto et al., 1989)

Df(3R)Drice

(Xu et al., 2006)

Df(3R)R61

(Mozer, 2001)

Dp(3;1)1A