FlyBase Gene Report: Dmel\car

General Information

Symbol

Dmel\car

Species

D. melanogaster

Name

carnation

Annotation Symbol

CG12230

Feature Type

protein_coding_gene

FlyBase ID

FBgn0000257

Gene Model Status

Current

Stock Availability

52 publicly available

Gene Snapshot

carnation (car) encodes a subunit of the conserved HOPS complex, which is required for pigment granule formation and membrane fusion events, such as fusions between endosomes or autophagosomes with lysosomes. car loss of function mutant flies exhibit altered eye color. [Date last reviewed: 2018-09-06]

Other Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

Vps33, Vps33A, l(1)G0447

Key Links

Genomic Location

Cytogenetic map

18D1-18D1

Sequence location

X:19,566,019..19,569,401 [+]

Recombination map

1-63

Sequence

Get Decorated FASTA

Genomic Maps

GBrowse JBrowse

Help me choose

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

[Detailed GO annotations]

Gene Group (FlyBase)

SM TRAFFICKING GENES

VPS-C COMPLEXES: HOPS AND CORVET

Protein Family (UniProt)

Belongs to the STXBP/unc-18/SEC1 family. (Q9Y1I2)

Protein Signatures (InterPro)

Molecular Function (GO)
[Detailed GO annotations]

Experimental Evidence

protein binding; contributes_to syntaxin binding

Predictions / Assertions

SNARE binding

Summaries

Gene Group (FlyBase)

SM TRAFFICKING GENES -: Members of the Sec1/Munc18 (SM) gene family interact with soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) to regulate SNARE complex assembly and vesicle membrane fusion. (Adapted from PMID:20471239).
VPS-C COMPLEXES: HOPS AND CORVET -: The heterohexameric VPS-C complexes, HOPS and CORVET have been extensively characterised in yeast. They interact with SNAREs and Rabs to promote vesicle tethering. The CORVET complex is involved in early endosome fusion, interacting with Rab5-GTP. The HOPS complex interacts with Rab7-GTP on late endosomes (multivesicular bodies) to promote fusion with the lysosomal compartment (and vacuoles) and also autophagosome-lysosome fusion. The VPS-C complexes share common subunits and CORVET to HOPS conversion intermediates (i-CORVET and i-HOPS) have been proposed to accompany early to late endosome maturation. (Adapted from PMID:19575650 and FBrf0223135).

Protein Function (UniProtKB)

Required for the biogenesis of eye pigment granules (PubMed:10549280). Plays a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane docking/fusion reactions of late endosomes/lysosomes probably as part of the class C core vacuole/endosome tethering (CORVET) complex (PubMed:10549280, PubMed:22160599, PubMed:27253064).

(UniProt, Q9Y1I2)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

car: carnation

Eye color dark ruby. Body shape and proportions seem rounded. With st, eye color is yellow-brown; with bw, brownish yellow to brown (Mainx, 1938, Z. Indukt. Abstamm. Vererbungsl. 75: 256-76). Malpighian tubes pale yellow in mature larva (Beadle, 1937, Genetics 22: 587-611) but hard to distinguish from wild type before third instar. Eye color autonomous in transplant into wild-type host (Beadle and Ephrussi, 1936, Genetics 21: 230). car dor is pupal lethal and shows reduced recovery in gynandromorphs with male parts car dor (Nash, 1971, DIS 47: 73). car lt also lethal, dies as larva when mother car;lt/+ or car/+;lt and as pupa when mother car/+;lt/+ (Nickla, 1977, Nature 268: 638-39); lethal focus domineering; fate maps to ventral nervous system (Nickla, Lilly, and McCarthy, 1980, Experientia 36: 402-05). Brain histology abnormal [McCarthy and Nickla, 1980, Experientia 36: 1361-63 (fig.)].

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\car or the JBrowse view of Dmel\car 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 5.40

gene_with_stop_codon_read_through ; SO:0000697

Gene model reviewed during 5.44

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene

gene_with_stop_codon_read_through

(Jungreis et al., 2011)

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

car-RA

FBtr0074728

NM_078686

3097

617

car-RB

FBtr0074727

NM_167664

3173

617

car-RC

FBtr0331158

NM_001272778

3173

639

Additional Transcript Data and Comments

Reported size (kB)

3.022 (longest cDNA)

(Sevrioukov et al., 1999)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

car-PA

FBpp0074497

68.8

617

6.74

NP_523410

AAF48972

car-PB

FBpp0074496

68.8

617

6.74

NP_728266

AAN09503

car-PC

FBpp0303585

71.2

639

7.13

NP_001259707

AGB95547

Polypeptides with Identical Sequences

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

617 aa isoforms: car-PA, car-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

617 (aa)

(Sevrioukov et al., 1999)

Comments

External Data

Subunit Structure (UniProtKB)

Component of the class C core vacuole/endosome tethering (CORVET) complex composed of at least dor/Vps18, Vps16A, Vps8 and car/Vps33A; unlike in other species, Vps11 is not part of the Drosophila complex (PubMed:27253064). Interacts with dor (PubMed:10549280). Interacts with ema (PubMed:20194640).

(UniProt, Q9Y1I2)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

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

External Data

Crossreferences

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

car_1
car_2

Linkouts

Gene Ontology (26 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

protein binding

inferred from physical interaction with UniProtKB:M9PF72,UniProtKB:Q24314,UniProtKB:Q9VHG1,UniProtKB:Q9VRX2

(assigned by UniProt )

(Lőrincz et al., 2016)

inferred from physical interaction with UniProtKB:A4V4S5,UniProtKB:Q24314,UniProtKB:Q9VHG1,UniProtKB:Q9VRX2

(assigned by UniProt )

(Lőrincz et al., 2016)

inferred from physical interaction with UniProtKB:Q24314

(assigned by UniProt )

(Sevrioukov et al., 1999)

syntaxin binding

inferred from physical interaction with FLYBASE:Syx16; FB:FBgn0031106

(Akbar et al., 2009)

contributes_to syntaxin binding

inferred from physical interaction with FLYBASE:Syx17; FB:FBgn0035540

(Takáts et al., 2014)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

SNARE binding

inferred from sequence or structural similarity

(Littleton, 2000)

Biological Process (18 terms)

Terms Based on Experimental Evidence (13 terms)

CV Term

Evidence

References

autophagosome maturation

inferred from mutant phenotype

(Takáts et al., 2014, Akbar et al., 2009)

cellular response to starvation

inferred from mutant phenotype

(Takáts et al., 2014)

compound eye pigmentation

inferred from mutant phenotype

(Chi et al., 2010)

inferred from genetic interaction with FLYBASE:p; FB:FBgn0086679

(Falcon-Perez et al., 2007)

determination of adult lifespan

inferred from mutant phenotype

(Simonsen et al., 2007)

endocytosis

inferred from mutant phenotype

(Wilkin et al., 2008)

endosomal vesicle fusion

inferred from mutant phenotype

(assigned by UniProt )

(Lőrincz et al., 2016)

endosome organization

inferred from mutant phenotype

(Sriram et al., 2003)

endosome to lysosome transport

inferred from mutant phenotype

(Akbar et al., 2009)

eye pigment granule organization

inferred from mutant phenotype

(Akbar et al., 2009)

inferred from mutant phenotype

(assigned by UniProt )

(Sevrioukov et al., 1999)

Notch receptor processing

inferred from mutant phenotype

(Wilkin et al., 2008)

ommochrome biosynthetic process

inferred from mutant phenotype

(Tearle, 1991)

protein targeting to lysosome

inferred from mutant phenotype

(assigned by UniProt )

(Sevrioukov et al., 1999)

regulation of protein ubiquitination

inferred from mutant phenotype

(Simonsen et al., 2007)

Terms Based on Predictions or Assertions (7 terms)

CV Term

Evidence

References

compound eye pigmentation

traceable author statement

(Toonen and Verhage, 2003)

endosomal transport

inferred from sequence or structural similarity with SGD:S000004388

(Solinger and Spang, 2013)

endosome to lysosome transport

traceable author statement

(Toonen and Verhage, 2003, Luzio et al., 2000)

intracellular transport

traceable author statement

(Narayanan and Ramaswami, 2001)

regulation of SNARE complex assembly

inferred from sequence or structural similarity with SGD:S000004388

(Solinger and Spang, 2013)

vesicle docking involved in exocytosis

inferred from electronic annotation with InterPro:IPR001619

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

vesicle-mediated transport

inferred from sequence or structural similarity

(Littleton, 2000)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

CORVET complex

inferred from direct assay

(assigned by UniProt )

(Lőrincz et al., 2016)

HOPS complex

inferred from direct assay

(Pulipparacharuvil et al., 2005)

inferred from mutant phenotype

(Takáts et al., 2014)

lysosome

inferred from direct assay

(assigned by UniProt )

(Sevrioukov et al., 1999)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

CORVET complex

inferred from sequence or structural similarity with SGD:S000004388

(Solinger and Spang, 2013)

cytosol

traceable author statement

(Toonen and Verhage, 2003)

HOPS complex

inferred from sequence or structural similarity with SGD:S000004388

(Solinger and Spang, 2013)

membrane

traceable author statement

(Toonen and Verhage, 2003)

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

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 11 -- 12

amnioserosa

(Fisher et al., 2012)

anterior midgut primordium

(Fisher et al., 2012)

fat body primordium

Comment: reported as fat body specific anlage

(Fisher et al., 2012)

fat body/gonad primordium

(Fisher et al., 2012)

garland cell primordium

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

plasmatocyte primordium

Comment: reported as plasmatocytes anlage

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 13 -- 16

crystal cell

(Fisher et al., 2012)

embryonic/larval fat body

(Fisher et al., 2012)

embryonic/larval garland cell

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

plasmatocyte

(Fisher et al., 2012)

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

CORVET complex

inferred from direct assay

(assigned by UniProt )

(Lőrincz et al., 2016)

HOPS complex

inferred from direct assay

(Pulipparacharuvil et al., 2005)

inferred from mutant phenotype

(Takáts et al., 2014)

lysosome

inferred from direct assay

(assigned by UniProt )

(Sevrioukov et al., 1999)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\car 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\car

View exonic expression by tissue for Dmel\car

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0000257

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

FBgn0000257

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG12230-RB

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

CG12230

Flygut - An atlas of the Drosophila adult midgut

FBgn0000257

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\car

Stages(s) 1-3
Stages(s) 4-6
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 10 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of car

Transgenic constructs containing regulatory region of car

Deletions and Duplications ( 37 )

Disrupted in

Df(1)14.4

(Gomez et al., 2012)

Df(1)268

(Patterson, 1932)

Df(1)BSC275

(Christensen and Cook, 2007.3.22)

(Pontecorvo, 1942)

Duplicated in

Dp(1;3)DC363

(Popodi, 2010.10.8, Venken et al., 2010)

Dp(1;3)DC364

(Popodi et al., 2010-, Venken et al., 2010)

Dp(1;f)3

(Schalet and Finnerty, 1968)

Dp(1;f)52

(Schalet and Finnerty, 1968)

(Morgan, 1938)

Not disrupted in

Not duplicated in

(Gethmann, 1967)

(Gethmann, 1967)

Partially disrupted in

Df(1)car^Δ33

(Akbar et al., 2009)

Df(1)car^Δ141

(Akbar et al., 2009)

Df(1)car^Δ163

(Akbar et al., 2009)

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal - all die before end of pupal stage, with Scer\GAL4^FRT.Act5C

car^dsRNA.UAS

lethal - all die before end of second instar larval stage | recessive

car^Δ146

partially lethal - majority die, with Scer\GAL4^pnr-MD237

car^GD1397

partially lethal - majority die | recessive

car^G0447

viable

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

car^GD1397

viable, with Scer\GAL4^tin.CΔ4

car^GD1397

Sterility

Allele

fertile

car^EY09656

Other Phenotypes

Allele

decreased cell death

car¹

eye color defective

eye color defective, with Scer\GAL4^FRT.Act5C

car^dsRNA.UAS

short lived | male

car¹

some die during pupal stage, with Scer\GAL4^FRT.Act5C

car^dsRNA.UAS

some die during pupal stage, with Scer\GAL4^pnr-MD237

car^GD1397

some die during second instar larval stage | recessive

car^Δ146

visible, with Scer\GAL4^pnr-MD237

car^GD1397

visible | recessive

visible | recessive | somatic clone

car^Δ146

wild-type

car^GMR.PS

Phenotype manifest in

Allele

autolysosome | somatic clone | wandering third instar larval stage | nutrition conditional, with Scer\GAL4^{FRT.Rnor\Cd2.Act5C}

car^GD1397

embryonic/larval brain

car¹

embryonic/larval fat body | somatic clone | wandering third instar larval stage | nutrition conditional, with Scer\GAL4^{FRT.Rnor\Cd2.Act5C}

car^GD1397

embryonic/larval garland cell | larval stage, with Scer\GAL4^unspecified

car^GD1397

endosome

car¹

eye

car¹

late endosome

car¹

late endosome | larval stage, with Scer\GAL4^unspecified

car^GD1397

male germline cell

car¹

Malpighian tubule

car¹

mesothoracic tergum, with Scer\GAL4^pnr-MD237

car^GD1397

ommatidium

car¹

ommatidium | somatic clone

car^Δ146

pigment cell

pigment cell | somatic clone

car^Δ146

rhabdomere

car¹

rhabdomere | cell autonomous | somatic clone

car^Δ146

spermatogonial cyst

car¹

wing | somatic clone

car^Δ146

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\VPS33A

15 of 15

Yes

Hsap\VPS33B

3 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Vps33a

14 of 15

Yes

Mmus\Vps33b

3 of 15

Rattus norvegicus (Norway rat) (2)

Rnor\Vps33a

10 of 13

Yes

Rnor\Vps33b

3 of 13

Xenopus tropicalis (Western clawed frog) (2)

Xtro\vps33a

3 of 12

Yes

Xtro\vps33b

3 of 12

Yes

Danio rerio (Zebrafish) (2)

Drer\vps33a

14 of 15

Yes

Drer\vps33b

2 of 15

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\vps-33.1

7 of 15

Yes

Cele\vps-33.2

6 of 15

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\ATVPS33

8 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\VPS33

10 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\vps33

12 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091906LZ )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\car

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA11493

Drosophila persimilis

Dper\GL14537

Drosophila persimilis

Dper\GL14536

Drosophila willistoni

Dwil\GK10350

Drosophila virilis

Dvir\GJ16477

Drosophila mojavensis

Dmoj\GI21456

Drosophila grimshawi

Dgri\GH12312

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091502ZK )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17016918

Glossina morsitans

Tsetse fly

Gmor\GMOY008491

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_05306

Mayetiola destructor

Hessian fly

Mdes\Mdes009998

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL000214

Anopheles darlingi

American malaria mosquito

Adar\ADAC004865

Anopheles gambiae

Malaria mosquito

Agam\AGAP003203

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ013822

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W03AV )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA008046

Danaus plexippus

Monarch butterfly

Dple\DPOGS206911-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL016091

Apis florea

Little honeybee

Aflo\2676033060

Apis mellifera

Western honey bee

Amel\car

Apis mellifera

Western honey bee

Amel\GB41103

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP10896

Bombus terrestris

Buff-tailed bumblebee

Bter\15203042

Linepithema humile

Argentine ant

Lhum\LH25249

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:000c64

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG013521

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_11755

Tribolium castaneum

Red flour beetle

Tcas\TC006102

Pediculus humanus

Human body louse

Phum\PHUM608030

Rhodnius prolixus

Kissing bug

Rpro\RPRC012001

Rhodnius prolixus

Kissing bug

Rpro\RPRC011995

Cimex lectularius

Bed bug

Clec\CLEC000057

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI004826

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_14410

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X037S )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR007845

Ixodes scapularis

Black-legged tick

Isca\ISCW000790

Stegodyphus mimosarum

African social velvet spider

Smim\KFM73712.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur05g03740

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_274981

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_107524

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_109112

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_119900

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_111119

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_301010

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_329944

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_113272

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_116308

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_120082

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_108305

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0AK0 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Vps33B_1

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Vps33B

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Vps33A

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_023451gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_011548gn

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000012212

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000021626

Gallus gallus

Domestic chicken

Ggal\VPS33B

Gallus gallus

Domestic chicken

Ggal\VPS33A

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (4)

Gene Symbol

Score

Source

Alignment

5 of 10

Rop

1 of 10

Slh

1 of 10

Vps45

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

cancer, multiple, RAS-Vps-C complex-related

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

car^dsRNA.UAS

model of cancer

CEA with Ras85D^V12.UAS

(Chi et al., 2010)

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 2 )

Allele

Disease

Interaction

References

car¹

ameliorates neurofibromatosis

modeled by Nf1^E2

(Walker et al., 2013)

car^Δ146

ameliorates neurofibromatosis

modeled by Nf1^E2

(Walker et al., 2013)

Comments on Models/Modifiers Based on Experimental Evidence ( 0 )

Disease Associations of Human Orthologs (via DIOPT v7.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

VPS33A; VPS33A core subunit of CORVET and HOPS complexes

15 of 15

610034

MUCOPOLYSACCHARIDOSIS-PLUS SYNDROME; MPSPS

VPS33B; VPS33B late endosome and lysosome associated

3 of 15

608552

ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 1; ARCS1

ARC syndrome

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

car - Rab2

pull down, peptide massfingerprinting

(Gillingham et al., 2014)

car - Rab5

pull down, peptide massfingerprinting

(Gillingham et al., 2014)

car - Syx16

anti bait coimmunoprecipitation, anti tag western blot

(Akbar et al., 2009)

car - Syx17

anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation, western blot

(Takáts et al., 2014)

car - Vps8

anti tag coimmunoprecipitation, western blot, peptide massfingerprinting

(Lőrincz et al., 2016)

car - Ykt6

pull down, western blot

(Takáts et al., 2018)

car - ema

anti tag coimmunoprecipitation, western blot

(Kim et al., 2010)

car - lt

anti tag coimmunoprecipitation, western blot

(Lőrincz et al., 2019)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

car

suppressible

Cys

(Kinser and Dolph, 2012)

car|rush

suppressible

sta

(Gailite et al., 2012)

car

enhanceable

(Lloyd et al., 2002)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

bchs

enhanceable

car

(Simonsen et al., 2007)

l(2)gd1

suppressible

car

(Schneider et al., 2013)

Nf1

suppressible

car

(Walker et al., 2013)

enhanceable

(Chi et al., 2010)

suppressible

(Yonamine et al., 2011)

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9Y1I2 )

Linkouts

BioGRID - A database of protein and genetic interactions.

59247

DroID - A comprehensive database of gene and protein interactions.

FBgn0000257

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

32947

MIST (genetic) - An integrated Molecular Interaction Database

MIST (protein-protein) - An integrated Molecular Interaction Database

Pathways

Gene Group - Pathway Membership (FlyBase)

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-63

Cytogenetic map

18D1-18D1

Sequence location

X:19,566,019..19,569,401 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

18D1-18D1

Limits computationally determined from genome sequence between P{EP}EP1526&P{EP}Pfrx^EP1150 and P{EP}Tao-1^EP1455

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

18D1-18D4

(determined by in situ hybridisation)

(Peter et al., 2002, Schäfer et al., 1999.12.2)

18D1-18D2

(Lindsley and Grell, 1968)

Experimentally Determined Recombination Data

Location

1-63

(FlyBase, 2016)

1-62.1

(Comeron et al., 2012)

1-62.5

Left of (cM)

(Homyk et al., 1986)

(Fischbach and Lyly-Hunerberg, 1983)

Right of (cM)

(Homyk et al., 1986)

Notes

Stocks and Reagents

Stocks (52)

Bloomington

car¹

car¹ su(f)⁸

579

Df(1)JF5, f¹ car¹/FM7a

12257

w^67c23 P{lacW}car^G0447

788

In(1)rst³, y¹ car¹

Kyoto

105680

car¹

101065

car¹ su(f)⁸

101194

v¹ f^3N car¹

105990

Df(1)JF5, f¹ car¹/FM7a

VDRC

v110756

P{KK108988}VIE-260B

v4548

w¹¹¹⁸; P{GD1397}v4548

v4547

w¹¹¹⁸; P{GD1397}v4547/CyO

More stocks available...

Genomic Clones (20)

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

cDNA Clones (72)

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 sequences

BDGP DGC clones

LD22396

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0000257

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0000257

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

32947

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Sevrioukov et al., 1999)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Source for merge of: car Vps33

(Sevrioukov et al., 1999)

Source for merge of: car l(1)G0447

(Peter et al., 2002)

Additional comments

"l(1)G0041" may affect "car".

(Peter et al., 2002)

Other Comments

car is required for endocytic trafficking to lysosomes. car is required for the biogenesis of pigment granules.

(Akbar et al., 2009)

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)

dor is part of a protein complex which includes car.

(Sevrioukov et al., 1999)

Lesions in car reduce eye and ocelli pigmentation and cause excretion of pigment from the tubules.

(Tearle, 1991)

Origin and Etymology

Discoverer

Patterson, 20th March 1928.

Etymology

Identification

External Crossreferences and Linkouts ( 45 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

32947

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9Y1I2

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0000257

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0000257

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

car_1
car_2

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

CG12230

Flygut - An atlas of the Drosophila adult midgut

FBgn0000257

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

32947

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC006102

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

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG12230

modMine - A data warehouse for the modENCODE project

FBgn0000257

Linkouts

BioGRID - A database of protein and genetic interactions.

59247

DroID - A comprehensive database of gene and protein interactions.

FBgn0000257

DRSC - Results frm RNAi screens

FBgn0000257

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

FBgn0000257

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG12230-RB

FlyMine - An integrated database for Drosophila genomics

FBgn0000257

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

32947

MIST (genetic) - An integrated Molecular Interaction Database

MIST (protein-protein) - An integrated Molecular Interaction Database

Synonyms and Secondary IDs (16)

Reported As

Symbol Synonym

CG12230

(Hosono et al., 2015, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Dorer et al., 2006)

Car

(Rosa-Ferreira et al., 2018, Takáts et al., 2018, Lee et al., 2014, Takáts et al., 2014, Kim et al., 2010, Williamson et al., 2010)

Dm-Vps33

(Sevrioukov et al., 1999)

VPS33a

(Dorer et al., 2006)

Vps33

(Rosa-Ferreira et al., 2018, Gupta et al., 2014, Kim et al., 2010, Littleton, 2000, Kramer, 1999.3.5)

Vps33/carnation

(Toonen and Verhage, 2003)

Vps33A

(Takáts et al., 2018, Li and Blissard, 2015, Takáts et al., 2014, Kim et al., 2010)

Vps33a

(Csizmadia et al., 2018, Solinger and Spang, 2013, Akbar et al., 2009)

Vps33p

(Littleton, 2000)

car

(Meltzer et al., 2019, Baranski et al., 2018, Csizmadia et al., 2018, Jin et al., 2018, Salazar and Yamamoto, 2018, Napoletano et al., 2017, Shimizu et al., 2017, Transgenic RNAi Project members, 2017-, Lőrincz et al., 2016, Lőrincz et al., 2016, Nemetschke and Knust, 2016, Gillingham et al., 2014, Issman-Zecharya and Schuldiner, 2014, Jalvingh et al., 2014, Shimizu et al., 2014, Takáts et al., 2014, Schneider et al., 2013, Solinger and Spang, 2013, Walker et al., 2013, Yacobi-Sharon et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Kinser and Dolph, 2012, Du et al., 2011, Harris et al., 2011, Jungreis et al., 2011, Yamada et al., 2011, Yonamine et al., 2011, Chi et al., 2010, Popodi, 2010.10.8, Popodi et al., 2010-, Venken et al., 2010, Akbar et al., 2009, Chinchore et al., 2009, Soukup et al., 2009, Anaka et al., 2008, Straub et al., 2008, Wilkin et al., 2008, Akbar et al., 2007, Christensen and Cook, 2007.3.22, Falcon-Perez et al., 2007, Pulipparacharuvil et al., 2005)

carn

(Simonsen et al., 2007)

l(1)G0447

(Schäfer et al., 1999.12.2)

vps33a

(Lőrincz et al., 2019)

Name Synonyms

Carnation

(Rosa-Ferreira et al., 2018, Yacobi-Sharon et al., 2013)

Vacuolar protein sorting protein 33

Secondary FlyBase IDs

FBgn0027357
FBgn0040160

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (139)

Report Sections

Open Close