FlyBase Gene Report: Dmel\vari

General Information

Symbol

Dmel\vari

Species

D. melanogaster

Name

varicose

Annotation Symbol

CG9326

Feature Type

protein_coding_gene

FlyBase ID

FBgn0250785

Gene Model Status

Stock Availability

16 publicly available

Gene Snapshot

varicose (vari) encodes a protein involved in tracheal system development and septate junction assembly. [Date last reviewed: 2019-09-19]

Other Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

l(2)03953, szar, 38E.21

Key Links

Genomic Location

Cytogenetic map

Sequence location

2L:20,788,662..20,797,042 [-]

Recombination map

2-54

RefSeq locus

NT_033779 REGION:20788662..20797042

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (7 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (5 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

involved_in dorsal trunk growth, open tracheal system

inferred from mutant phenotype

(Baer et al., 2007)

involved_in open tracheal system development

inferred from mutant phenotype

(Moyer and Jacobs, 2008, Beitel and Krasnow, 2000)

involved_in regulation of tube length, open tracheal system

inferred from mutant phenotype

(Wu et al., 2007)

involved_in regulation of tube size, open tracheal system

inferred from mutant phenotype

(Beitel and Krasnow, 2000)

involved_in septate junction assembly

inferred from mutant phenotype

(Bachmann et al., 2008, Wu et al., 2007)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in lateral plasma membrane

inferred from direct assay

(Moyer and Jacobs, 2008)

located_in septate junction

inferred from direct assay

(Bachmann et al., 2008, Wu et al., 2007)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

-

Protein Signatures (InterPro)

Summaries

Summary (Interactive Fly)

Essential septate junction gene encoding a membrane associated guanylate kinase (MAGUK) - required for accumulation of the tracheal size-control proteins Vermiform and Serpentine in the tracheal lumen

Interactive Fly

Gene Model and Products

Number of Transcripts

5

Number of Unique Polypeptides

4

Please see the JBrowse view of Dmel\vari 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

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0089947

2610

636

FBtr0089946

2320

469

FBtr0089945

2717

615

FBtr0335146

2535

611

FBtr0335501

2379

469

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

FBpp0088886

72.4

636

7.34

FBpp0088885

53.4

469

6.43

FBpp0088884

70.3

615

6.95

FBpp0307145

69.4

611

6.95

FBpp0307469

53.4

469

6.43

Polypeptides with Identical Sequences

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

469 aa isoforms: vari-PC, vari-PF

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

Nucleotide / Polypeptide Records

Mapped Features

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

External Data

Crossreferences

Linkouts

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

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

(Fisher et al., 2012)

embryonic stage 11 -- 12

dorsal epidermis primordium

(Fisher et al., 2012)

foregut primordium

(Fisher et al., 2012)

hindgut proper primordium

(Fisher et al., 2012)

tracheal primordium

(Fisher et al., 2012)

embryonic stage 10 -- 11

embryonic/larval trachea

(Chung et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 12 -- 16

embryonic dorsal epidermis

(Wu et al., 2007)

embryonic stage 14 -- 16

embryonic/larval salivary gland

(Wu et al., 2007)

embryonic/larval hindgut

(Wu et al., 2007)

embryonic/larval trachea

(Wu et al., 2007)

embryonic stage 13 -- 17

embryonic/larval epidermis

(Moyer and Jacobs, 2008)

embryonic/larval trachea

(Moyer and Jacobs, 2008)

embryonic/larval proventriculus

(Moyer and Jacobs, 2008)

embryonic/larval salivary gland

(Moyer and Jacobs, 2008)

embryonic/larval hindgut

(Moyer and Jacobs, 2008)

embryonic/larval optic lobe

(Moyer and Jacobs, 2008)

third instar larval stage

larval neuroblast

(Moyer and Jacobs, 2008)

neuron | subset of adult brain

(Moyer and Jacobs, 2008)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

vari protein expression was detected from embryonic stage 13-17 and is observed in septate junctions in epithelial tissues including the epidermis, trachea, proventriculus, salivary gland and hindgut. In larvae, vari protein is observed in the neurepithelium of the optic lobe and in central brain neuroblasts in third instar larvae. In the adult nervous system, vari localizes to a subset of differentiated neurons surrounding neuropile regions.

(Moyer and Jacobs, 2008)

vari protein is predominantly expressed in the septate junctions in trachea and hindgut by embryonic stage 14 but is also detected in the dorsal epidermis as early as stage 12. It is also observed in salivary gland in stages 15,16.

(Wu et al., 2007)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in lateral plasma membrane

inferred from direct assay

(Moyer and Jacobs, 2008)

located_in septate junction

inferred from direct assay

(Bachmann et al., 2008, Wu et al., 2007)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\vari 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\vari

View exonic expression by tissue for Dmel\vari

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

FBgn0250785

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

FBgn0250785

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG9326-RB

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

CG9326

Flygut - An atlas of the Drosophila adult midgut

FBgn0250785

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\vari

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

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 27 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of vari

Transgenic constructs containing regulatory region of vari

Aberrations (Deficiencies and Duplications) ( 14 )

Inferred from experimentation

Gene disrupted in

Gene partially disrupted in

Df(2L)vari^48EP

(Moyer and Jacobs, 2008)

Gene not disrupted in

(Butler et al., 2001)

(Butler et al., 2001)

Df(2L)Fs(2)Ket-RX32

(Butler et al., 2001, Kozlova et al., 1998)

(Butler et al., 2001)

Inferred from location

Phenotypes

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

Lethality

Allele

FlyBase_internaltransgene_features:cell lethal:cell lethal | somatic clone

lethal (with Df(2L)Exel7079)

lethal (with Df(2L)TW2)

lethal (with vari^38EFa2)

lethal (with vari^48EP)

vari^GE13049

lethal (with vari³²⁷)

lethal (with vari^03953b)

lethal (with vari^B4)

vari^GE13049

lethal (with vari^B5)

vari^GE13049

lethal (with vari^f00033)

lethal (with vari^GE13049)

lethal (with vari^HM2043)

lethal (with vari^K4)

vari^GE13049

lethal (with vari^L4)

vari^GE13049

lethal (with vari^R3)

lethal (with vari^R979)

lethal (with vari^R2376)

lethal | pharate adult stage P15(ii), with Scer\GAL4^pnr-MD237

vari^GD13798

lethal | pupal stage, with Scer\GAL4^pnr-MD237

vari^GD13798

lethal | recessive

lethal - all die before end of P-stage, with Scer\GAL4^sd-SG29.1

vari^{dsRNA.UAS.cBa}

lethal - all die during embryonic stage

lethal - all die during embryonic stage (with vari^03953b)

vari^MD109

lethal - all die during embryonic stage (with vari^MD109)

vari^03953b

partially lethal (with vari^38EFa2)

partially lethal (with vari^HM2043)

vari^38EFa2

partially lethal (with vari^R979)

vari^38EFa2

partially lethal (with vari^R2376)

vari^38EFa2

partially lethal - majority live

vari^38EFa2

partially lethal - majority live (with vari^38EFa2)

vari^03953b

partially lethal - majority live (with vari^03953b)

vari^38EFa2

viable, with Scer\GAL4^Mef2.PR

vari^GD13798

viable, with Scer\GAL4^tin.CΔ4

vari^GD13798

Other Phenotypes

Allele

abnormal neuroanatomy | embryonic stage

vari³²⁷

abnormal neuroanatomy | embryonic stage, with Scer\GAL4^elav.PLu

vari^HM05087

abnormal neuroanatomy | embryonic stage (with vari^48EP)

vari³²⁷

abnormal neuroanatomy | embryonic stage (with vari³²⁷)

abnormal neuroanatomy | embryonic stage (with vari^R3)

vari³²⁷

some die during embryonic stage

some die during embryonic stage (with vari^03953b)

vari^MD109

some die during embryonic stage (with vari^MD109)

vari^03953b

some die during pharate adult stage, with Scer\GAL4^sd-SG29.1

vari^{dsRNA.UAS.cBa}

visible, with Scer\GAL4^da.G32

vari^UAS.cMa

visible, with Scer\GAL4^dpp.PU

vari^GD13798

visible, with Scer\GAL4^ey.PH

vari^{dsRNA.UAS.cBa}

visible, with Scer\GAL4^sd-SG29.1

vari^{dsRNA.UAS.cBa}

Phenotype manifest in

Allele

axon | embryonic stage

vari³²⁷

axon | embryonic stage, with Scer\GAL4^elav.PLu

vari^HM05087

axon | embryonic stage (with vari^48EP)

vari³²⁷

axon | embryonic stage (with vari³²⁷)

axon | embryonic stage (with vari^R3)

vari³²⁷

dorsal trunk primordium

dorsal trunk primordium, with Scer\GAL4^da.G32

vari^GD13798

dorsal trunk primordium (with vari^48EP)

vari^03953b

dorsal trunk primordium (with vari^03953b)

vari^48EP

embryonic/larval dorsal trunk

embryonic/larval tracheal system

embryonic/larval tracheal system (with vari^03953b)

vari^MD109

embryonic/larval tracheal system (with vari^MD109)

vari^03953b

embryonic/larval transverse connective

vari^03953b

embryonic hindgut

vari^48EP

eye, with Scer\GAL4^ey.PH

vari^{dsRNA.UAS.cBa}

ganglionic branch primordium

vari^f00033

interommatidial bristle, with Scer\GAL4^da.G32

vari^UAS.cMa

intersegmental nerve | embryonic stage

vari³²⁷

intersegmental nerve branch ISNb of A1-7 | embryonic stage

vari³²⁷

intersegmental nerve branch ISNb of A1-7 | embryonic stage, with Scer\GAL4^elav.PLu

vari^HM05087

intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari^48EP)

vari³²⁷

intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari³²⁷)

intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari^R3)

vari³²⁷

lateral trunk primordium

vari^48EP

ocellus, with Scer\GAL4^ey.PH

vari^{dsRNA.UAS.cBa}

pleated septate junction

presumptive embryonic/larval tracheal system

segmental nerve branch SNa of A1-7 | embryonic stage

vari³²⁷

septate junction

wing, with Scer\GAL4^sd-SG29.1

vari^{dsRNA.UAS.cBa}

wing hair, with Scer\GAL4^dpp.PU

vari^GD13798

wing margin, with Scer\GAL4^sd-SG29.1

vari^{dsRNA.UAS.cBa}

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (21)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

13 of 15

Yes

Yes

10 of 15

No

Yes

3 of 15

No

No

2 of 15

No

No

2

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

1 of 15

No

Yes

1 of 15

No

Yes

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

2

1 of 15

No

No

1 of 15

No

No

1

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (22)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

12 of 15

Yes

Yes

11 of 15

No

Yes

3 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

1 of 15

No

Yes

1 of 15

No

Yes

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Rattus norvegicus (Norway rat) (21)

10 of 13

Yes

Yes

7 of 13

No

Yes

2 of 13

No

No

2 of 13

No

No

2 of 13

No

No

1 of 13

No

Yes

1 of 13

No

Yes

1 of 13

No

Yes

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

Rnor\LOC100910506

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

Xenopus tropicalis (Western clawed frog) (13)

9 of 12

Yes

Yes

8 of 12

No

Yes

3 of 12

No

No

2 of 12

No

No

2 of 12

No

No

1 of 12

No

Yes

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

Danio rerio (Zebrafish) (28)

13 of 15

Yes

Yes

11 of 15

No

Yes

10 of 15

No

Yes

9 of 15

No

Yes

3 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

2 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Drer\LOC100534780

1 of 15

No

Yes

Drer\LOC100537443

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Caenorhabditis elegans (Nematode, roundworm) (8)

3 of 15

Yes

Yes

2 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Arabidopsis thaliana (thale-cress) (3)

1 of 9

Yes

No

1 of 9

Yes

Yes

1 of 9

Yes

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

2 of 15

Yes

No

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPBC1198.05

1 of 12

Yes

No

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919041G )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Dsuz\DS10_00000812

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Drosophila persimilis

Drosophila willistoni

Drosophila virilis

Drosophila mojavensis

Drosophila grimshawi

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091501TA )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Glossina morsitans

Tsetse fly

Gmor\GMOY008944

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_08885

Mayetiola destructor

Hessian fly

Mdes\Mdes010674

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL009937

Anopheles darlingi

American malaria mosquito

Adar\ADAC010206

Anopheles gambiae

Malaria mosquito

Agam\AGAP008321

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ005514

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W035W )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA001334

Danaus plexippus

Monarch butterfly

Dple\DPOGS214116-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL011395

Apis florea

Little honeybee

Aflo\2342674148

Apis mellifera

Western honey bee

Bombus impatiens

Common eastern bumble bee

Bombus terrestris

Buff-tailed bumblebee

Linepithema humile

Argentine ant

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:00289b

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG023752

Dendroctonus ponderosae

Mountain pine beetle

Tribolium castaneum

Red flour beetle

Pediculus humanus

Human body louse

Phum\PHUM091990

Rhodnius prolixus

Kissing bug

Rpro\RPRC005796

Cimex lectularius

Bed bug

Clec\CLEC005609

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI069428

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_11518

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X032R )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR014361

Stegodyphus mimosarum

African social velvet spider

Smim\KFM80756.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur32g01300

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_7952

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_195819

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G065I )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_023432gn

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000020496

Ciona intestinalis

Vase tunicate

Cint\LOC100181746

Ciona intestinalis

Vase tunicate

Cint\LOC100179311

Ciona intestinalis

Vase tunicate

Cint\LOC100176249

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (6)

Gene Symbol

Score

Source

Alignment

4 of 10

3 of 10

3 of 10

1 of 10

1 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v8.0 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?

MPP6; membrane palmitoylated protein 6

13 of 15

MPP2; membrane palmitoylated protein 2

10 of 15

MPP1; membrane palmitoylated protein 1

3 of 15

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

anti bait coimmunoprecipitation, western blot

(Wells et al., 2013)

pull down, western blot, anti tag coimmunoprecipitation

(Bachmann et al., 2008)

anti bait coimmunoprecipitation, western blot, two hybrid, anti tag coimmunoprecipitation, anti tag western blot

(Jeong et al., 2017)

pull down, western blot

(Bachmann et al., 2008)

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

enhanceable

(Swanson et al., 2009)

enhanceable

(Swanson et al., 2009)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Jeong et al., 2017)

suppressible

(Song et al., 2013)

enhanceable

(Jeong et al., 2017)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

61306

DroID - A comprehensive database of gene and protein interactions.

FBgn0250785

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

35343

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

vari

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

guanosine ribonucleotides <i>de novo</i> biosynthesis

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

2L

Recombination map

2-54

Cytogenetic map

Sequence location

2L:20,788,662..20,797,042 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

39D3-40B1

Left limit from non-inclusion within Df(2L)TW84 (FBrf0128394) Right limit from inclusion within Df(2L)TW161 (FBrf0128394)

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-54

(FlyBase, 2016)

2-54.1

(Comeron et al., 2012)

2-

(Kozlova et al., 1998)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (16)

36271

w^*; P{UAS-vari.M}93

18289

w¹¹¹⁸; PBac{WH}vari^f00033

5319

vari^38EFa2 dpy^ov1 bw¹/CyO

44732

y¹ w^*; Mi{MIC}vari^MI08013/SM6a

22225

y¹ w^*; P{Mae-UAS.6.11}vari^LA00256

28599

y¹ v¹; P{TRiP.HM05087}attP2/TM3, Sb¹

76191

y¹ w^*; Mi{Trojan-GAL4.0}vari^{MI08013-TG4.0}

108174

vari^38EFa2 dpy^ov1 bw¹/CyO

120256

y^* w^*; P{Mae-UAS.6.11}vari^LA00256

v104548

P{KK110006}VIE-260B

v24156

w¹¹¹⁸ P{GD13798}v24156

v24157

w¹¹¹⁸; P{GD13798}v24157

More stocks available...

Genomic Clones (14)

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

cDNA Clones (124)

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

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.

FBgn0250785

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0250785

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

35343

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Jeong et al., 2017, Bachmann et al., 2008, Moyer and Jacobs, 2008)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: vari l(2)03953

(Beitel and Krasnow, 2000)

Source for identity of: szar CG9326

(Moyer and Jacobs, 2007)

Source for database merge of

Source for merge of: vari szar l(2)38EFa

(Wu et al., 2007)

Additional comments

Other Comments

vari is required for septate junction formation in the tracheal system.

(Wu 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)

Mutation in vari alters tracheal tube size in embryos without affecting other aspects of tracheal development including primary branch budding and outgrowth or branch fusion.

(Beitel and Krasnow, 2000)

Origin and Etymology

Discoverer

Etymology

The gene is named "senz'aria", the Italian for "airless", as the trachea fail to inflate in mutant embryos.

(Moyer and Jacobs, 2007)

Identification

External Crossreferences and Linkouts ( 95 )

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.

35343

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

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0250785

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

FBgn0250785

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

CG9326

Flygut - An atlas of the Drosophila adult midgut

FBgn0250785

FlyMine - An integrated database for Drosophila genomics

FBgn0250785

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

35343

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

TC033082

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

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

Dmel_CG9326

modMine - A data warehouse for the modENCODE project

FBgn0250785

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

A1XXK3

Linkouts

BioGRID - A database of protein and genetic interactions.

61306

DroID - A comprehensive database of gene and protein interactions.

FBgn0250785

DRSC - Results frm RNAi screens

FBgn0250785

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

FBgn0250785

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG9326-RB

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0250785

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

guanosine ribonucleotides <i>de novo</i> biosynthesis

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

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

35343

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

vari

Synonyms and Secondary IDs (13)

Reported As

Symbol Synonym

38E.21

(Butler, 2001, Butler et al., 2001, McGill Drosophila Genome Project, 2001.9.25)

CG9326

(Hosono et al., 2015, Rosa-Ferreira et al., 2015, Fukuoh et al., 2014, Ni et al., 2011.7.19, Keleman et al., 2009.8.5, Krejcí et al., 2009, Perkins et al., 2009, Bachmann et al., 2008, Moyer and Jacobs, 2008, Moyer and Jacobs, 2007, Tomancak et al., 2007, Wu et al., 2007)

Vari

(Song et al., 2013, Laprise et al., 2010)

l(2)03953

(Gelbart, 1999.7.20, BDGP Project Members, 1994-1999, Timmons et al., 1993)

l(2)03953b

(Beitel and Krasnow, 2000)

l(2)38EFa

szar

(Japanese National Institute of Genetics, 2012.5.21, Krejcí et al., 2009, Moyer and Jacobs, 2007)

vari

(Königsmann et al., 2020, Lee et al., 2018, Jeong et al., 2017, Gajan et al., 2016, Gene Disruption Project members, 2016-, Hildebrandt et al., 2015, Matthews et al., 2015, Zang et al., 2015, Moyer and Jacobs, 2013.11.6, Wells et al., 2013, Aranjuez et al., 2012, Chung et al., 2011, Laprise et al., 2009, Swanson et al., 2009, Bachmann et al., 2008, Laval et al., 2008, Moyer and Jacobs, 2008, Wu et al., 2007, Tonning et al., 2005)

Name Synonyms

CG9326

Varicose

(De et al., 2018, Juarez, 2016, Song et al., 2013, Wells et al., 2013, Leiserson and Keshishian, 2011, Rodrigues et al., 2011, Laprise et al., 2010, Laval et al., 2008, Moyer and Jacobs, 2008)

lethal (2) 38EFa

senz'aria

(Moyer and Jacobs, 2007)

senz-aria

varicose

(Saito et al., 2018, Song et al., 2013, Juarez et al., 2011, Laprise et al., 2009, Swanson et al., 2009, Bachmann et al., 2008, Baer et al., 2007, Wu et al., 2007, Beitel and Krasnow, 2000)

Secondary FlyBase IDs

FBgn0010560
FBgn0032885
FBgn0025170

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (85)