FB2020_01, released Feb 12, 2020

Gene: Dmel\vari

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General Information
Symbol
Dmel\vari
Species
D. melanogaster
Name
varicose
Annotation Symbol
CG9326
Feature Type
protein_coding_gene
FlyBase ID
FBgn0250785
Gene Model Status
Current
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
Also Known As

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

Key Links
Genomic Location
Cytogenetic map
38E1-39A3
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
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
-
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

Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
4

Please see the GBrowse view of Dmel\vari or 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
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
vari-RB
FBtr0089947
NM_165342
2610
636
vari-RC
FBtr0089946
NM_165343
2320
469
vari-RD
FBtr0089945
NM_206011
2717
615
vari-RE
FBtr0335146
NM_001273715
2535
611
vari-RF
FBtr0335501
NM_001273716
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
vari-PB
FBpp0088886
72.4
636
7.34
NP_724288
AAN11089
vari-PC
FBpp0088885
53.4
469
6.43
NP_724289
AAN11090
vari-PD
FBpp0088884
70.3
615
6.95
NP_995733
AAF53925
vari-PE
FBpp0307145
69.4
611
6.95
NP_001260644
AGB93179
vari-PF
FBpp0307469
53.4
469
6.43
NP_001260645
AGB93180
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
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
Gene Ontology (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
dorsal trunk growth, open tracheal system
inferred from mutant phenotype
(Baer et al., 2007)
open tracheal system development
inferred from mutant phenotype
(Moyer and Jacobs, 2008, Beitel and Krasnow, 2000)
regulation of tube length, open tracheal system
inferred from mutant phenotype
(Wu et al., 2007)
regulation of tube size, open tracheal system
inferred from mutant phenotype
(Beitel and Krasnow, 2000)
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
lateral plasma membrane
inferred from direct assay
(Moyer and Jacobs, 2008)
septate junction
inferred from direct assay
(Bachmann et al., 2008, Wu et al., 2007)
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
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)
larval stage
embryonic/larval optic lobe
(Moyer and Jacobs, 2008)
third instar larval stage
larval neuroblast
(Moyer and Jacobs, 2008)
adult stage
neuron | subset of adult brain
(Moyer and Jacobs, 2008)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(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
lateral plasma membrane
inferred from direct assay
(Moyer and Jacobs, 2008)
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
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
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
Deletions and Duplications ( 14 )
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 vari38EFa2)
lethal (with vari48EP)
lethal (with vari327)
lethal (with vari03953b)
lethal (with variB4)
lethal (with variB5)
lethal (with varif00033)
lethal (with variGE13049)
lethal (with variHM2043)
lethal (with variK4)
lethal (with variL4)
lethal (with variR3)
lethal (with variR979)
lethal (with variR2376)
lethal | pharate adult stage P15(ii), with Scer\GAL4pnr-MD237
lethal | pupal stage, with Scer\GAL4pnr-MD237
lethal | recessive
lethal - all die before end of embryonic stage
lethal - all die before end of embryonic stage (with vari03953b)
lethal - all die before end of embryonic stage (with variMD109)
lethal - all die before end of P-stage, with Scer\GAL4sd-SG29.1
partially lethal (with vari38EFa2)
partially lethal (with variHM2043)
partially lethal (with variR979)
partially lethal (with variR2376)
partially lethal - majority live
partially lethal - majority live (with vari38EFa2)
partially lethal - majority live (with vari03953b)
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
neuroanatomy defective | embryonic stage
neuroanatomy defective | embryonic stage, with Scer\GAL4elav.PLu
neuroanatomy defective | embryonic stage (with vari48EP)
neuroanatomy defective | embryonic stage (with vari327)
neuroanatomy defective | embryonic stage (with variR3)
some die during embryonic stage
some die during embryonic stage (with vari03953b)
some die during embryonic stage (with variMD109)
some die during pharate adult stage, with Scer\GAL4sd-SG29.1
visible, with Scer\GAL4da.G32
visible, with Scer\GAL4dpp.PU
visible, with Scer\GAL4ey.PH
visible, with Scer\GAL4sd-SG29.1
Phenotype manifest in
Allele
axon | embryonic stage
axon | embryonic stage, with Scer\GAL4elav.PLu
axon | embryonic stage (with vari48EP)
axon | embryonic stage (with vari327)
axon | embryonic stage (with variR3)
dorsal trunk primordium
dorsal trunk primordium, with Scer\GAL4da.G32
dorsal trunk primordium (with vari48EP)
dorsal trunk primordium (with vari03953b)
embryonic/larval dorsal trunk
embryonic/larval tracheal system
embryonic/larval tracheal system (with vari03953b)
embryonic/larval tracheal system (with variMD109)
embryonic/larval transverse connective
embryonic hindgut
eye, with Scer\GAL4ey.PH
ganglionic branch primordium
interommatidial bristle, with Scer\GAL4da.G32
intersegmental nerve | embryonic stage
intersegmental nerve branch ISNb of A1-7 | embryonic stage
intersegmental nerve branch ISNb of A1-7 | embryonic stage, with Scer\GAL4elav.PLu
intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari48EP)
intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari327)
intersegmental nerve branch ISNb of A1-7 | embryonic stage (with variR3)
lateral trunk primordium
ocellus, with Scer\GAL4ey.PH
pleated septate junction
presumptive embryonic/larval tracheal system
segmental nerve branch SNa of A1-7 | embryonic stage
septate junction
wing, with Scer\GAL4sd-SG29.1
wing hair, with Scer\GAL4dpp.PU
wing margin, with Scer\GAL4sd-SG29.1
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\MPP6
12 of 15
Yes
Yes
Hsap\MPP2
9 of 15
No
Yes
Hsap\CASK
1 of 15
No
No
 
Hsap\MPP1
1 of 15
No
No
Hsap\MPP3
1 of 15
No
No
Hsap\MPP4
1 of 15
No
No
Hsap\MPP5
1 of 15
No
No
Hsap\MPP7
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Mpp6
12 of 15
Yes
Yes
Mmus\Mpp2
10 of 15
No
Yes
Mmus\Cask
1 of 15
No
No
Mmus\Mpp1
1 of 15
No
No
Mmus\Mpp3
1 of 15
No
No
Mmus\Mpp4
1 of 15
No
No
Mmus\Mpp5
1 of 15
No
No
Mmus\Mpp7
1 of 15
No
No
Rattus norvegicus (Norway rat) (6)
Rnor\Mpp6
7 of 13
Yes
Yes
Rnor\Mpp2
4 of 13
No
Yes
Rnor\Mpp3
1 of 13
No
No
Rnor\Mpp4
1 of 13
No
No
Rnor\Mpp5
1 of 13
No
No
Rnor\Mpp7
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (6)
Xtro\mpp2
8 of 12
Yes
Yes
Xtro\mpp6
6 of 12
No
Yes
Xtro\cask
1 of 12
No
No
Xtro\mpp1
1 of 12
No
No
Xtro\mpp5
1 of 12
No
No
Xtro\mpp7
1 of 12
No
No
Danio rerio (Zebrafish) (14)
Drer\mpp6b
12 of 15
Yes
Yes
Drer\mpp6a
9 of 15
No
Yes
Drer\mpp2a
8 of 15
No
Yes
Drer\mpp2b
8 of 15
No
Yes
Drer\caska
1 of 15
No
No
Drer\LOC556594
1 of 15
No
No
Drer\mpp1
1 of 15
No
No
Drer\mpp3a
1 of 15
No
No
Drer\mpp3b
1 of 15
No
No
Drer\mpp4a
1 of 15
No
No
Drer\mpp5b
1 of 15
No
No
Drer\mpp7a
1 of 15
No
No
Drer\mpp7b
1 of 15
No
No
Drer\si:ch73-272h16.4
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\magu-3
2 of 15
Yes
Yes
Cele\lin-2
1 of 15
No
No
Cele\magu-1
1 of 15
No
No
Cele\magu-2
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (3)
Atha\GK-1
1 of 9
Yes
No
Atha\MAPKKK6
1 of 9
Yes
No
Atha\MAPKKK7
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\GUK1
2 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC1198.05
1 of 12
Yes
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919041G )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\vari
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00000812
Drosophila simulans
Dsim\GD21680
Drosophila sechellia
Dsec\GM23306
Drosophila erecta
Dere\GG21549
Drosophila yakuba
Dyak\GE13543
Drosophila ananassae
Dana\GF14547
Drosophila pseudoobscura pseudoobscura
Dpse\GA21703
Drosophila persimilis
Dper\GL19590
Drosophila willistoni
Dwil\GK24864
Drosophila virilis
Dvir\GJ20335
Drosophila mojavensis
Dmoj\GI22442
Drosophila grimshawi
Dgri\GH10158
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
Mdoa\17014792
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
Amel\GB45145
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP15047
Bombus terrestris
Buff-tailed bumblebee
Bter\15212359
Linepithema humile
Argentine ant
Lhum\LH18643
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:00289b
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG023752
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_10338
Tribolium castaneum
Red flour beetle
Tcas\TC033082
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
Spur\Sp-Cask
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Mpp5-2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Cask_2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Mpp5-3
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Mpp5
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Mpp6
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
Ggal\MPP1
Gallus gallus
Domestic chicken
Ggal\MPP3
Gallus gallus
Domestic chicken
Ggal\MPP4
Gallus gallus
Domestic chicken
Ggal\MPP6
Gallus gallus
Domestic chicken
Ggal\CASK
Gallus gallus
Domestic chicken
Ggal\MPP7
Gallus gallus
Domestic chicken
Ggal\MPP5
Gallus gallus
Domestic chicken
Ggal\MPP2
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (7)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CASK
3 of 10
metro
3 of 10
sdt
3 of 10
CG11811
1 of 10
dlg1
1 of 10
Dlg5
1 of 10
pyd
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 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?
    MPP6; membrane palmitoylated protein 6
    12 of 15
    606959
        MPP2; membrane palmitoylated protein 2
        9 of 15
        600723
            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
            Show neighbor-neighbor interactions:
            Select Layout:
            Legend:
            Protein
            RNA
            Selected Interactor(s)
            Interactions Browser
            View in Interactions Browser
            Please see the Physical Interaction reports below for full details
            protein-protein
            Physical Interaction
            Assay
            References
            vari - Fas3
            anti bait coimmunoprecipitation, western blot
            (Wells et al., 2013)
            vari - Nrx-IV
            pull down, western blot, anti tag coimmunoprecipitation
            (Bachmann et al., 2008)
            vari - Sema1a
            two hybrid, anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot
            (Jeong et al., 2017)
            vari - veli
            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
            vari
            enhanceable
            dpy
            (Swanson et al., 2009)
            vari
            enhanceable
            pio
            (Swanson et al., 2009)
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            cher
            enhanceable
            vari
            (Jeong et al., 2017)
            GckIII
            suppressible
            vari
            (Song et al., 2013)
            Sema1a
            enhanceable
            vari
            (Jeong et al., 2017)
            External Data
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            DroID - A comprehensive database of gene and protein interactions.
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2L
            Recombination map

            2-54

            Cytogenetic map
            38E1-39A3
            Sequence location
            2L:20,788,662..20,797,042 [-]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            38E1-39A3
            Left limit from non-inclusion within Df(2L)Fs(2)Ket-RX32 (FBrf0102956) Right limit from inclusion within Df(2L)DS6 (FBrf0102956)
            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)
            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 sequences
            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.

            cDNA Clones, End Sequenced (ESTs)
            BDGP DGC clones
            Other clones
            RNAi and Array Information
            Linkouts
            DRSC - Results frm RNAi screens
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            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.
            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
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            Flygut - An atlas of the Drosophila adult midgut
            FlyMine - An integrated database for Drosophila genomics
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            modMine - A data warehouse for the modENCODE project
            SignaLink - A signaling pathway resource with multi-layered regulatory networks.
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            FLIGHT - Cell culture data for RNAi and other high-throughput technologies
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
            Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            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
            (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
            • FBpp0088886
            • FBtr0089947
            • FBpp0088885
            • FBtr0089946
            • FBpp0088884
            • FBtr0089945
            • FBgn0032885
            • FBgn0025170
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (83)