FB2022_02, released March 29, 2022

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
15 publicly available
Gene Summary
varicose (vari) encodes a protein involved in tracheal system development and septate junction assembly. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)
All Summaries
Also Known As

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

Key Links
Genomic Location
Cytogenetic map
39D3-40B1
Sequence location
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
Gene Ontology (GO) Annotations (9 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 (4 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 (2 terms)
CV Term
Evidence
References
is_active_in cell-cell junction
inferred from biological aspect of ancestor with PANTHER:PTN001137125
(assigned by GO_Central )
(Gaudet et al., 2011)
is_active_in plasma membrane
inferred from biological aspect of ancestor with PANTHER:PTN001137125
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
varicose (vari) encodes a protein involved in tracheal system development and septate junction assembly. [Date last reviewed: 2019-09-19]
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 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
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q7KT16)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

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
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 13 -- 17
embryonic/larval epidermis
(Moyer and Jacobs, 2008)
embryonic/larval tracheal section
(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 stage 14 -- 16
embryonic/larval salivary gland
(Wu et al., 2007)
embryonic/larval hindgut
(Wu et al., 2007)
embryonic/larval tracheal section
(Wu et al., 2007)
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
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
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
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, 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 )
Alleles Representing Disease-Implicated Variants
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 P-stage, with Scer\GAL4sd-SG29.1
lethal - all die during embryonic stage
lethal - all die during embryonic stage (with vari03953b)
lethal - all die during embryonic stage (with variMD109)
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
abnormal neuroanatomy | embryonic stage
abnormal neuroanatomy | embryonic stage, with Scer\GAL4elav.PLu
abnormal neuroanatomy | embryonic stage (with vari48EP)
abnormal neuroanatomy | embryonic stage (with vari327)
abnormal neuroanatomy | 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)
embryonic/larval tracheal dorsal trunk
embryonic/larval tracheal system
embryonic/larval tracheal system (with vari03953b)
embryonic/larval tracheal system (with variMD109)
embryonic/larval tracheal transverse connective
embryonic hindgut
epidermal cell | embryonic stage
eye, with Scer\GAL4ey.PH
ganglionic tracheal branch primordium
interommatidial bristle, with Scer\GAL4da.G32
larval intersegmental nerve | embryonic stage
larval intersegmental nerve branch ISNb of A1-7 | embryonic stage
larval intersegmental nerve branch ISNb of A1-7 | embryonic stage, with Scer\GAL4elav.PLu
larval intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari48EP)
larval intersegmental nerve branch ISNb of A1-7 | embryonic stage (with vari327)
larval intersegmental nerve branch ISNb of A1-7 | embryonic stage (with variR3)
larval segmental nerve branch SNa of A1-7 | embryonic stage
ocellus, with Scer\GAL4ey.PH
pleated septate junction
presumptive embryonic/larval tracheal system
septate junction
tracheal dorsal trunk primordium
tracheal dorsal trunk primordium, with Scer\GAL4da.G32
tracheal dorsal trunk primordium (with vari48EP)
tracheal dorsal trunk primordium (with vari03953b)
tracheal lateral trunk primordium
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
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (21)
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
13 of 15
Yes
Yes
Hsap\MPP2
10 of 15
No
Yes
Hsap\MPP1
3 of 15
No
No
Hsap\CASK
2 of 15
No
No
2  
Hsap\MPP3
2 of 15
No
No
Hsap\MPP4
2 of 15
No
No
Hsap\MPP7
2 of 15
No
No
Hsap\CARD10
1 of 15
No
Yes
Hsap\CARD11
1 of 15
No
Yes
Hsap\CARD14
1 of 15
No
Yes
Hsap\DLG1
1 of 15
No
No
Hsap\DLG2
1 of 15
No
No
Hsap\DLG3
1 of 15
No
No
Hsap\DLG4
1 of 15
No
No
2  
Hsap\DLG5
1 of 15
No
No
Hsap\GUK1
1 of 15
No
No
1  
Hsap\LRGUK
1 of 15
No
No
Hsap\MAGI3
1 of 15
No
No
Hsap\MPP5
1 of 15
No
No
Hsap\PATJ
1 of 15
No
No
Hsap\PDZD2
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
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
11 of 15
No
Yes
Mmus\Mpp1
3 of 15
No
No
Mmus\Cask
2 of 15
No
No
Mmus\Mpp3
2 of 15
No
No
Mmus\Mpp4
2 of 15
No
No
Mmus\Mpp7
2 of 15
No
No
Mmus\Card10
1 of 15
No
Yes
Mmus\Card11
1 of 15
No
Yes
Mmus\Card14
1 of 15
No
Yes
Mmus\Dlg1
1 of 15
No
No
Mmus\Dlg2
1 of 15
No
No
Mmus\Dlg3
1 of 15
No
No
Mmus\Dlg4
1 of 15
No
No
Mmus\Dlg5
1 of 15
No
No
Mmus\Furin
1 of 15
No
No
Mmus\Guk1
1 of 15
No
No
Mmus\Lrguk
1 of 15
No
No
Mmus\Magi3
1 of 15
No
No
Mmus\Mpp5
1 of 15
No
No
Mmus\Patj
1 of 15
No
No
Mmus\Pdzd2
1 of 15
No
No
Rattus norvegicus (Norway rat) (21)
Rnor\Mpp6
10 of 13
Yes
Yes
Rnor\Mpp2
7 of 13
No
Yes
Rnor\Mpp3
2 of 13
No
No
Rnor\Mpp4
2 of 13
No
No
Rnor\Mpp7
2 of 13
No
No
Rnor\Card10
1 of 13
No
Yes
Rnor\Card11
1 of 13
No
Yes
Rnor\Card14
1 of 13
No
Yes
Rnor\Cask
1 of 13
No
No
Rnor\Dlg1
1 of 13
No
No
Rnor\Dlg2
1 of 13
No
No
Rnor\Dlg3
1 of 13
No
No
Rnor\Dlg4
1 of 13
No
No
Rnor\Dlg5
1 of 13
No
No
Rnor\Guk1
1 of 13
No
No
Rnor\LOC100910506
1 of 13
No
No
Rnor\Lrguk
1 of 13
No
No
Rnor\Magi3
1 of 13
No
No
Rnor\Mpp1
1 of 13
No
No
Rnor\Mpp5
1 of 13
No
No
Rnor\Patj
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (13)
Xtro\mpp2
9 of 12
Yes
Yes
Xtro\mpp6
8 of 12
No
Yes
Xtro\mpp1
3 of 12
No
No
Xtro\cask
2 of 12
No
No
Xtro\mpp7
2 of 12
No
No
Xtro\card14
1 of 12
No
Yes
Xtro\dlg1
1 of 12
No
No
Xtro\dlg2
1 of 12
No
No
Xtro\dlg4
1 of 12
No
No
Xtro\dlg5
1 of 12
No
No
Xtro\guk1
1 of 12
No
No
Xtro\magi3
1 of 12
No
No
Xtro\mpp5
1 of 12
No
No
Danio rerio (Zebrafish) (28)
Drer\mpp6b
13 of 15
Yes
Yes
Drer\mpp6a
11 of 15
No
Yes
Drer\mpp2a
10 of 15
No
Yes
Drer\mpp2b
9 of 15
No
Yes
Drer\mpp1
3 of 15
No
No
Drer\caska
2 of 15
No
No
Drer\LOC556594
2 of 15
No
No
Drer\mpp3a
2 of 15
No
No
Drer\mpp3b
2 of 15
No
No
Drer\mpp4a
2 of 15
No
No
Drer\mpp4b
2 of 15
No
No
Drer\mpp7a
2 of 15
No
No
Drer\mpp7b
2 of 15
No
No
Drer\card11
1 of 15
No
Yes
Drer\caskb
1 of 15
No
No
Drer\dlg1
1 of 15
No
No
Drer\dlg3
1 of 15
No
No
Drer\dlg4b
1 of 15
No
No
Drer\dlg4
1 of 15
No
No
Drer\dlg5a
1 of 15
No
No
Drer\dlg5b.1
1 of 15
No
No
Drer\guk1b
1 of 15
No
No
Drer\LOC564220
1 of 15
No
No
Drer\LOC100534780
1 of 15
No
Yes
Drer\LOC100537443
1 of 15
No
No
Drer\lrguk
1 of 15
No
No
Drer\magi3a
1 of 15
No
No
Drer\mpp5b
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (8)
Cele\magu-3
3 of 15
Yes
Yes
Cele\lin-2
2 of 15
No
No
Cele\dlg-1
1 of 15
No
No
Cele\guk-1
1 of 15
No
No
Cele\magi-1
1 of 15
No
No
Cele\magu-1
1 of 15
No
No
Cele\magu-2
1 of 15
No
No
Cele\magu-4
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (3)
Atha\GK-1
1 of 9
Yes
No
Atha\MAPKKK6
1 of 9
Yes
Yes
Atha\MAPKKK7
1 of 9
Yes
Yes
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
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (6)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CASK
4 of 10
metro
3 of 10
sdt
3 of 10
CG11811
1 of 10
dlg1
1 of 10
Dlg5
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?
    PALS2; protein associated with LIN7 2, MAGUK p55 family member
    13 of 15
    606959
        MPP2; MAGUK p55 scaffold protein 2
        10 of 15
        600723
            MPP1; MAGUK p55 scaffold protein 1
            3 of 15
            305360
                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
                anti tag coimmunoprecipitation, anti tag western blot, two hybrid, anti bait coimmunoprecipitation, 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.
                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
                39D3-40B1
                Sequence location
                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 (15)
                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.

                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 ( 99 )
                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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
                UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                Other crossreferences
                AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
                BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                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.
                MARRVEL_MODEL - MARRVEL (model organism gene)
                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
                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
                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
                (Khoury et al., 2021, 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
                (Anqueira-González et al., 2021, Lebo et al., 2021, Lindsey et al., 2021, Pang et al., 2021, Rouka et al., 2021, 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
                (Rice et al., 2021, 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 (8)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (8)
                Result
                Result Type
                Title
                scRNAseq_2020_Cattenoz_NI_seq_clustering
                Clustering analysis of hemocytes from non-infested third instar larvae
                scRNAseq_2020_Cattenoz_WI_seq_clustering
                Clustering analysis of hemocytes from wasp-infested third instar larvae
                scRNAseq_2020_Cho_NI72LG_seq_clustering
                Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
                scRNAseq_2020_Cho_NI96LG_seq_clustering
                Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
                scRNAseq_2020_Cho_NI120LG_seq_clustering
                Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
                scRNAseq_2020_Cho_WI96LG_seq_clustering
                Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
                scRNAseq_2020_Cho_NI96HL_seq_clustering
                Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
                scRNAseq_2020_Cho_NI120HL_seq_clustering
                Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
                References (93)