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    vari varicose [ Drosophila melanogaster (fruit fly) ]

    Gene ID: 35343, updated on 9-Dec-2024

    Summary

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    Official Symbol
    variprovided by FlyBase
    Official Full Name
    varicoseprovided by FlyBase
    Primary source
    FLYBASE:FBgn0250785
    Locus tag
    Dmel_CG9326
    See related
    AllianceGenome:FB:FBgn0250785
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Drosophila melanogaster
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
    Also known as
    38E.21; CG9326; Dmel\CG9326; l(2)03953; l(2)03953b; l(2)38EFa; szar; Vari
    Summary
    Involved in dorsal trunk growth, open tracheal system; regulation of tube length, open tracheal system; and septate junction assembly. Located in lateral plasma membrane and septate junction. Is expressed in several structures, including adult brain; adult head; dorsal epidermis primordium; epidermis; and gut section. Orthologous to several human genes including PALS2 (protein associated with LIN7 2, MAGUK p55 family member). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See vari in Genome Data Viewer
    Location:
    38E10-38E10; 2-54 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) 2L NT_033779.5 (20788662..20797042, complement)
    Release 5.57 previous assembly Release 5 (GCF_000001215.2) 2L NT_033779.4 (20788662..20797042, complement)

    Chromosome 2L - NT_033779.5Genomic Context describing neighboring genes Neighboring gene diaphanous Neighboring gene caudal Neighboring gene long non-coding RNA:CR44146 Neighboring gene pomp Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Multi-ethnic GWAS and meta-analysis of sleep quality identify MPP6 as a novel gene that functions in sleep center neurons. Khoury S, et al. Sleep, 2021 Mar 12. PMID 33034629, Free PMC Article
    2. O-GlcNAcylation of boundary element associated factor (BEAF 32) in Drosophila melanogaster correlates with active histone marks at the promoters of its target genes. De D, et al. Nucleus, 2018 Jan 1. PMID 28910574, Free PMC Article
    3. The lateral mobility of cell adhesion molecules is highly restricted at septate junctions in Drosophila. Laval M, et al. BMC Cell Biol, 2008 Jul 18. PMID 18638384, Free PMC Article
    4. Varicose and cheerio collaborate with pebble to mediate semaphorin-1a reverse signaling in Drosophila. Jeong S, et al. Proc Natl Acad Sci U S A, 2017 Sep 26. PMID 28894005, Free PMC Article
    5. The expression of the Drosophila awd gene during normal development and in neoplastic brain tumors caused by lgl mutations. Timmons L, et al. Dev Biol, 1993 Aug. PMID 8393813

    See all (80) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The PDZ domain binding motif found in the most C-terminal region of the Sema-1a ICD is necessary for interaction with Vari, but not Cher, indicative of distinct binding modalities. Pbl/Sema-1a-mediated repulsive guidance is potentiated by both vari and cher Genetic analyses further suggest that scaffolding functions of Vari and Cher play an important role in Pbl-mediated Sema-1a reverse signaling.
      Title: Varicose and cheerio collaborate with pebble to mediate semaphorin-1a reverse signaling in Drosophila.
    2. Vari fundamentally extends the similarity of Drosophila and vertebrate basolateral regions from sharing only polarity complexes to sharing both polarity and cell-adhesion complexes.
      Title: Drosophila Varicose, a member of a new subgroup of basolateral MAGUKs, is required for septate junctions and tracheal morphogenesis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by FlyBase

    Process Evidence Code Pubs
    involved_in dorsal trunk growth, open tracheal system IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in open tracheal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of tube length, open tracheal system IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of tube size, open tracheal system IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in septate junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in septate junction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    varicose
    Names
    CG9326-PB
    CG9326-PC
    CG9326-PD
    CG9326-PE
    CG9326-PF
    lethal (2) 38EFa
    senz'aria
    senz-aria
    vari-PB
    vari-PC
    vari-PD
    vari-PE
    vari-PF

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NT_033779.5 Reference assembly

      Range
      20788662..20797042 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_206011.3 → NP_995733.2  varicose, isoform D [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_995733.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q8SXI6, Q9VIJ4
      Conserved Domains (5) summary
      cd11862
      Location:266 → 326
      SH3_MPP; Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins
      smart00072
      Location:397 → 601
      GuKc; Guanylate kinase homologues
      cd00992
      Location:173 → 250
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam00625
      Location:387 → 601
      Guanylate_kin; Guanylate kinase
      pfam02828
      Location:105 → 128
      L27; L27 domain

    2. NM_165343.3 → NP_724289.2  varicose, isoform C [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_724289.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q2PDR9, Q8MR96
      Related
      FBpp0088885
      Conserved Domains (4) summary
      cd11862
      Location:120 → 180
      SH3_MPP; Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins
      smart00072
      Location:251 → 455
      GuKc; Guanylate kinase homologues
      cd00992
      Location:6 → 83
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam00625
      Location:241 → 455
      Guanylate_kin; Guanylate kinase

    3. NM_001273716.1 → NP_001260645.1  varicose, isoform F [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_001260645.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q2PDR9, Q8MR96
      Conserved Domains (4) summary
      cd11862
      Location:120 → 180
      SH3_MPP; Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins
      smart00072
      Location:251 → 455
      GuKc; Guanylate kinase homologues
      cd00992
      Location:6 → 83
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam00625
      Location:241 → 455
      Guanylate_kin; Guanylate kinase

    4. NM_001273715.1 → NP_001260644.1  varicose, isoform E [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_001260644.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      M9PDB2, Q8SXI6
      Conserved Domains (5) summary
      cd11862
      Location:287 → 347
      SH3_MPP; Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins
      smart00072
      Location:418 → 597
      GuKc; Guanylate kinase homologues
      cd00992
      Location:173 → 250
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam00625
      Location:408 → 597
      Guanylate_kin; Guanylate kinase
      pfam02828
      Location:105 → 128
      L27; L27 domain

    5. NM_165342.4 → NP_724288.3  varicose, isoform B [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_724288.3

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q7KT16, Q8SXI6
      Conserved Domains (5) summary
      cd11862
      Location:287 → 347
      SH3_MPP; Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins
      smart00072
      Location:418 → 622
      GuKc; Guanylate kinase homologues
      cd00992
      Location:173 → 250
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam00625
      Location:408 → 622
      Guanylate_kin; Guanylate kinase
      pfam02828
      Location:105 → 128
      L27; L27 domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A1XXK0 A1XXK0
    A1XXK1 A1XXK1
    A1XXK2 A1XXK2
    A1XXK3 A1XXK3
    A1XXK4 A1XXK4
    A1XXK5 A1XXK5
    A1XXK7 A1XXK7
    M9PDB2 M9PDB2
    Q2PDR9 Q2PDR9
    Q7KT16 Q7KT16
    Q8MR96 Q8MR96
    Q8SXI6 Q8SXI6
    Q9VIJ4 Q9VIJ4

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