FB2025_05 , released December 11, 2025
Gene: Dmel\vimar
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General Information
Symbol
Dmel\vimar
Species
D. melanogaster
Name
visceral mesodermal armadillo-repeats
Annotation Symbol
CG3572
Feature Type
protein_coding_gene
FlyBase ID
FBgn0022960
Gene Model Status
Current
Stock Availability
20 publicly available
Gene Summary
visceral mesodermal armadillo-repeats (vimar) encodes a protein involved in regulation of muscle homeostasis and rhabdomere development. Its expression in the visceral mesoderm is controlled by the product of bap. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(2)k16722

Key Links
Genomic Location
Cytogenetic map
42E1-42E1
Sequence location
Recombination map
2-55
RefSeq locus
NT_033778 REGION:6975285..6985712
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
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables guanyl-nucleotide exchange factor activity
inferred from genetic interaction with UniProtKB:Q8IMX7
(Ding et al., 2016)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables guanyl-nucleotide exchange factor activity
inferred from electronic annotation with InterPro:IPR040144
(InterPro Project Members, 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in muscle cell cellular homeostasis
inferred from mutant phenotype
(Kucherenko et al., 2011)
inferred from genetic interaction with FLYBASE:Dg; FB:FBgn0034072
(Kucherenko et al., 2011)
involved_in regulation of mitochondrion organization
inferred from genetic interaction with UniProtKB:Q8IMX7
(Ding et al., 2016)
involved_in rhabdomere development
inferred from mutant phenotype
(Marrone et al., 2011)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
(Ding et al., 2016)
located_in endoplasmic reticulum
inferred from direct assay
(Ding et al., 2016)
located_in mitochondrion
inferred from direct assay
(Ding et al., 2016)
located_in plasma membrane
inferred from high throughput direct assay
(Lye et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in cytosol
inferred from biological aspect of ancestor with PANTHER:PTN000102921
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
visceral mesodermal armadillo-repeats (vimar) encodes a protein involved in regulation of muscle homeostasis and rhabdomere development. Its expression in the visceral mesoderm is controlled by the product of bap. [Date last reviewed: 2019-03-21]
Protein Function (UniProtKB)
Probably acts as a GEF (guanine nucleotide exchange factor) for the Rho family of small GTP-binding proteins (G proteins) that stimulates the dissociation of GDP to enable subsequent binding of GTP (By similarity). May also chaperone the processing and/or trafficking of small GTPases independently of GEF activity (By similarity). By interacting with Miro, promotes mitochondrial fission in response to high calcium concentrations (PubMed:27716788).
(UniProt, A1Z6S7)
Summary (Interactive Fly)

guanine nucleotide exchange factor for Miro - involved in mitochondrial fusion - functional targets of miR-277 that modulates rCGG repeat-mediated neurodegeneration - expressed embryonically in the midgut and hindgut visceral mesoderm, as well as in the CNS and PNS - mutation causes shortened rhabdomere length in the eye

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\vimar 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
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry A1Z6S7)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

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

Gene model reviewed during 5.48

Shares 5' UTR with upstream gene.

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
vimar-RB
FBtr0086183
NM_057957
3467
634
vimar-RC
FBtr0086182
NM_206045
3470
635
Additional Transcript Data and Comments
Reported size (kB)

3.7, 3.2 (northern blot)

(Lo and Frasch, 1998)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
vimar-PB
FBpp0089175
70.3
634
4.80
A1Z6S6
NP_477305
AAF57418
vimar-PC
FBpp0085514
70.3
635
4.80
A1Z6S7
NP_995767
AAS64794
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Miro.

(UniProt, A1Z6S7)
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\vimar using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.78

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 11 -- 12
dorsal pharyngeal muscle primordium
(Fisher et al., 2012)
embryonic optic lobe primordium
(Fisher et al., 2012)
longitudinal trunk visceral muscle primordium
(Fisher et al., 2012)
somatic muscle primordium

Comment: reported as muscle system primordium

(Fisher et al., 2012)
trunk visceral muscle primordium

Comment: reported as muscle system primordium

(Fisher et al., 2012)
embryonic stage 13 -- 16
larval somatic muscle cell
(Fisher et al., 2012)
larval visceral muscle cell
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage -- larval stage
(Lo and Frasch, 1998)
embryonic stage 1 -- 4
organism

Comment: 0-2 hrs AEL

(Lo and Frasch, 1998)
embryonic stage 9 -- 17

Comment: 4-24 hrs AEL

(Lo and Frasch, 1998)
first instar larval stage
(Lo and Frasch, 1998)
adult stage | female
organism
(Lo and Frasch, 1998)
Additional Descriptive Data

The 3.2 kb vimar maternal transcript is detected at high levels in adult females, and in early embryos. Transcripts are detected at very low levels through the first instar larval stage.

(Lo and Frasch, 1998)

vimar zygotic transcripts are first detected in embryos at 4 hours, and until the first instar larval stage.

(Lo and Frasch, 1998)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
(Ding et al., 2016)
located_in endoplasmic reticulum
inferred from direct assay
(Ding et al., 2016)
located_in mitochondrion
inferred from direct assay
(Ding et al., 2016)
located_in plasma membrane
inferred from high throughput direct assay
(Lye et al., 2014)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\vimar in JBrowse
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) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 20 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of vimar
Transgenic constructs containing regulatory region of vimar
Aberrations (Deficiencies and Duplications) ( 12 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
Hsap\RAP1GDS1
13 of 14
Yes
Yes
1  
Hsap\KPNA5
1 of 14
No
No
1  
Hsap\KPNA7
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (2)
Rnor\Rap1gds1
13 of 14
Yes
Yes
Rnor\Odad2
1 of 14
No
No
Mus musculus (laboratory mouse) (4)
Mmus\Rap1gds1
12 of 14
Yes
Yes
Mmus\Gm10184
1 of 14
No
No
Mmus\Kpna2
1 of 14
No
No
Mmus\Kpna7
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\rap1gds1
10 of 13
Yes
Yes
Xtro\LOC100496678
9 of 13
No
Yes
Xtro\ankar
1 of 13
No
Yes
Xtro\apom
1 of 13
No
Yes
Danio rerio (Zebrafish) (5)
Drer\rap1gds1
13 of 14
Yes
Yes
Drer\si:dkey-191g9.5
11 of 14
No
Yes
Drer\si:dkey-21e13.3
4 of 14
No
Yes
Drer\armc3
1 of 14
No
No
Drer\kpna7
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP005262
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\ABAP1
1 of 13
Yes
No
Atha\ARIA
1 of 13
Yes
No
Atha\MOS6
1 of 13
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\BEM4
1 of 13
Yes
Yes
Scer\VAC8
1 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\arz1
5 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:vimar. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    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 ( 2 )
    Disease Associations of Human Orthologs (via DIOPT v9.1 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?
    RAP1GDS1; Rap1 GTPase-GDP dissociation stimulator 1
    13 of 14
    179502
       
      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
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please see the Physical Interaction reports below for full details
      RNA-RNA
      Physical Interaction
      Assay
      References
      vimar - mir-277
      luminiscence technology, necessary binding region
      (Tan et al., 2012)
      protein-protein
      Physical Interaction
      Assay
      References
      vimar - Miro
      anti tag coimmunoprecipitation, anti tag western blot
      (Ding et al., 2016)
      Summary of Genetic Interactions
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Dg
      enhanceable
      vimar
      (Kucherenko et al., 2011, Kucherenko et al., 2008)
      Dys
      suppressible
      vimar
      (Kucherenko et al., 2008)
      trc
      suppressible
      vimar
      (He et al., 2005)
      External Data
      Subunit Structure (UniProtKB)
      Interacts with Miro.
      (UniProt, A1Z6S7 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyBase
      External Links
      External Data
      Linkouts
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      2R
      Recombination map
      2-55
      Cytogenetic map
      42E1-42E1
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      42E1-42E1
      Limits computationally determined from genome sequence between P{EP}EP2303&P{EP}EP2105 and P{lacW}vimark16722
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      42E2-42E3
      (Lo, 1997.11.12)
      42E3-42E4
      (determined by in situ hybridisation)
      (Spradling et al., 1999, BDGP Project Members, 1994-1999)
      42E2-42E3
      (determined by in situ hybridisation)
      (Lo and Frasch, 1998)
      Experimentally Determined Recombination Data
      Location

      2-55

      (FlyBase, 2016)

      2-56.1

      (Comeron et al., 2012)

      2-

      (Lo, 1997.11.12)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (20)
      Genomic Clones (18)
       

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

      cDNA Clones (90)
       

      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 JBrowse 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
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: vimar l(2)k16722

          (Spradling et al., 1999)

          Source for merge of: vimar anon- EST:Posey213

          (Bayraktaroglu, 2000.11.2)
          Additional comments

          l(2)k04909b may correspond to CG30156 and/or vimar: the P{lacW}l(2)k04909bk04909b insertion maps within the transcription units.

          (Gene Disruption Project members, 2015.10.8)
          Nomenclature History
          Source for database identify of
          Nomenclature comments
          Etymology

          Gene name is 'visceral mesodermal armadillo-repeats' based on the gene's tissue-specific expression and sequence of its encoded protein.

          (Lo and Frasch, 1998)
          Synonyms and Secondary IDs (9)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 53 )
          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/Swiss-Prot - Manually annotated and reviewed 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
          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
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          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)
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
          MIST (genetic) - An integrated Molecular Interaction Database
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (81)