FB2020_06, released Dec 22, 2020

Gene: Dmel\vig

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General Information
Symbol
Dmel\vig
Species
D. melanogaster
Name
vasa intronic gene
Annotation Symbol
CG4170
Feature Type
protein_coding_gene
FlyBase ID
FBgn0024183
Gene Model Status
Current
Stock Availability
12 publicly available
Gene Snapshot
vasa intronic gene (vig) encodes a protein involved in RNA interference and heterochromatin organization. [Date last reviewed: 2019-09-19]
Other Summaries
Also Known As

BG:DS00929.13

Key Links
Genomic Location
Cytogenetic map
35C1-35C1
Sequence location
2L:15,062,931..15,070,316 [-]
Recombination map

2-50

RefSeq locus
NT_033779 REGION:15062931..15070316
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 (11 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with UniProtKB:Q9NFU0,UniProtKB:Q9VUQ5,UniProtKB:Q9W0S7
(assigned by UniProt )
(Caudy et al., 2003)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables mRNA binding
inferred from sequence model
(Caudy et al., 2002)
enables RNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000266096
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in heterochromatin organization
inferred from mutant phenotype
(Gracheva et al., 2009)
involved_in RNA interference
inferred from physical interaction with FLYBASE:AGO2; FB:FBgn0087035
(Caudy et al., 2002)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Gracheva et al., 2009)
located_in cytosol
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from direct assay
(Gracheva et al., 2009)
located_in polytene chromosome puff
inferred from direct assay
(Gracheva et al., 2009)
located_in polytene chromosome
inferred from direct assay
(Gracheva et al., 2009)
part_of RISC complex
inferred from physical interaction with FLYBASE:AGO2; FB:FBgn0087035
(Caudy et al., 2002)
inferred from direct assay
(assigned by UniProt )
(Caudy et al., 2003)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000266096
(assigned by GO_Central )
(Gaudet et al., 2011)
located_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000266096
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\vig 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

Gene model reviewed during 5.45

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

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
vig-RA
FBtr0080720
NM_078848
1918
490
vig-RB
FBtr0080721
NM_165100
3164
490
vig-RC
FBtr0080719
NM_165101
1838
490
vig-RD
FBtr0080718
NM_165102
3209
490
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
vig-PA
FBpp0080279
52.7
490
10.41
NP_523572
AAF53437
vig-PB
FBpp0080280
52.7
490
10.41
NP_723896
AAN10887
vig-PC
FBpp0080278
52.7
490
10.41
NP_723897
AAN10888
vig-PD
FBpp0080277
52.7
490
10.41
NP_723898
AAN10889
Polypeptides with Identical Sequences

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

490 aa isoforms: vig-PA, vig-PB, vig-PC, vig-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

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

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
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
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 5 of adulthood & male -- day 7 of adulthood & male
spermatozoon
(Wasbrough et al., 2010)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Gracheva et al., 2009)
located_in cytosol
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from direct assay
(Gracheva et al., 2009)
located_in polytene chromosome puff
inferred from direct assay
(Gracheva et al., 2009)
located_in polytene chromosome
inferred from direct assay
(Gracheva et al., 2009)
part_of RISC complex
inferred from physical interaction with FLYBASE:AGO2; FB:FBgn0087035
(Caudy et al., 2002)
inferred from direct assay
(assigned by UniProt )
(Caudy et al., 2003)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\vig 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) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 8 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of vig
Transgenic constructs containing regulatory region of vig
Deletions and Duplications ( 8 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
female sterile
fertile
Other Phenotypes
Allele
short lived, with Scer\GAL4Mef2.PR
suppressor of variegation | dominant
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (2)
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\SERBP1
12 of 15
Yes
Yes
2  
Hsap\HABP4
7 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
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\Serbp1
11 of 15
Yes
Yes
Mmus\Habp4
8 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Serbp1
10 of 13
Yes
Yes
Rnor\Habp4
8 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\serbp1
10 of 12
Yes
Yes
Xtro\habp4
4 of 12
No
Yes
Danio rerio (Zebrafish) (3)
Drer\serbp1a
11 of 15
Yes
Yes
Drer\serbp1b
10 of 15
No
Yes
Drer\zgc:103482
4 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\vig-1
6 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\AT4G17520
4 of 9
Yes
No
Atha\AT5G47210
4 of 9
Yes
No
Atha\AT4G16830
3 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\STM1
1 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC16A3.08c
2 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190IAK )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00000197
Drosophila simulans
Dsim\GD21970
Drosophila sechellia
Dsec\GM14534
Drosophila erecta
Dere\GG24224
Drosophila yakuba
Dyak\GE19416
Drosophila ananassae
Dana\GF15560
Drosophila pseudoobscura pseudoobscura
Dpse\GA18005
Drosophila persimilis
Dper\GL25726
Drosophila willistoni
Dwil\GK18065
Drosophila virilis
Dvir\GJ15963
Drosophila mojavensis
Dmoj\GI17329
Drosophila grimshawi
Dgri\GH10817
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150EI1 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17007688
Glossina morsitans
Tsetse fly
Gmor\GMOY004545
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_00488
Mayetiola destructor
Hessian fly
Mdes\Mdes013409
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0HZY )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ixodes scapularis
Black-legged tick
Isca\ISCW000538
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (3)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
vig2
7 of 10
FDY
5 of 10
PPYR1
3 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?
    SERBP1; SERPINE1 mRNA binding protein 1
    12 of 15
    607378
         
        HABP4; hyaluronan binding protein 4
        7 of 15
        617369
            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
            vig - AGO1
            anti tag coimmunoprecipitation, western blot
            (Zhou et al., 2008)
            vig - AGO2
            molecular sieving, ion exchange chromatography, peptide massfingerprinting, anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation
            (Zhou et al., 2008, Caudy et al., 2003, Caudy et al., 2002)
            vig - CG4806
            experimental knowledge based
            (Guruharsha et al., 2011)
            vig - Fmr1
            anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, molecular sieving, ion exchange chromatography, peptide massfingerprinting
            (Lee et al., 2018, Zhou et al., 2008, Caudy et al., 2003, Caudy et al., 2002)
            vig - Nelf-E
            anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
            (Rhee et al., 2014)
            vig - Pi3K92E
            anti tag coimmunoprecipitation, Identification by mass spectrometry
            (Vinayagam et al., 2016)
            vig - RpL21
            anti tag coimmunoprecipitation, western blot
            (Zhou et al., 2008)
            vig - RpL22
            anti tag coimmunoprecipitation, western blot
            (Zhou et al., 2008)
            vig - S6kII
            anti tag coimmunoprecipitation, Identification by mass spectrometry
            (Vinayagam et al., 2016)
            vig - Su(var)2-HP2
            anti bait coimmunoprecipitation, western blot
            (Gracheva et al., 2009)
            vig - Su(var)205
            anti bait coimmunoprecipitation, western blot
            (Gracheva et al., 2009)
            vig - Tdrd3
            anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, Identification by mass spectrometry
            (Lee et al., 2018)
            vig - Tsc1
            anti tag coimmunoprecipitation, Identification by mass spectrometry
            (Vinayagam et al., 2016)
            vig - Tudor-SN
            molecular sieving, ion exchange chromatography, western blot, anti bait coimmunoprecipitation
            (Caudy et al., 2003)
            vig - bel
            anti tag coimmunoprecipitation, western blot
            (Zhou et al., 2008)
            vig - foxo
            anti tag coimmunoprecipitation, Identification by mass spectrometry
            (Vinayagam et al., 2016)
            vig - gig
            anti tag coimmunoprecipitation, Identification by mass spectrometry
            (Vinayagam et al., 2016)
            RNA-protein
            Physical Interaction
            Assay
            References
            vig - His2A
            anti tag coimmunoprecipitation, quantitative reverse transcription pcr, electrophoretic mobility shift assay, autoradiography
            (Tsui et al., 2018)
            vig - His3
            anti tag coimmunoprecipitation, quantitative reverse transcription pcr
            (Tsui et al., 2018)
            vig - hpRNA:CR46342
            anti tag coimmunoprecipitation, northern blot
            (Zhou et al., 2008)
            vig - mir-2b-1
            anti bait coimmunoprecipitation, northern blot
            (Caudy et al., 2003)
            vig - mir-2b-2
            anti bait coimmunoprecipitation, northern blot
            (Caudy et al., 2003)
            vig - mir-ban
            anti tag coimmunoprecipitation, northern blot
            (Zhou et al., 2008)
            Summary of Genetic Interactions
            esyN Network Diagram
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            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
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2L
            Recombination map

            2-50

            Cytogenetic map
            35C1-35C1
            Sequence location
            2L:15,062,931..15,070,316 [-]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            35C1-35C1
            Limits computationally determined from genome sequence between P{lacW}Su(H)k07904 and P{EP}vigEP812&P{PZ}stc05441
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location

            2-50

            (FlyBase, 2016)

            2-47.8

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (12)
            Genomic Clones (14)
             

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

            cDNA Clones (187)
             

            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

            (Gracheva et al., 2009, Caudy et al., 2003)
            Commercially Available Antibodies
             
            Other Information
            Relationship to Other Genes
            Source for database identify of

            Source for identity of: vig CG4170

            (Kodira, 1999.11)
            Source for database merge of
            Additional comments
            Other Comments

            Shows particularly robust cycling of transcription in adult heads, as assessed by expression analysis using high density oligonucleotide arrays with probe generated during three 12-point time course experiments over the course of 6 days.

            (Claridge-Chang et al., 2001)
            Origin and Etymology
            Discoverer
            Etymology
            Identification
            External Crossreferences and Linkouts ( 45 )
            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
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            Flygut - An atlas of the Drosophila adult midgut
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            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
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            DPiM - Drosophila Protein interaction map
            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
            FlyMine - An integrated database for Drosophila genomics
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            Synonyms and Secondary IDs (8)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (99)