FB2020_06, released Dec 22, 2020

Gene: Dmel\bonsai

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General Information
Symbol
Dmel\bonsai
Species
D. melanogaster
Name
bonsai
Annotation Symbol
CG4207
Feature Type
protein_coding_gene
FlyBase ID
FBgn0026261
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Snapshot
bonsai (bonsai) encodes a mitochondrial small ribosomal protein that belongs to the universal S15 ribosomal protein US15m family. It is involved in growth regulation. [Date last reviewed: 2018-10-18]
Other Summaries
Also Known As

mRpS15

Key Links
Genomic Location
Cytogenetic map
58F3-58F3
Sequence location
2R:22,637,770..22,638,868 [+]
Recombination map

2-100

RefSeq locus
NT_033778 REGION:22637770..22638868
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 (6 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables structural constituent of ribosome
inferred from sequence or structural similarity with UniProtKB:P82914
(Sardiello et al., 2003.6.11, Koc et al., 2001)
inferred from sequence or structural similarity with UniProtKB:P82913
(assigned by UniProt )
(Suzuki et al., 2001)
traceable author statement
(Marygold et al., 2007)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in regulation of growth
inferred from mutant phenotype
(assigned by UniProt )
(Galloni and Edgar, 1999)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in mitochondrial translation
traceable author statement
(Marygold et al., 2007)
inferred from sequence or structural similarity with UniProtKB:P82913
(assigned by UniProt )
(Suzuki et al., 2001)
involved_in translation
inferred from sequence or structural similarity with UniProtKB:P82914
(Sardiello et al., 2003.6.11, Koc et al., 2001)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in mitochondrion
inferred from direct assay
(Galloni, 2003)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of mitochondrial small ribosomal subunit
inferred from sequence or structural similarity with UniProtKB:P82914
(Sardiello et al., 2003.6.11, Koc et al., 2001)
traceable author statement
(Marygold et al., 2007)
inferred from sequence or structural similarity with UniProtKB:P82913
(assigned by UniProt )
(UniProt Curators, 2002-, Suzuki et al., 2001)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the universal ribosomal protein uS15 family. (Q8WTC1)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
MITOCHONDRIAL SMALL RIBOSOMAL PROTEINS -
Mitochondrial ribosomes are found in the mitochondrial matrix and translate genes involved in oxidative phosphorylation encoded by the mitochondrial genome. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the small subunit is to bind mRNA. (Adapted from FBrf0205398).
Protein Function (UniProtKB)
Essential for gut mitochondrial activity. Might be involved in tissue specific growth factor production.
(UniProt, Q8WTC1)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\bonsai 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 5.51

Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
bonsai-RA
FBtr0071860
NM_137847
981
280
Additional Transcript Data and Comments
Reported size (kB)

1 (northern blot)

(Galloni, 2003)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
bonsai-PA
FBpp0071771
33.5
280
9.73
NP_611691
AAF46869
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)

280 (aa)

(Galloni, 2003)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins.

(UniProt, Q8WTC1)
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\bonsai 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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
extended germ band stage
anterior midgut primordium & posterior midgut primordium
(Galloni, 2003)
larval stage
embryonic/larval midgut
(Galloni, 2003)
embryonic stage 1 -- 3
organism | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism | faint | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
head mesoderm
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
embryonic stage 9 -- 10
head mesoderm
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
head mesoderm
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
embryonic stage 13 -- 16
dorsal pharyngeal muscle
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
embryonic/larval visceral muscle
(Fisher et al., 2012)
embryonic stage 2
organism | ubiquitous
(Galloni, 2003)
embryonic stage 16
embryonic/larval midgut primordium | restricted
(Galloni, 2003)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage -- adult stage
(Galloni, 2003)
Additional Descriptive Data

In early embryos bonsai transcript is detected throughout the organism suggesting maternal deposition. At the end of germband extension bonsai is expressed in the anterior and poster midgut primordia and as development proceeds expression occurs in regions corresponding to the midgut constrictions. Expression is also detected in the larval midgut.

(Galloni, 2003)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
distribution deduced from reporter or direct label
Stage
Tissue/Position (including subcellular localization)
Reference
(Galloni, 2003)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
Additional Descriptive Data

A ubiquitously expressedGFP::bonsai fusion protein was used to localize the bonsai protein to the mitochondrion.

(Galloni, 2003)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in mitochondrion
inferred from direct assay
(Galloni, 2003)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\bonsai 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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of bonsai
Transgenic constructs containing regulatory region of bonsai
Deletions and Duplications ( 3 )
Phenotypes
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\MRPS15
11 of 15
Yes
Yes
Hsap\RPS13
1 of 15
No
No
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\Mrps15
10 of 15
Yes
Yes
Mmus\Rps13
1 of 15
No
No
Rattus norvegicus (Norway rat) (2)
Rnor\Mrps15
11 of 13
Yes
Yes
Rnor\LOC684988
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\mrps15
7 of 12
Yes
Yes
Xtro\rps13
1 of 12
No
No
Danio rerio (Zebrafish) (2)
Drer\mrps15
9 of 15
Yes
Yes
Drer\rps13
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\mrps-15
11 of 15
Yes
Yes
Cele\rps-13
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT1G15810
2 of 9
Yes
Yes
Atha\AT1G80620
2 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\MRPS28
8 of 15
Yes
Yes
Scer\RPS13
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\mrps28
5 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190CPH )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00002117
Drosophila simulans
Dsim\GD11682
Drosophila sechellia
Dsec\GM15929
Drosophila erecta
Dere\GG21060
Drosophila yakuba
Dyak\GE14002
Drosophila ananassae
Dana\GF11906
Drosophila pseudoobscura pseudoobscura
Dpse\GA18031
Drosophila persimilis
Dper\GL11592
Drosophila willistoni
Dwil\GK17900
Drosophila virilis
Dvir\GJ21104
Drosophila mojavensis
Dmoj\GI19535
Drosophila grimshawi
Dgri\GH21563
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091508OC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17015229
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07818
Mayetiola destructor
Hessian fly
Mdes\Mdes003124
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL001280
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL014836
Anopheles darlingi
American malaria mosquito
Adar\ADAC006684
Anopheles gambiae
Malaria mosquito
Agam\AGAP005615
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002310
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09FJ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA012954
Danaus plexippus
Monarch butterfly
Dple\DPOGS206948-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL014368
Apis florea
Little honeybee
Aflo\2330096612
Apis mellifera
Western honey bee
Amel\GB48064
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP15456
Bombus terrestris
Buff-tailed bumblebee
Bter\15208246
Linepithema humile
Argentine ant
Lhum\LH15954
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0008fa
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG011359
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_06216
Tribolium castaneum
Red flour beetle
Tcas\TC013234
Pediculus humanus
Human body louse
Phum\PHUM167470
Rhodnius prolixus
Kissing bug
Rpro\RPRC003299
Cimex lectularius
Bed bug
Clec\CLEC012189
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI007377
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01750
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X09BQ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR006105
Ixodes scapularis
Black-legged tick
Isca\ISCW020518
Stegodyphus mimosarum
African social velvet spider
Smim\KFM67383.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur18g00740
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_300200
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0EM6 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_009251gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_022526gn
Ciona intestinalis
Vase tunicate
Cint\LOC100180232
Gallus gallus
Domestic chicken
Ggal\ENSGALG00000027648
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
RpS13
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?
    MRPS15; mitochondrial ribosomal protein S15
    11 of 15
    611979
        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
        bonsai - rictor
        anti tag coimmunoprecipitation, Identification by mass spectrometry
        (Vinayagam et al., 2016)
        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
        bonsai
        suppressible
        Dp
        (Galloni and Edgar, 1999)
        bonsai
        suppressible
        E2f1
        (Galloni and Edgar, 1999)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins.
        (UniProt, Q8WTC1 )
        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
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map

        2-100

        Cytogenetic map
        58F3-58F3
        Sequence location
        2R:22,637,770..22,638,868 [+]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        58F3-58F3
        Limits computationally determined from genome sequence between P{PZ}l(2)rG270rG270 and P{EP}EP718EP718
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        58F-58F
        (Galloni, 1999.3.4)
        Experimentally Determined Recombination Data
        Location

        2-100

        (FlyBase, 2016)

        2-105.5

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (6)
        Genomic Clones (15)
         

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

        cDNA Clones (54)
         

        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
         
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of
        Source for database merge of

        Source for merge of: bonsai CG4207

        (Millburn, 2000.10.26)
        Additional comments
        Other Comments

        bonsai mutants appear to have defective mitochondrial activity in the gut.

        (Galloni, 2003)

        Mutants have a growth defect that is not cell-autonomous.

        (Galloni and Edgar, 1999)

        Identification: One of a collection of genes identified with defective larval growth that extend larval life.

        (Galloni and Edgar, 1999)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 37 )
        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/Swiss-Prot - Manually annotated and reviewed 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
        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
        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.
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        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 (6)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (48)