FB2022_02, released March 29, 2022

Gene: Dmel\BomS3

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General Information
Symbol
Dmel\BomS3
Species
D. melanogaster
Name
Bomanin Short 3
Annotation Symbol
CG16844
Feature Type
protein_coding_gene
FlyBase ID
FBgn0040736
Gene Model Status
Current
Stock Availability
2 publicly available
Gene Summary
Secreted immune-induced peptide induced by Toll signaling (PubMed:29920489). Has a role in resistance bacterial and fungal infections (PubMed:25915418, PubMed:29920489). The strength of antimicrobial activity appears to correlate with the overall level of expression (PubMed:29920489). Has no activity against the fungus C.glabrata in vitro (PubMed:29920489). (UniProt, Q9V8G0)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

IM3, Immune induced molecule 3, DIM 3, Bom3

Key Links
Genomic Location
Cytogenetic map
55C4-55C4
Sequence location
Recombination map
2-85
RefSeq locus
NT_033778 REGION:18387895..18388734
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 (3 terms)
Molecular Function (0 terms)
There is no information supporting a Molecular Function term for this gene. (Based on a review of available data before: 2006-08-03 )
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in antibacterial humoral response
inferred from direct assay
(assigned by UniProt )
(Uttenweiler-Joseph et al., 1998)
involved_in response to bacterium
inferred from high throughput expression pattern
(Levy et al., 2004)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in extracellular region
inferred from direct assay
(assigned by UniProt )
(Uttenweiler-Joseph et al., 1998)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the bomanin family. (Q9V8G0)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
BOMANINS -
Bomanins are a family of small, secreted immune-induced peptides that are induced by Toll signalling. These proteins may confer resistance to bacterial infection. (Adapted from FBrf0228271).
Protein Function (UniProtKB)
Secreted immune-induced peptide induced by Toll signaling (PubMed:29920489). Has a role in resistance bacterial and fungal infections (PubMed:25915418, PubMed:29920489). The strength of antimicrobial activity appears to correlate with the overall level of expression (PubMed:29920489). Has no activity against the fungus C.glabrata in vitro (PubMed:29920489).
(UniProt, Q9V8G0)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\BomS3 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 Q9V8G0)

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

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
BomS3-RA
FBtr0086665
NM_144111
301
39
BomS3-RB
FBtr0340328
NM_001299640
769
39
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
BomS3-PA
FBpp0085846
4.1
39
8.83
NP_652368
AAF57707
BomS3-PB
FBpp0309289
4.1
39
8.83
NP_001286569
AHN56364
Polypeptides with Identical Sequences

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

39 aa isoforms: BomS3-PA, BomS3-PB
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\BomS3 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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in extracellular region
inferred from direct assay
(assigned by UniProt )
(Uttenweiler-Joseph et al., 1998)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\BomS3 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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of BomS3
Transgenic constructs containing regulatory region of BomS3
Aberrations (Deficiencies and Duplications) ( 3 )
Inferred from experimentation ( 3 )
Gene disrupted in
Df(2R)BomΔ55C-2
(Lindsay et al., 2018)
Df(2R)BomΔ55C
(Clemmons et al., 2015)
Gene not disrupted in
Df(2R)BomΔleft
(Clemmons et al., 2015)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (0)
No records found.
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (0)
No records found.
Rattus norvegicus (Norway rat) (0)
No records found.
Xenopus tropicalis (Western clawed frog) (0)
No records found.
Danio rerio (Zebrafish) (0)
No records found.
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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?
    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
    Interactions Browser
    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.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-85
    Cytogenetic map
    55C4-55C4
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    55C4-55C4
    Limits computationally determined from genome sequence between P{PZ}sbb04525&P{EP}EP1081EP1081 and P{lacW}l(2)08770k04808
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-85

    (FlyBase, 2016)

    2-89.6

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (2)
    Genomic Clones (12)
     

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

    cDNA Clones (48)
     

    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 identity of: CG16844 IM3

    (FlyBase, 1996-)

    Source for identity of: Bom3 IM3

    (Lindsay et al., 2018)

    Source for identity of: BomS3 Bom3

    (Wasserman et al., 2019.8.12)
    Source for database merge of

    Source for merge of: CG16844 BcDNA:RH58911

    (FlyBase, 1996-)
    Additional comments

    The genes CG15065 and IM3 share >70% identity and close proximity, and so may have been derived from a DNA-based tandem duplication.

    (Langille and Clark, 2007)

    Source for identity of CG16844 IM3 was sequence identity ( date:031215 ).

    (FlyBase, 1996-)

    Source for merge of CG16844 BcDNA:RH58911 was a shared cDNA ( date:030728 ).

    (FlyBase, 1996-)
    Other Comments

    Identification: Encodes a protein that is induced by immune challenge.

    (Uttenweiler-Joseph et al., 1998)
    Origin and Etymology
    Discoverer
    Etymology

    Renamed to have a systematic 'Bom' (Bomanin) prefix for all family members while retaining the last digit of the previous 'IM' number for continuity with prior literature.

    (Lindsay et al., 2018)
    Identification
    External Crossreferences and Linkouts ( 33 )
    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
    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
    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.
    MARRVEL_MODEL - MARRVEL (model organism gene)
    modMine - A data warehouse for the modENCODE project
    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
    FlyMine - An integrated database for Drosophila genomics
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Synonyms and Secondary IDs (12)
    Datasets (4)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    Study result (4)
    Result
    Result Type
    Title
    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_NI120HL_seq_clustering
    Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
    References (69)