FlyBase Gene Report: Dmel\mir-278

General Information

Symbol

Dmel\mir-278

Species

D. melanogaster

Name

mir-278 stem loop

Annotation Symbol

CR42945

Feature Type

miRNA_gene

FlyBase ID

FBgn0262403

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

dme-miR-278, EP1229, miR-278-3p, mirvana

Key Links

Genomic Location

Cytogenetic map

52B3-52B3

Sequence location

2R:15,657,066..15,657,163 [+]

Recombination map

2-75

RefSeq locus

NT_033778 REGION:15657066..15657163

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (6 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables mRNA 3'-UTR binding

inferred from direct assay

(Yu et al., 2009, Easow et al., 2007, Teleman and Cohen, 2006)

enables mRNA base-pairing translational repressor activity

inferred from direct assay

(Yu et al., 2009, Easow et al., 2007, Teleman and Cohen, 2006)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (4 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in energy homeostasis

inferred from mutant phenotype

(Teleman and Cohen, 2006)

involved_in female germ-line stem cell asymmetric division

inferred from mutant phenotype

(Yu et al., 2009)

involved_in miRNA-mediated post-transcriptional gene silencing

inferred from direct assay

(Yu et al., 2009, Easow et al., 2007, Teleman and Cohen, 2006)

involved_in negative regulation of apoptotic process

inferred from mutant phenotype

(Nairz et al., 2006)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in miRNA-mediated post-transcriptional gene silencing

inferred from electronic annotation with Rfam:RF00729

(RNAcentral, 2018-)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\mir-278 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

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Locations and structures of miRNA models as mapped by miRBase (FBrf0220601).

miRNA support: accession MI0000361 at http://www.sanger.ac.uk/Software/Rfam/mirna/ and FBrf0160711; FBrf0162058;

Conserved: found throughout the Drosophila genus (FBrf0230987).

Sequence Ontology: Class of Gene

gene

miRNA_gene

(FlyBase Genome Annotators, 2010)

nuclear_gene

(FlyBase Genome Annotators, 2010)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0304316

FBtr0472722

FBtr0304315

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

miRBase - A searchable database of published miRNA sequences and annotation.

MI0000361

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\mir-278 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).

NA

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\mir-278 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\mir-278

View exonic expression by tissue for Dmel\mir-278

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

12798482/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262403

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262403

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 10 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mir-278

Transgenic constructs containing regulatory region of mir-278

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal, with Scer\GAL4^Act5C.PU

mir-278^UAS.cSa

lethal, with Scer\GAL4^Bx-MS1096

mir-278^{UAS.DsRed(Unk)}

lethal, with Scer\GAL4^ey.PU

mir-278^UAS.cSa

lethal, with Scer\GAL4^ptc-559.1

mir-278^{UAS.DsRed(Unk)}

lethal, with Scer\GAL4^sd-SG29.1

mir-278^{UAS.DsRed(Unk)}

lethal - all die before end of P-stage, with Scer\GAL4^Bx-MS1096

mir-278^UAS.cSa

lethal - all die before end of P-stage, with Scer\GAL4^sd-SG29.1

mir-278^UAS.pLUC

viable

viable, with Scer\GAL4^Tub.PU

mir-278^{sponge.V2.UAS.mCherry}

Sterility

Allele

female fertile

mir-278^KO

fertile

mir-278^mirvana-1

male fertile

mir-278^KO

Other Phenotypes

Allele

increased cell number, with Scer\GAL4^GMR.PF

some die during pharate adult stage, with Scer\GAL4^Bx-MS1096

mir-278^UAS.cSa

some die during pharate adult stage, with Scer\GAL4^sd-SG29.1

mir-278^UAS.pLUC

visible, with Scer\GAL4^dpp.blk1

mir-278^UAS.cTa

visible, with Scer\GAL4^dpp.PU

mir-278^{UAS.DsRed(Unk)}

visible, with Scer\GAL4^en-e16E

visible, with Scer\GAL4^GMR.PF

mir-278^EP2316

visible, with Scer\GAL4^sca-537.4

Phenotype manifest in

Allele

1st posterior cell, with Scer\GAL4^dpp.blk1

mir-278^UAS.cTa

1st posterior cell, with Scer\GAL4^dpp.PU

mir-278^{UAS.DsRed(Unk)}

dorsocentral bristle, with Scer\GAL4^sca-537.4

dorsocentral bristle | ectopic, with Scer\GAL4^sca-537.4

eye, with Scer\GAL4^ey.PU

mir-278^UAS.cSa

eye, with Scer\GAL4^GMR.PF

female germline stem cell (with mir-278^Gal4KI)

mir-278^KO

female germline stem cell (with mir-278^KO)

mir-278^Gal4KI

female germline stem cell | germline clone

germline cell | embryonic stage

mir-278^KO

interommatidial bristle

mir-278^mirvana-1

interommatidial bristle, with Scer\GAL4^GMR.PF

ommatidial precursor cluster, with Scer\GAL4^GMR.PF

ommatidium

mir-278^mirvana-1

ommatidium, with Scer\GAL4^GMR.PF

ommatidium | somatic clone, with Scer\GAL4^GMR.PB

mir-278^KN447.UAS

posterior crossvein, with Scer\GAL4^en-e16E

mir-278^UAS.cTa

scutellar bristle, with Scer\GAL4^sca-537.4

scutellar bristle | ectopic, with Scer\GAL4^sca-537.4

tormogen cell, with Scer\GAL4^sca-537.4

tormogen cell | ectopic, with Scer\GAL4^sca-537.4

mir-278^EP1229

trichogen cell, with Scer\GAL4^sca-537.4

trichogen cell | ectopic, with Scer\GAL4^sca-537.4

mir-278^EP1229

wing blade posterior compartment, with Scer\GAL4^en-e16E

wing disc, with Scer\GAL4^ap-md544

mir-278^UAS.cTa

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:mir-278. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (0)

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 ( 0 )

Allele

Disease

Interaction

References

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?

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:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

MIST Molecular Interaction Search Tool

View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

RNA-RNA

Physical Interaction

Assay

References

mir-278 - dap

luminiscence technology, necessary binding region

(Yu et al., 2009)

mir-278 - ex

immunohistochemistry, luminiscence technology, necessary binding region

(Easow et al., 2007, Teleman and Cohen, 2006)

Summary of Genetic Interactions

esyN Network Diagram

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

View in 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

mir-278

suppressible

Pi3K92E

(Teleman and Cohen, 2006)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

chico

suppressible

mir-278

(Teleman and Cohen, 2006)

suppressible

mir-278

(Teleman and Cohen, 2006)

grim

suppressible

mir-278

(Nairz et al., 2006, Müller et al., 2005)

hid

suppressible

mir-278

(Müller et al., 2005)

suppressible

mir-278

(Singh et al., 2005)

enhanceable

mir-278

(Abdelilah-Seyfried et al., 2000)

p53

suppressible

mir-278

(Müller et al., 2005)

pnr

enhanceable

mir-278

(Pena-Rangel et al., 2002)

rpr

suppressible

mir-278

(Müller et al., 2005)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262403

MIST (genetic) - An integrated Molecular Interaction Database

12798482

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-75

Cytogenetic map

52B3-52B3

Sequence location

2R:15,657,066..15,657,163 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

52B3-52B3

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-75

(FlyBase, 2016)

2-79.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

58909

w^*; TI{TI}mir-278^KO

41180

w¹¹¹⁸; P{UAS-LUC-mir-278.T}attP2

60598

w^*; P{UAS-mir-278.T}3/TM3, Ser¹

61409

w^*; P{UAS-mCherry.mir-278.sponge.V2}attP40/CyO; P{UAS-mCherry.mir-278.sponge.V2}attP2

FlyORF

F002060

M{UAS-mir-278.S}ZH-86Fb

Kyoto

122040

w¹¹¹⁸; P{EP}mir-278^EP1229

Genomic Clones (23)

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

cDNA Clones (0)

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

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

mir-278 does not appear to belong to an miRNA family and is insect specific.

(Nairz et al., 2006)

mir-278 mutants have elevated insulin production and are correspondingly lean. Despite the elevated insulin levels, mir-278 mutants have elevated circulating sugar, mobilised from adipose-tissue glycogen stores. mir-278 mutants appear to be insulin resistant.

(Teleman and Cohen, 2006)

New annotation (CR33589) in release 4.1 of the genome annotation.

(FlyBase Genome Annotators, 2005)

Relationship to Other Genes

Source for database merge of

Source for merge of: EP1229 EP2316

(Pena-Rangel et al., 2002)

Source for merge of: mir-278 EP1229

(Nairz et al., 2006)

Additional comments

The annotation for mir-278 has been changed in release 5.31 of the genome annotation, so that instead of representing a mature miRNA it now represents the precursor stem loop pre-miRNA. The symbol of the annotation has been changed from CR33589 to CR42945 to reflect this change.

(FlyBase Genome Annotators, 2010)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

CR33589

(FlyBase Genome Annotators, 2005)

CR42945

(FlyBase Genome Annotators, 2010)

EP(2)1229

(Pena-Rangel et al., 2002)

EP1229

EP2316

MIR-278

(Ylla et al., 2016)

Mir-278

(Robins et al., 2005)

dme-miR-278

(Volin et al., 2018, Chandra et al., 2017, Dhahbi et al., 2016, Lucas et al., 2015, Towler et al., 2015, Esslinger et al., 2013)

dme-mir-278

(He et al., 2022, Mohammed et al., 2014, miRBase, 2013, Krishnan et al., 2006)

miR-278-3p

(Gartland et al., 2022, Hotzy et al., 2022)

mirvana

(Nairz, 2006.8.18, Nairz et al., 2006)

Name Synonyms

EP1229

miR-278

(Kühnlein, 2010, Easow et al., 2007)

micro RNA hidden in a nirvana

(Nairz et al., 2006)

mir-278

mir-278 stem loop

Secondary FlyBase IDs

FBgn0086369
FBgn0082178
FBgn0043373
FBgn0043361
FBgn0262238

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 18 )

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.

12798482

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms

Other crossreferences

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

12798482/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262403

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262403

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CR42945

MARRVEL_MODEL - MARRVEL (model organism gene)

12798482

miRBase - A searchable database of published miRNA sequences and annotation.

MI0000361

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262403

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262403

MIST (genetic) - An integrated Molecular Interaction Database

12798482

References (82)

The following external sites may use different assemblies or annotations than FlyBase.

NA

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