FlyBase Gene Report: Dmel\mir-308

General Information

Symbol

Dmel\mir-308

Species

D. melanogaster

Name

mir-308 stem loop

Annotation Symbol

CR42951

Feature Type

miRNA_gene

FlyBase ID

FBgn0262407

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Pathway
Interactive Fly

Also Known As

dme-mir-308

Key Links

Genomic Location

Cytogenetic map

50E4-50E4

Sequence location

2R:14,215,802..14,215,864 [-]

Recombination map

2-69

RefSeq locus

NT_033778 REGION:14215802..14215864

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

(Daneshvar et al., 2013, Leaman et al., 2005)

enables mRNA base-pairing translational repressor activity

inferred from direct assay

(Yao et al., 2023, Daneshvar et al., 2013, Leaman et al., 2005)

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 miRNA-mediated post-transcriptional gene silencing

inferred from direct assay

(Yao et al., 2023, Daneshvar et al., 2013, Leaman et al., 2005)

involved_in negative regulation of apoptotic process

inferred from mutant phenotype

(Leaman et al., 2005)

involved_in negative regulation of translation

inferred from mutant phenotype

(Rödel et al., 2013)

involved_in peptidoglycan recognition protein signaling pathway

inferred from mutant phenotype

(Yao et al., 2023)

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:RF00743

(RNAcentral, 2018-)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Pathway (FlyBase)

Negative Regulators of Imd Signaling Pathway

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Pathway (FlyBase)

Negative Regulators of Imd Signaling Pathway -: Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\mir-308 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).

Conserved: found throughout the Drosophila genus (FBrf0230987).

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0304328

FBtr0472749

FBtr0304327

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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

MI0000419

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-308 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-308 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-308

View exonic expression by tissue for Dmel\mir-308

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

12798452/tissue=All

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

FBgn0262407

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

FBgn0262407

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mir-308

Transgenic constructs containing regulatory region of mir-308

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 2 )

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-308^UAS.cSa

partially lethal - majority die, with Scer\GAL4^da.G32

mir-308^UAS.cDa

viable, with Scer\GAL4^Tub.PU

mir-308^{sponge.V2.UAS.mCherry}

Sterility

Allele

female fertile (with Df(2R)BSC361)

mir-308^KO

male fertile (with Df(2R)BSC361)

mir-308^KO

Other Phenotypes

Allele

some die during embryonic stage (with Df(2R)BSC361)

mir-308^KO

visible, with Scer\GAL4^Bx-MS1096

mir-308^UAS.cSa

visible, with Scer\GAL4^sca.PU

mir-308^UAS.cSb

Phenotype manifest in

Allele

chaeta | ectopic, with Scer\GAL4^sca.PU

mir-308^UAS.cSb

wing, with Scer\GAL4^Bx-MS1096

mir-308^UAS.cSa

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-308. 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)

Other 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

mir-308 - Myc

western blot, quantitative reverse transcription pcr

(Daneshvar et al., 2013)

mir-308 - grim

fluorescence technology

(Leaman et al., 2005)

mir-308 - skl

fluorescence technology

(Leaman et al., 2005)

Summary of Genetic Interactions

esyN Network Diagram

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

esyN Network Key:

Suppression

Enhancement

Other 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

mir-308

suppressible

Myc

(Daneshvar et al., 2013)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

mir-308

(Szuplewski et al., 2012)

Myc

suppressible

mir-308

(Daneshvar et al., 2013)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262407

Pathways

Signaling Pathways (FlyBase)

Negative Regulators of Imd Signaling Pathway

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

miRNA_gene

(FlyBase Genome Annotators, 2010, Stark et al., 2003, Stark et al., 2003)

nuclear_gene

(FlyBase Genome Annotators, 2010, Stark et al., 2003, Stark et al., 2003)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-69

Cytogenetic map

50E4-50E4

Sequence location

2R:14,215,802..14,215,864 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

50E4-50E4

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-69

(FlyBase, 2016)

2-74.9

(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

41809

w^*; P{UAS-mir-308.D}10

41159

w¹¹¹⁸; P{UAS-LUC-mir-308.T}attP2

59909

w^*; PBac{UAS-mir-308.S}VK00037/CyO

58921

w^*; TI{TI}mir-308^KO/CyO, P{GAL4-twi.G}2.2, P{UAS-2xEGFP}AH2.2

61425

w^*; P{UAS-mCherry.mir-308.sponge.V2}attP40/CyO; P{UAS-mCherry.mir-308.sponge.V2}attP2

FlyORF

F002087

M{UAS-mir-308.S}ZH-86Fb

Genomic Clones (18)

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

New annotation (CR33612) in release 4.1 of the genome annotation.

(FlyBase Genome Annotators, 2005)

Relationship to Other Genes

Source for database merge of

Additional comments

The annotation for mir-308 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 CR33612 to CR42951 to reflect this change.

(FlyBase Genome Annotators, 2010)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

308

(Han et al., 2011)

CR33612

(FlyBase Genome Annotators, 2005)

CR42951

(FlyBase Genome Annotators, 2010)

dme-miR-308

(Volin et al., 2018, Towler et al., 2015)

dme-mir-308

(He et al., 2022, miRBase, 2013, Gesellchen and Boutros, 2004)

mir-308

(Hanyu-Nakamura et al., 2019, Ghezzi et al., 2016, Mohammed and Lai, 2016.2.8, Chen et al., 2014, Mohammed et al., 2014, Naqvi et al., 2014, Wang et al., 2014, Daneshvar et al., 2013, Bejarano et al., 2012, Schertel et al., 2012, Szuplewski et al., 2012, FlyBase Genome Annotators, 2010, Okamura et al., 2009, Ruby et al., 2007, Leaman et al., 2005)

Name Synonyms

mir-308

mir-308 stem loop

Secondary FlyBase IDs

FBgn0067696
FBgn0262244

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 14 )

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.

12798452

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

12798452/tissue=All

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

FBgn0262407

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

FBgn0262407

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

dme:Dmel_CR42951

MARRVEL_MODEL - MARRVEL (model organism gene)

12798452

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

MI0000419

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262407

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262407

References (58)

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

NA

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