FlyBase Gene Report: Dmel\mir-6-3

General Information

Symbol

Dmel\mir-6-3

Species

D. melanogaster

Name

mir-6-3 stem loop

Annotation Symbol

CR42966

Feature Type

miRNA_gene

FlyBase ID

FBgn0262418

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

miR-6, dme-mir-6-3

Key Links

Genomic Location

Cytogenetic map

56E1-56E1

Sequence location

2R:19,660,716..19,660,795 [-]

Recombination map

2-90

RefSeq locus

NT_033778 REGION:19660716..19660795

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 (2 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

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:RF00143

(RNAcentral, 2018-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of RISC complex

inferred from electronic annotation with Rfam:RF00143

(RNAcentral, 2018-)

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-6-3 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)

FBtr0304358

FBtr0309744

FBtr0304357

Additional Transcript Data and Comments

Reported size (kB)

Comments

This miRNA exists in multiple copies in the genome.

(Aravin et al., 2003)

External Data

Crossreferences

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

MI0000126

Rfam - A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements

RF00143

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

AJ421766

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-6-3 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

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4

organism | ubiquitous

• nucleus

Comment: probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018

(Biemar et al., 2005)

organism | ubiquitous

(Aboobaker et al., 2005)

embryonic stage 5

organism | 10-90% egg length

• nucleus

Comment: probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018

(Biemar et al., 2005)

organism | restricted

Comment: along anterior-posterior axis

(Aboobaker et al., 2005)

organism | striped

Comment: restricted dorsally late stage 5

(Aboobaker et al., 2005)

embryonic stage 5 -- 7

dorsal ectoderm | striped

• nucleus

Comment: probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018

(Biemar et al., 2005)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Sempere et al., 2003)

embryonic stage -- second instar larval stage

organism

(Aravin et al., 2003)

first instar larval stage

(Sempere et al., 2003)

Additional Descriptive Data

mir-6-3 transcript is ubquitously expressed in precellular embryos. At stage 5, transcript expression is repressed, first at the posterior pole of the embryo, then in a dorsal patch at the anterior of the embryo. Late in stage 5, transcript expression begins to be lost in the mesoderm and neural ectoderm in ventral and lateral regions. By late embryonic stage 5, expression is refined to transient stripes in the dorsal ectoderm These stripes become further refined to a single central band by embryonic stage 7. Expression is essentially lost by the onset of germband elongation, except for residual expression at the anterior tip of the embryo, and in the dorsal ectoderm. mir-6-3 transcript is localized to the nucleus at all stages.

(Biemar et al., 2005)

Expression has a broad peak from the fourth hour until the end of embryonic development. Probe

(Aravin et al., 2003)

Northern analysis of 24 microRNAs showed that the expression of mir-4, mir-5, mir-124 and mir-6 isoforms (mir-6-1, mir-6-2 and mir-6-3) is restricted to embryogenesis and the first larval instar with levels decreasing during the latter part of the first larval stage.

(Sempere et al., 2003)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{mir-3.eve-lacZ.0.8}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4

organism | ubiquitous

(Biemar et al., 2005)

embryonic stage 5

organism | 10-90% egg length

(Biemar et al., 2005)

embryonic stage 5 -- 7

dorsal ectoderm | striped

(Biemar et al., 2005)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\mir-6-3 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-6-3

View exonic expression by tissue for Dmel\mir-6-3

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

12798351/tissue=All

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

FBgn0262418

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

FBgn0262418

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 ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mir-6-3

Transgenic constructs containing regulatory region of mir-6-3

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)mir-309-6^Δ1

(Bushati et al., 2008)

Inferred from location ( 5 )

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

viable, with Scer\GAL4^Act5C.PU

mir-6-3^UAS.cSa

Phenotype manifest in

Allele

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-6-3. 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

alcohol, response to, microRNA-related

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

mir-6-3^{UAS.cluster.pLUC}

model of alcohol use disorder

CEA with mir-6-1^{UAS.cluster.pLUC}, mir-6-2^{UAS.cluster.pLUC}

(Ghezzi et al., 2016)

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-6-3 - hid

luminiscence technology, fluorescence technology

(Leaman et al., 2005)

mir-6-3 - rpr

luminiscence technology

(Leaman et al., 2005)

mir-6-3 - skl

fluorescence technology

(Brennecke et al., 2005, Leaman et al., 2005)

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262418

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

miRNA_gene

(FlyBase Genome Annotators, 2010, Lagos-Quintana et al., 2001)

nuclear_gene

(FlyBase Genome Annotators, 2010, Lagos-Quintana et al., 2001)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-90

Cytogenetic map

56E1-56E1

Sequence location

2R:19,660,716..19,660,795 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

56E1-56E1

Limits computationally determined from genome sequence between P{PZ}sm⁰⁵³³⁸&P{PZ}emm¹ and P{lacW}l(2)k08002^k08002

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-90

(FlyBase, 2016)

2-95.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

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

Bloomington

41136

w¹¹¹⁸; P{UAS-LUC-mir-6-1.mir-6-2.mir-6-3.T}attP2

61372

w^*; P{UAS-mCherry.mir-6.sponge.V2}attP40/CyO; P{UAS-mCherry.mir-6.sponge.V2}attP2

FlyORF

F001941

M{UAS-mir-6-3.S}ZH-86Fb

Genomic Clones (19)

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-3, mir-4, mir-5, mir-6-1, mir-6-2 and mir-6-3 sequences are clustered within 900bp in 56D7-56E3.

(Sempere et al., 2003)

New annotation (CR33039) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Additional comments

The annotation for mir-6-3 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 CR33039 to CR42966 to reflect this change.

(FlyBase Genome Annotators, 2010)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

6-3

(Chen et al., 2014)

CR33039

CR42966

(FlyBase Genome Annotators, 2010)

Dme-miR-6

(Zhou et al., 2009)

dme-miR-6-3

(Volin et al., 2018)

dme-mir-6-3

(He et al., 2022, Chen et al., 2013, miRBase, 2013, Wang and Liu, 2011)

miR-6

(Tat et al., 2016, Lucas and Raikhel, 2013, Ge et al., 2012, Behura et al., 2011, Thomsen et al., 2010, Nahvi et al., 2009, Bushati et al., 2008, Behura, 2007, Carthew, 2006, Rehwinkel et al., 2006, Alvarez-Garcia and Miska, 2005, Leaman et al., 2005, Boutla et al., 2003, Sempere et al., 2003, Stark et al., 2003, Stark et al., 2003, Lagos-Quintana et al., 2001, Lee et al., 2001, Ruvkun, 2001)

miR-6-3

(Atilano et al., 2017, Li et al., 2017, Pancratov et al., 2013, Bejarano et al., 2012, Biemar et al., 2005, Lai et al., 2004, Lai, 2002)

miR6-3

(Lai et al., 2003)

mir-6

(Daneshvar et al., 2013, Schnall-Levin et al., 2010, Burgler and Macdonald, 2005, Stark et al., 2005, Sempere et al., 2003)

mir-6-3

(Örkenby et al., 2023, Zhe et al., 2020, Hanyu-Nakamura et al., 2019, Ghezzi et al., 2016, Mohammed and Lai, 2016.2.8, Cook and Van Vactor, 2015.6.15, Suh et al., 2015, Mohammed et al., 2014, Ninova et al., 2014, Wang et al., 2014, Zhou et al., 2014, Smibert et al., 2013, Bejarano et al., 2012, Schertel et al., 2012, Szuplewski et al., 2012, FlyBase Genome Annotators, 2010, Okamura et al., 2008, Ruby et al., 2007, Moss, 2002)

Name Synonyms

mir-6-3

mir-6-3 stem loop

Secondary FlyBase IDs

FBgn0046817
FBgn0262259

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 17 )

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.

12798351

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

AJ421766

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

12798351/tissue=All

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

FBgn0262418

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

FBgn0262418

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

dme:Dmel_CR42966

MARRVEL_MODEL - MARRVEL (model organism gene)

12798351

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

MI0000126

Rfam - A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements

RF00143

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262418

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262418

References (75)

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

NA

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