FlyBase Gene Report: Dmel\mir-1017

General Information

Symbol

Dmel\mir-1017

Species

D. melanogaster

Name

mir-1017 stem loop

Annotation Symbol

CR42919

Feature Type

miRNA_gene

FlyBase ID

FBgn0262389

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-1017

Key Links

Genomic Location

Cytogenetic map

96A3-96A3

Sequence location

3R:24,488,612..24,488,682 [+]

Recombination map

3-85

RefSeq locus

NT_033777 REGION:24488612..24488682

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 (4 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables mRNA base-pairing post-transcriptional repressor activity

inferred from direct assay

(Khanal et al., 2024)

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 miRNA-mediated post-transcriptional gene silencing

inferred from mutant phenotype

(Khanal et al., 2024)

involved_in regulation of synaptic transmission, cholinergic

inferred from mutant phenotype

(Khanal et al., 2024)

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:RF02517

(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:RF02517

(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-1017 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)

FBtr0304260

FBtr0304259

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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

MI0005878

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-1017 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-1017 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-1017

View exonic expression by tissue for Dmel\mir-1017

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

12798527/tissue=All

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

FBgn0262389

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

FBgn0262389

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mir-1017

Transgenic constructs containing regulatory region of mir-1017

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 6 )

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-1017^UAS.cSa

viable, with Scer\GAL4^Tub.PU

mir-1017^{sponge.V2.UAS.mCherry}

Sterility

Allele

female fertile

mir-1017^KO

male fertile

mir-1017^KO

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-1017. 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

Interaction Browsers

Summary of Genetic Interactions

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.

FBgn0262389

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

miRNA_gene

(FlyBase Genome Annotators, 2010, Ruby et al., 2007)

nuclear_gene

(FlyBase Genome Annotators, 2010, Ruby et al., 2007)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-85

Cytogenetic map

96A3-96A3

Sequence location

3R:24,488,612..24,488,682 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

96A3-96A3

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-85

(FlyBase, 2016)

3-83.8

(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

60670

w^*; P{UAS-mir-1017.S}attP2

60669

w^*; P{UAS-mir-1017.S}attP16

41208

w¹¹¹⁸; P{UAS-LUC-mir-1017.T}attP2/TM3, Sb¹

58889

w^*; TI{TI}mir-1017^KO/TM3, P{GAL4-twi.G}2.3, P{UAS-2xEGFP}AH2.3, Sb¹ Ser¹

61500

w^*; P{UAS-mCherry.mir-1017.sponge.V2}attP40; P{UAS-mCherry.mir-1017.sponge.V2}attP2/TM6B, Tb¹

FlyORF

F001994

M{UAS-mir-1017.S}ZH-86Fb

Genomic Clones (16)

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 CR42919 (which corresponds to mir-1017) in release 5.31 of the genome annotation.

(FlyBase Genome Annotators, 2010)

mir-1017 is a 3' tailed mirtron. A mature miRNA is produced from mir-1017 via a multi-step process involving intron splicing and debranching, exosome-mediated trimming of the 3' tail and dicing.

(Flynt et al., 2010)

The mir-1017 miRNA is located in the intron of another gene. Its 5' end, but not 3' end matches the splice site of its host intron. Thus unlike true "mirtrons" (which are encoded as an intron of another gene and which accumulate as lariats after splicing and require debranching enzyme for conversion into a functional miRNA), this miRNA would depend on a nuclease to cleave its extensive 3' overhang.

(Ruby et al., 2007)

Relationship to Other Genes

Source for database merge of

Additional comments

mir-1017 is a 3' tailed mirtron produced from an intron of nAcRα-96Ab.

(Flynt et al., 2010)

mir-1017 is a potential miRNA that is located in the intron of another gene (nAcRα-96Ab).

(Ruby et al., 2007)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CR42919

(FlyBase Genome Annotators, 2010)

dme-miR-1017

(Wang et al., 2019, Volin et al., 2018)

dme-mir-1017

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

miR-1017

(Kitatani et al., 2020, Eyk et al., 2019, Atilano et al., 2017, Chandra et al., 2017, Li et al., 2017, Li et al., 2017, Picao-Osorio et al., 2017, Suh et al., 2015, Van Vactor, 2015.6.15, Kong et al., 2014, Mezan et al., 2013, Nesler et al., 2013, Behura et al., 2011)

miR-1017-3p

(Wei et al., 2018)

mir-1017

(Khanal et al., 2024, Iftikhar et al., 2019, Niu et al., 2019, Ueda et al., 2018, Mohammed and Lai, 2016.2.8, Chen et al., 2014, Bejarano et al., 2012, Schertel et al., 2012, Szuplewski et al., 2012, FlyBase Genome Annotators, 2010, Flynt et al., 2010, Ruby et al., 2007, Ruby et al., 2007)

Name Synonyms

mir-1017 stem loop

Secondary FlyBase IDs

FBgn0250813
FBgn0262212

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 13 )

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.

12798527

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

12798527/tissue=All

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

FBgn0262389

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

FBgn0262389

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

dme:Dmel_CR42919

MARRVEL_MODEL - MARRVEL (model organism gene)

12798527

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

MI0005878

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262389

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262389

References (40)

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

NA

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