FlyBase Gene Report: Dmel\mir-10404-2

General Information

Symbol

Dmel\mir-10404-2

Species

D. melanogaster

Name

mir-10404-2 stem loop

Annotation Symbol

CR46347

Feature Type

miRNA_gene

FlyBase ID

FBgn0285976

Gene Model Status

Current

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

mir-10404

Key Links

Genomic Location

Cytogenetic map

Sequence location

rDNA:70,290..70,358 [+]

Recombination map

RefSeq locus

NW_007931121 REGION:70290..70358

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

NCBI

UCSC

Ensembl

Function

Gene Ontology (GO) Annotations (4 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

(Morita et al., 2020)

enables mRNA base-pairing post-transcriptional repressor activity

inferred from direct assay

(Morita et al., 2020)

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 direct assay

(Morita et al., 2020)

involved_in positive regulation of G1/S transition of mitotic cell cycle

inferred from mutant phenotype

(Morita et al., 2020)

Terms Based on Predictions or Assertions (0 terms)

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-10404-2 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

Gene model based on RNA hairpin predictions and miRNA identified by RNA-Seq, as described in Chak et. al, 2013 (FBrf0227634).

Multiple copies of the mir-10404 sequence exist in the Release 6 genome assembly: 10 perfect and 4 near perfect matches (all contain a perfect mir-10404-5p sequence). These copies are found on the rDNA, proximal X chromosome and six other minor scaffolds. Only the two copies that are localized to fully intact ribosomal precursor transcripts are annotated.

Gene model reviewed during 6.17

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0472933

FBtr0472934

FBtr0472927

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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

MI0033427

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-10404-2 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-10404-2 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-10404-2

View exonic expression by tissue for Dmel\mir-10404-2

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

36786394/tissue=All

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

FBgn0285976

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

FBgn0285976

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 ( 0 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mir-10404-2

Transgenic constructs containing regulatory region of mir-10404-2

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.

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-10404-2. 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) (4)

1 of 13

1 of 13

1 of 13

1 of 13

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

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-10404-2 - dap

fluorescence microscopy

(Morita et al., 2020)

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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

miRNA_gene

(FlyBase Genome Annotators, 2017, Chak et al., 2015)

nuclear_gene

(FlyBase Genome Annotators, 2017, Chak et al., 2015)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

rDNA

Recombination map

Cytogenetic map

Sequence location

rDNA:70,290..70,358 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (0)

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

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 (CR46347) in release 6.17 of the genome annotation.

(FlyBase Genome Annotators, 2017)

Located in the internal transcribed spacer 1 (ITS1) region of the rDNA array.

(Chak et al., 2015)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: mir-10404-2 CR46347

(FlyBase, 1992-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CR46347

(FlyBase Genome Annotators, 2017)

dme-mir-10404

(He et al., 2022)

miR-10404

(Morita et al., 2020)

mir-10404

(Mohammed et al., 2018, Mohammed and Lai, 2016.2.8, Chak et al., 2015)

mir-10404-2

mir-ITS1

(Chak et al., 2015)

Name Synonyms

mir-10404-2 stem loop

Secondary FlyBase IDs

FBgn0283460

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 12 )

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.

36786394

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

NR_156799

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

36786394/tissue=All

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

FBgn0285976

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

FBgn0285976

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

dme:Dmel_CR46347

MARRVEL_MODEL - MARRVEL (model organism gene)

36786394

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

MI0033427

Linkouts

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0285976

References (7)

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

NA

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