FlyBase Gene Report: Dmel\mir-iab-4

General Information

Symbol

Dmel\mir-iab-4

Species

D. melanogaster

Name

mir-iab-4 stem loop

Annotation Symbol

CR43043

Feature Type

miRNA_gene

FlyBase ID

FBgn0262462

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

directly inhibits Ubx activity in vivo - ectopic expression induces a classical homeotic mutant phenotype, the transformation of halteres into wings (Interactive Fly, mir-iab-4 )

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

miR-iab4, mir-iab-4-5p, iab-4-5p, iab-4-3p, mir-iab-4-3p

Key Links

Genomic Location

Cytogenetic map

89E3-89E3

Sequence location

3R:16,856,275..16,856,342 [+]

Recombination map

3-59

RefSeq locus

NT_033777 REGION:16856275..16856342

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 (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables mRNA 3'-UTR binding

inferred from direct assay

(Tyler et al., 2008, Ronshaugen et al., 2005)

enables mRNA base-pairing post-transcriptional repressor activity

inferred from direct assay

(Tyler et al., 2008, Ronshaugen et al., 2005)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in miRNA-mediated post-transcriptional gene silencing

inferred from mutant phenotype

(Tyler et al., 2008, Ronshaugen et al., 2005)

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:RF00725

(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:RF00725

(RNAcentral, 2018-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Summary (Interactive Fly)

directly inhibits Ubx activity in vivo - ectopic expression induces a classical homeotic mutant phenotype, the transformation of halteres into wings

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\mir-iab-4 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)

FBtr0304521

FBtr0304522

FBtr0304520

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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

MI0000432

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-iab-4 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 -- 5

organism | restricted

Comment: along anterior-posterior axis

(Aboobaker et al., 2005)

organism | 60-90% egg length

(Lemons et al., 2012)

embryonic stage 5

parasegment 8 -- parasegment 12

(Tyler et al., 2008)

embryonic stage 11

embryonic abdominal segment 5 -- embryonic abdominal segment 7

(Stark et al., 2008)

germ band | restricted | ventral

(Lemons et al., 2012)

embryonic stage 14

embryonic abdominal segment 2 -- embryonic abdominal segment 7

(Tyler et al., 2008)

lateral ectoderm

(Lemons et al., 2012)

larval ventral nerve cord of embryonic abdominal segment 4 -- embryonic abdominal segment 7

(Lemons et al., 2012)

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-iab-4 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-iab-4

View exonic expression by tissue for Dmel\mir-iab-4

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

12798431/tissue=All

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

FBgn0262462

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

FBgn0262462

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 ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mir-iab-4

Transgenic constructs containing regulatory region of mir-iab-4

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3R)ΔmiRNA

(Bender, 2008)

Gene partially disrupted in

Df(3R)mir-C11

(Garaulet et al., 2020)

Inferred from location ( 3 )

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-iab-4^UAS.cSa

lethal, with Scer\GAL4^ptc-559.1

mir-iab-4^{UAS.DsRed(Unk)}

Other Phenotypes

Allele

visible, with Scer\GAL4^Bx-MS1096

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

visible | homeotic, with Scer\GAL4^Bx-MS1096

mir-iab-4^{UAS.cRa.DsRed2}

visible | homeotic, with Scer\GAL4^sd-SG29.1

mir-iab-4^{UAS.cRa.DsRed2}

Phenotype manifest in

Allele

haltere, with Scer\GAL4^Bx-MS1096

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

mir-iab-4^{UAS.cRa.DsRed2}

wing, with Scer\GAL4^Bx-MS1096

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

wing margin, with Scer\GAL4^sd-SG29.1

mir-iab-4^{UAS.DsRed(Unk)}

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-iab-4. 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

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-iab-4 - Ubx

immunohistochemistry, fluorescence technology

(Tyler et al., 2008, Ronshaugen et al., 2005)

RNA-protein

Physical Interaction

Assay

References

mir-iab-4 - DIP1

electrophoretic mobility shift assay, autoradiography

(Catanese and Matthews, 2010)

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.

FBgn0262462

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

miRNA_gene

(FlyBase Genome Annotators, 2010, Bartel, 2004)

nuclear_gene

(FlyBase Genome Annotators, 2010, Bartel, 2004)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-59

Cytogenetic map

89E3-89E3

Sequence location

3R:16,856,275..16,856,342 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

89E3-89E3

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-59

(FlyBase, 2016)

3-58.9

(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

41173

w¹¹¹⁸; P{UAS-LUC-mir-iab-4.T}attP2

60673

w^*; P{UAS-DsRed2-mir-iab-4.S}2/CyO

FlyORF

F002021

M{UAS-mir-iab-4.S}ZH-86Fb

Genomic Clones (25)

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 (CR33624) in release 4.1 of the genome annotation.

(FlyBase Genome Annotators, 2005)

New annotation (CR33623) in release 4.1 of the genome annotation.

(FlyBase Genome Annotators, 2005)

Ectopic expression of the mir-iab-4 microRNAs induces a classical homeotic mutant phenotype; the transformation of halteres into wings.

(Ronshaugen et al., 2005)

The Ubx 3'UTR contains predicted target sites for the mir-iab-4 5p microRNA.

(Ronshaugen et al., 2005)

Relationship to Other Genes

Source for database merge of

Source for merge of: mir-iab-4-5p mir-iab-4-3p

(FlyBase Genome Annotators, 2010)

Additional comments

The annotation for mir-iab-4 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. Thus the separate annotations (CR33624 and CR33623) which previously each represented one of the two mature miRNAs made from the mir-iab-4 stem loop precursor have been converted into a single annotation (CR43043).

(FlyBase Genome Annotators, 2010)

The "iab-8" non-coding transcript encodes a microRNA (represented by "mir-iab-8") derived from a hairpin which is complementary to the hairpin present in the "iab-4" non-coding transcript (the hairpin in the "iab-4" transcript is represented by "mir-iab-4").

(Bender, 2008)

The "mir-iab-4" and "mir-iab-8" precursor hairpins are encoded on opposite strands of the same genomic region. The mature miRNAs derived from each hairpin have very similar sequences, but are shifted by 2 nucleotides at the 5' end and also differ in four positions at the 3' region.

(Stark et al., 2008)

The "mir-iab-4" and "mir-iab-8" precursor hairpins are encoded on opposite strands of the same genomic region. The major products of both hairpins are their respective "5p" species. While the 5' ends of the mature microRNA from each hairpin (mir-iab-4-5p and mir-iab-8-5p respectively) are related, the mir-iab-8-5p microRNA contains a strict 2 nucleotide "UU" extension.

(Tyler et al., 2008)

The "iab-4" locus produces two microRNAs, represented by "mir-iab-4".

(Ronshaugen et al., 2005)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (22)

Reported As

Symbol Synonym

CR33623

(FlyBase Genome Annotators, 2005)

CR33624

(FlyBase Genome Annotators, 2005)

CR43043

(FlyBase Genome Annotators, 2010)

MIR-iab-4

(Miura et al., 2011)

MIR-iab4

(Ylla et al., 2016)

dme-iab-4

(Hui et al., 2013)

dme-miR-iab-4

(Volin et al., 2018, Chandra et al., 2017, Lucas et al., 2015)

dme-mir-iab-4

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

iab-4

(Garaulet et al., 2021, Szuplewski et al., 2012, Aboobaker et al., 2005)

iab-4-3p

(Chopra and Mishra, 2006, Lai et al., 2006, Ronshaugen et al., 2005)

iab-4-5p

(Chopra and Mishra, 2006, Lai et al., 2006, Ronshaugen et al., 2005)

miR-Iab4

(Li et al., 2024)

miR-iab-4

(Garaulet et al., 2020, Song and Zhou, 2020, Cosacak et al., 2018, Kim et al., 2017, Fu et al., 2014, Gummalla et al., 2014, Mallo and Alonso, 2013, Lemons et al., 2012, Bender, 2008, Paré et al., 2008, Stark et al., 2008, Behura, 2007, Stark et al., 2007, Lemons and McGinnis, 2006)

miR-iab-4-3p

(Patraquim et al., 2011, Stark et al., 2005)

miR-iab-4-5p

(Nesler et al., 2013, Patraquim et al., 2011, Stark et al., 2005)

miR-iab4

(Joshi et al., 2021, Issa et al., 2019, Picao-Osorio et al., 2017, Lucas and Raikhel, 2013, Thomsen et al., 2010)

mir-iab-4-3p

(Prasanth and Spector, 2007)

mir-iab-4-5p

(Daneshvar et al., 2013, Prasanth and Spector, 2007, Chopra and Mishra, 2006)

mir-iab4

(Enderle et al., 2011)

Name Synonyms

iab-4 microRNA

(Hui et al., 2013)

mir-iab-4 stem loop

mir-iab-4-3p

mir-iab-4-5p

Secondary FlyBase IDs

FBgn0082170
FBgn0067677
FBgn0082171
FBgn0262336

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 16 )

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.

12798431

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

12798431/tissue=All

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

FBgn0262462

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

FBgn0262462

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

dme:Dmel_CR43043

MARRVEL_MODEL - MARRVEL (model organism gene)

12798431

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

MI0000432

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262462

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262462

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

References (74)

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

NA

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