FlyBase Gene Report: Dmel\lncRNA:iab4

General Information

Symbol

Dmel\lncRNA:iab4

Species

D. melanogaster

Name

long non-coding RNA:iab4

Annotation Symbol

CR31271

Feature Type

lncRNA_gene

FlyBase ID

FBgn0020546

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

iab-4

Key Links

Genomic Location

Cytogenetic map

89E3-89E3

Sequence location

3R:16,850,004..16,856,497 [+]

Recombination map

3-59

RefSeq locus

NT_033777 REGION:16850004..16856497

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: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

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\lncRNA:iab4 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

miRNA(s) located within the transcribed region of this non-coding RNA gene.

Gene model reviewed during 5.48

Supported by strand-specific RNA-Seq and/or EST data.

Gene model reviewed during 5.55

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0083362

2113

FBtr0083363

1807

FBtr0345273

1841

FBtr0345274

6175

Additional Transcript Data and Comments

Reported size (kB)

2.0, 1.7 (northern blot)

(Cumberledge et al., 1990)

Comments

External Data

Crossreferences

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\lncRNA:iab4 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

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4

organism | posterior

(Cumberledge et al., 1990)

embryonic stage 8

parasegment 8 -- parasegment 14

(Cumberledge et al., 1990)

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 17

(Cumberledge et al., 1990)

embryonic stage 4

organism | 10-60% egg length

(Cumberledge et al., 1990)

embryonic stage 5 -- 15

parasegment 8 -- parasegment 12

(Bender, 2008)

Additional Descriptive Data

iab-4 is expressed from parasegment 8-12

(Bender, 2008)

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\lncRNA:iab4 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\lncRNA:iab4

View exonic expression by tissue for Dmel\lncRNA:iab4

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

3772110/tissue=All

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

FBgn0020546

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

FBgn0020546

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of lncRNA:iab4

Transgenic constructs containing regulatory region of lncRNA:iab4

Aberrations (Deficiencies and Duplications) ( 6 )

Inferred from experimentation ( 6 )

Gene disrupted in

Df(3R)abd-A^iab4,5-DB

(Cumberledge et al., 1990, Karch et al., 1985)

Df(3R)McR1

(Karch et al., 1990)

In(3LR)iab4¹⁶⁶

(Cumberledge et al., 1990)

T(2;3;4)iab4³⁰²

(Cumberledge et al., 1990)

T(2;3)iab4⁴⁵

(Cumberledge et al., 1990, Karch et al., 1985)

T(3;4)iab4¹²⁵

(Cumberledge et al., 1990)

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

viable

Sterility

Allele

female sterile

lncRNA:iab4³⁰²

female sterile | recessive

lncRNA:iab4^DB

male sterile

lncRNA:iab4³⁰²

male sterile | recessive

lncRNA:iab4^DB

Other Phenotypes

Allele

visible | homeotic

visible | recessive

lncRNA:iab4^DB

Phenotype manifest in

Allele

adult abdominal segment 1

lncRNA:iab4^MX4

adult abdominal segment 2

adult abdominal segment 4

adult abdominal segment 5

lncRNA:iab4³⁰²

gonad | precursor

ovary

lncRNA:iab4⁴⁵

oviduct

lncRNA:iab4⁴⁵

primordial germ cell

testis

lncRNA:iab4⁴⁵

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:lncRNA:iab4. 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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

lncRNA_gene

nuclear_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-59

Cytogenetic map

89E3-89E3

Sequence location

3R:16,850,004..16,856,497 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

89E3-89E3

Limits computationally determined from genome sequence between P{lacW}CSN5^L4032 and P{EP}MESK4^EP1015

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

89E2-89E2

(Martin et al., 1995)

Based on proximity to abd-A.

(Martin et al., 1995)

Experimentally Determined Recombination Data

Location

3-59

(FlyBase, 2016)

3-58.9

(Comeron et al., 2012)

(Martin et al., 1995)

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

601156

w¹¹¹⁸; P{VT042810-p65.AD}attP40

74839

w¹¹¹⁸; P{VT042810-GAL4.DBD}attP2

88417

w¹¹¹⁸; P{VT042810-p65.AD}attP40; P{R51G03-GAL4.DBD}attP2

87717

w¹¹¹⁸; P{VT027104-p65.AD}attP40; P{VT042810-GAL4.DBD}attP2

607136

w¹¹¹⁸; P{VT042810-p65.AD}attP40; P{VT048854-GAL4.DBD}attP2

Korea

15232

P{VT042810-GAL4}attP2

Genomic Clones (26)

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

DRSC - Results frm RNAi screens

FBgn0020546

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CR31271) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

The transcription unit that produces the noncoding iab-4 transcript has been identified.

(Lewis et al., 1995)

Non-coding RNA regulating abd-A.

(Martin et al., 1995)

Relationship to Other Genes

Source for database merge of

Additional comments

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

(Ronshaugen et al., 2005)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:iab4 iab-4

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

CR31271

(Casares and Sanchez-Herrero, 1995)

iab

(Mattick and Gagen, 2001)

iab-4

(Zhou et al., 2022, Szabad et al., 2019, Garaulet and Lai, 2015, Ríos-Barrera et al., 2015, Fu et al., 2014, Saunders et al., 2013, Lemons et al., 2012, Enderle et al., 2011, Graveley et al., 2011, Bender, 2008, Stark et al., 2008, Tyler et al., 2008, Holohan et al., 2007, Prasanth and Spector, 2007, Chopra and Mishra, 2006, Lemons and McGinnis, 2006, Zhimulev et al., 2003)

lncRNA:iab4

pri-mir-iab-4_mir-iab-4as

(Graveley et al., 2011)

Name Synonyms

domain I

(Sanchez-Herrero and Akam, 1989)

iab-4

(Holohan et al., 2007)

long non-coding RNA:iab4

Secondary FlyBase IDs

FBan0031271
FBgn0051271

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 22 )

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.

3772110

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

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

3772110/tissue=All

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

FBgn0020546

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

FBgn0020546

FlyMine - An integrated database for Drosophila genomics

FBgn0020546

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

dme:Dmel_CR31271

MARRVEL_MODEL - MARRVEL (model organism gene)

3772110

Linkouts

DRSC - Results frm RNAi screens

FBgn0020546

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0020546

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

References (58)

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

NA

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