FlyBase Gene Report: Dmel\hpRNA:CR18854

General Information

Symbol

Dmel\hpRNA:CR18854

Species

D. melanogaster

Name

hairpin RNA:CR18854

Annotation Symbol

CR18854

Feature Type

hpRNA_gene

FlyBase ID

FBgn0285991

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

esi-1, hp-CG18854, esi-1.1, esi-1.2

Key Links

Genomic Location

Cytogenetic map

30D1-30D1

Sequence location

2L:9,787,294..9,790,745 [-]

Recombination map

2-36

RefSeq locus

NT_033779 REGION:9787294..9790745

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 (0 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

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\hpRNA:CR18854 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

RNA 2D structure (Predicted by RNAcentral) (RNAcentral entry URS0000CD473A)

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 6.17

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.47

Antisense (in part): 3' portion overlaps IP3K1 on opposite strand.

Supported by strand-specific RNA-Seq data.

Pseudogene (in part): incorporates a pseudogene similar to CG4036; proximate; partial.

Sequence Ontology: Class of Gene

gene_with_edited_transcript

(Rodriguez et al., 2012)

hpRNA_gene

(FlyBase Genome Annotators, 2010)

nuclear_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0472915

2499

FBtr0472916

2557

FBtr0472917

2564

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Polypeptides with Identical Sequences

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\hpRNA:CR18854 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).

0.19

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

salivary gland body primordium

Comment: reported as salivary gland primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

dorsal pharyngeal muscle cell

(Fisher et al., 2012)

embryonic foregut

(Fisher et al., 2012)

embryonic hindgut

(Fisher et al., 2012)

embryonic proventriculus

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

embryonic/larval salivary gland

(Fisher et al., 2012)

embryonic/larval somatic muscle cell

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

microinjection

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

imaginal disc

Comment: library contains gonads

(Wen et al., 2015)

adult stage | male

testis

(Wen et al., 2015)

Additional Descriptive Data

Tissue-specific RNA-seq reveals that hairpin RNA is dominantly expressed in testis and also accumulates in lbraries from mass-isolated imaginal discs containing larval gonads.

(Wen et al., 2015)

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\hpRNA:CR18854 in JBrowse

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

View exonic expression by developmental stage for Dmel\hpRNA:CR18854

View exonic expression by tissue for Dmel\hpRNA:CR18854

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

10178800/tissue=All

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

FBgn0285991

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0042174

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

FBgn0285991

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of hpRNA:CR18854

Transgenic constructs containing regulatory region of hpRNA:CR18854

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)Exel6025

(Ryder, 2004.4.26)

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

embryonic/larval hemocyte | third instar larval stage, with Scer\GAL4^Pxn.PS

hpRNA:CR18854^EY00141

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:hpRNA:CR18854. 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 ( 1 )

Allele

Disease

Interaction

References

hpRNA:CR18854^RNAi.UAS.cUa

ameliorates neurodegenerative disease

modeled by FIG4^KK102943

(Muraoka et al., 2018)

ameliorates amyotrophic lateral sclerosis type 6

modeled by caz^KK107486

(Muraoka et al., 2018)

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-protein

Physical Interaction

Assay

References

hpRNA:CR18854 - AGO1

nucleic acid uv cross-linking assay, autoradiography, anti tag coimmunoprecipitation, full identification by RNA sequencing

(Kingston and Bartel, 2021, Ameres et al., 2011)

hpRNA:CR18854 - AGO2

nucleic acid uv cross-linking assay, autoradiography

(Ameres et al., 2011)

hpRNA:CR18854 - stau

anti tag coimmunoprecipitation, partial DNA sequence identification by hybridization, anti bait coimmunoprecipitation

(Laver et al., 2013)

RNA-RNA

Physical Interaction

Assay

References

hpRNA:CR18854 - CG8289

anti tag western blot, sequence based prediction

(Czech et al., 2008, Okamura et al., 2008)

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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-36

Cytogenetic map

30D1-30D1

Sequence location

2L:9,787,294..9,790,745 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

30D1-30D1

Limits computationally determined from genome sequence between P{lacW}zf30C^k02506&P{EP}und^EP424 and P{lacW}l(2)k06416^k06416&P{lacW}sop^k04603

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

30D-30D

(Gray, 2000.3.23)

Experimentally Determined Recombination Data

Location

2-36

(FlyBase, 2016)

2-31.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

603920

w¹¹¹⁸; P{SX4.lexA::HG}hpRNA:CR18854^S14-9/CyO

31732

y¹ v¹; P{TRiP.HM04041}attP2/TM3, Sb¹

14810

y¹ w^67c23; P{EPgy2}hpRNA:CR18854^EY00141

35304

y¹ sc^* v¹ sev²¹; P{TRiP.GL00208}attP2

VDRC

v330538

P{VSH330538}attP40

Genomic Clones (9)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (58)

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

DPiM_GH14831

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

Annotation CG18854 renamed CR18854 in release 5.24 of the genome annotation.

(FlyBase Genome Annotators, 2010)

The siRNAs derived from esi-1 all arise from one genomic strand.

(Czech et al., 2008)

The Hrp59 protein binds preferentially to a subset of mRNAs, including CG18854 mRNA.

(Kiesler et al., 2005)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG18854 CG13122

(FlyBase, 1996-)

Source for merge of: CR18854 esi-1

(Wen et al., 2015)

Additional comments

The CG18854 annotation can produce an approximately 400bp dsRNA through interaction of its 5' and 3' untranslated regions. These regions are represented in FlyBase by the "esi-1" gene.

(Czech et al., 2008)

esi-1 consists of a duplex of more than 400bp separated by a large loop.

(Okamura et al., 2008)

Source for merge of CG18854 CG13122 was a shared cDNA ( date:010720 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: hpRNA:CR18854 esi-1

(Wen et al., 2015)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (14)

Reported As

Symbol Synonym

CG13122

(Lundgren et al., 2005, Egger et al., 2002, Tricoire, 2001.3.6)

CG18854

(Ninova et al., 2020, Murray et al., 2012, Zhan et al., 2011, Cunha et al., 2010, Marques et al., 2010, Czech et al., 2008, Okamura et al., 2008, Okamura et al., 2008, Stofanko et al., 2008, Firth and Baker, 2007, Zeitlinger et al., 2007, Burgler and Macdonald, 2005, Kiesler et al., 2005)

CR18854

(Kingston and Bartel, 2021, Pang et al., 2021, Yamaguchi et al., 2021, Yamaguchi et al., 2021, Li et al., 2019, Laver et al., 2013, FlyBase Genome Annotators, 2012, Rodriguez et al., 2012, Ni et al., 2011.7.19, FlyBase Genome Annotators, 2010, Ni et al., 2008)

esi-1

(Porrazzo et al., 2022, Donelick et al., 2020, Ameres et al., 2011, Han et al., 2011, Marques et al., 2010, Czech et al., 2009, Czech et al., 2008)

esi-1.1

(Liao et al., 2019, Xiong et al., 2013, Fukunaga et al., 2012)

esi-1.2

(Liao et al., 2019, Fukunaga et al., 2012)

esiRNA-sl-1

(Miyoshi et al., 2010)

hp-CG18854

(Wen et al., 2015, Ameres et al., 2011, Han et al., 2011, Okamura et al., 2008)

hp-CG18854A

(Okamura et al., 2011)

hpRNA:CR18854

lncRNA-CR18854

(Li et al., 2019)

Name Synonyms

1D-myo-Inositol-trisphosphate-3-kinase

(Lundgren et al., 2005)

endogenous siRNA 1

hairpin RNA:CR18854

Secondary FlyBase IDs

FBgn0261271
FBgn0042174
FBgn0032148

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 21 )

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.

10178800

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

10178800/tissue=All

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

FBgn0285991

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

FBgn0285991

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

dme:Dmel_CR18854

MARRVEL_MODEL - MARRVEL (model organism gene)

10178800

Linkouts

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0042174

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0285991

References (57)

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

0.19

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