FlyBase Gene Report: Dmel\hpRNA:LINR-1

General Information

Symbol

Dmel\hpRNA:LINR-1

Species

D. melanogaster

Name

hairpin RNA:Lsd1-interacting non-coding RNA 1

Annotation Symbol

CR32205

Feature Type

hpRNA_gene

FlyBase ID

FBgn0052205

Gene Model Status

Current

Stock Availability

10 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

hp-CR32205

Key Links

Genomic Location

Cytogenetic map

76B2-76B3

Sequence location

3L:19,420,390..19,424,183 [-]

Recombination map

3-45

RefSeq locus

NT_037436 REGION:19420390..19424183

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 (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables enzyme binding

inferred from physical interaction with FLYBASE:Su(var)3-3; FB:FBgn0260397

(Shao et al., 2022)

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 negative regulation of proteasomal ubiquitin-dependent protein catabolic process

inferred from genetic interaction with FLYBASE:hpRNA:LINR-2; FB:FBgn0062928

(Lin et al., 2024)

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:LINR-1 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 URS00001B3011)

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.46

Gene model reviewed during 5.51

5' portion overlaps pseudogene CR33255 on opposite strand.

May play role similar to antisense gene.

Gene model reviewed during 6.02

Supported by strand-specific RNA-Seq data.

Gene model reviewed during 6.17

Pseudogene (in part): incorporates a pseudogene similar to CG32212 and related genes; proximate; partial.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0075000

1085

FBtr0472918

3145

FBtr0472919

1291

Additional Transcript Data and Comments

Reported size (kB)

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\hpRNA:LINR-1 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).

4.88

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(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:LINR-1 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:LINR-1

View exonic expression by tissue for Dmel\hpRNA:LINR-1

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0052205

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3772102/tissue=All

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

FBgn0052205

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

FBgn0052205

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

CR32205

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 2 )

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 hpRNA:LINR-1

Transgenic constructs containing regulatory region of hpRNA:LINR-1

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

hpRNA:LINR-1^Δ

Sterility

Allele

female semi-sterile

hpRNA:LINR-1^Δ

Other Phenotypes

Allele

some die during embryonic stage | maternal effect

hpRNA:LINR-1^Δ

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:hpRNA:LINR-1. 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

hpRNA:LINR-1 - CG14096

luminiscence technology

(Wen et al., 2015)

hpRNA:LINR-1 - CG32212

luminiscence technology

(Wen et al., 2015)

hpRNA:LINR-1 - CG32213

luminiscence technology

(Wen et al., 2015)

hpRNA:LINR-1 - CR33255

luminiscence technology

(Wen et al., 2015)

RNA-protein

Physical Interaction

Assay

References

hpRNA:LINR-1 - CoRest

pull down, western blot

(Shao et al., 2022)

hpRNA:LINR-1 - Lsd-1

anti bait coimmunoprecipitation, full identification by RNA sequencing, pull down, western blot

(Shao et al., 2022)

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

BioGRID - A database of protein and genetic interactions.

533699

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

hpRNA_gene

nuclear_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-45

Cytogenetic map

76B2-76B3

Sequence location

3L:19,420,390..19,424,183 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

76B2-76B3

; Limits computationally determined from genome sequence between P{EP}MESR6^EP3142 and P{lacW}l(3)L3809^L3809

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-45

(FlyBase, 2016)

3-42.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

73176

w¹¹¹⁸; P{VT033301-p65.AD}attP40

65645

w¹¹¹⁸; PBac{IT.GAL4}hpRNA:LINR-1^1262-G4

73717

w¹¹¹⁸; P{VT033301-GAL4.DBD}attP2/TM3, Sb¹ Ser¹

89064

w¹¹¹⁸; P{VT033301-p65.AD}attP40/CyO, P{2xTb¹-RFP}CyO; P{R86F02-GAL4.DBD}attP2

603462

w¹¹¹⁸; P{VT033301-p65.AD}attP40/CyO, P{2xTb¹-RFP}CyO; P{R27G01-GAL4.DBD}attP2

603691

w¹¹¹⁸; P{VT033301-p65.AD}attP40/CyO, P{2xTb¹-RFP}CyO; P{R48E11-GAL4.DBD}attP2

603102

w¹¹¹⁸; P{VT033301-p65.AD}attP40/CyO, P{2xTb¹-RFP}CyO; P{R13D05-GAL4.DBD}attP2/TM6B, Tb¹

Korea

13489

P{VT033301-GAL4}attP2

15895

P{VT033301-lexA}JK73A

16345

P{VT033301-lexA}JK22C

Genomic Clones (28)

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

cDNA Clones (18)

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

RE73739

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.

FBgn0052205

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0052205

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

CR32205 reclassified as a pseudogene in release 6.02 of the genome annotation.

(FlyBase Genome Annotators, 2014)

The CR32205 annotation contains sequence encoding a small-RNA-generating hairpin that produces 21-22 nucleotide RNAs.

(Okamura et al., 2008)

New annotation (CR32205) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: CR32205 BcDNA:RE73739

(FlyBase, 1996-)

Additional comments

Source for merge of CR32205 BcDNA:RE73739 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: hpRNA:CR32205 CR32205

(Wen et al., 2015)

Source for identity of: hpRNA:LINR-1 hpRNA:CR32205

(Shao et al., 2022)

Nomenclature comments

Etymology

The gene is named 'LINR-1' based on function as an Lsd1(Su(var)3-3)-interacting non-coding RNA.

(Shao et al., 2022)

Synonyms and Secondary IDs (9)

Reported As

Symbol Synonym

BcDNA:RE73739

CR32205

(Nitschko et al., 2020, Clandinin and Owens, 2016-, FlyBase Genome Annotators, 2014, Cooper et al., 2010, Hiller et al., 2009, Okamura et al., 2008, FlyBase Genome Annotators, 2002-2003)

LINR-1

(Lin et al., 2024)

esi-4.1

(Zhou et al., 2009)

hp-CR32205

(Wen et al., 2015, Han et al., 2011)

hpRNA:CR32205

hpRNA:LINR-1

Name Synonyms

hairpin RNA:CR32205

hairpin RNA:Lsd1-interacting non-coding RNA 1

Secondary FlyBase IDs

FBgn0064855
FBgn0262151

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.

3772102

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0052205

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3772102/tissue=All

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

FBgn0052205

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

FBgn0052205

FlyMine - An integrated database for Drosophila genomics

FBgn0052205

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

dme:Dmel_CR32205

MARRVEL_MODEL - MARRVEL (model organism gene)

3772102

Linkouts

BioGRID - A database of protein and genetic interactions.

533699

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0052205

DRSC - Results frm RNAi screens

FBgn0052205

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0052205

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

CR32205

References (16)

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

4.88

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