FlyBase Gene Report: Dmel\snRNA:U1:82Ec

General Information

Symbol

Dmel\snRNA:U1:82Ec

Species

D. melanogaster

Name

small nuclear RNA U1 at 82Ec

Annotation Symbol

Feature Type

pseudogene

FlyBase ID

FBgn0004184

Gene Model Status

Unannotated

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

U1, U1 snRNA

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

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

Transcript Data

Annotated Transcripts

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

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\snRNA:U1:82Ec 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\snRNA:U1:82Ec in JBrowse

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

View exonic expression by developmental stage for Dmel\snRNA:U1:82Ec

View exonic expression by tissue for Dmel\snRNA:U1:82Ec

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

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 snRNA:U1:82Ec

Transgenic constructs containing regulatory region of snRNA:U1:82Ec

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:snRNA:U1:82Ec. 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

nuclear_gene

(Lo and Mount, 1990)

pseudogene

(Mount, 2000.5, Lo and Mount, 1990)

snRNA_gene

(Lo and Mount, 1990)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-[47.1]

Cytogenetic map

82E-82E

Sequence location

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

82E-82E

Left limit from molecular mapping relative to snRNA:U1:82Eb (FBrf0052749) Right limit from molecular mapping relative to snRNA:U1:82Ea (FBrf0041598)

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-[47.1]

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 (0)

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

snRNA:U1:82Ec does not appear to be present in the D.melanogaster strain used for sequencing the genome; only one copy of a U1 snRNA gene (CR32862) has been detected at 82E in the sequenced strain, although 3 copies have previously been reported in clones derived from Oregon R flies - snRNA:U1:82Eb , snRNA:U1:82Ec and snRNA:U1:82Ea (FBrf0052749). The copy present in the sequenced strain appears to correspond to snRNA:U1:82Eb , while snRNA:U1:82Ec and snRNA:U1:82Ea appear to be missing from the sequenced strain (see FBrf0128209).

(FlyBase Genome Annotators, 2002-2003)

Sequences corresponding to snRNA:U1:82Ec have not been found on the Celera assembly on the date of analysis.

(Mount, 2000.5)

snRNA:U1:82Ec has been cloned and sequenced.

(Lo and Mount, 1990)

snRNA:U1:82Ec has been cloned and sequenced. snRNA:U1:82Ec is a pseudogene, it is deleted at the 5' end, missing the first 50 bases.

(Kejzlarova-Lepesant et al., 1984)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (11)

Reported As

Symbol Synonym

82.2

(Mount, 2000.5)

(Cheng et al., 2020, Li et al., 2020, Chen et al., 2012, Rau et al., 2012, Gonsalvez et al., 2010, Kim et al., 2010, Gonsalvez et al., 2008, Kroiss et al., 2008, Li et al., 2004, Dominski et al., 2003, Yuan et al., 2003, Saluz et al., 1988)

U1 82E(pDm6Y)

(Kejzlarova-Lepesant et al., 1984)

U1 snRNA

(Natalizio and Matera, 2013, Deryusheva and Gall, 2009, Rajendra et al., 2007, Gonsalvez et al., 2006, Labourier and Rio, 2001, Labourier et al., 2001)

U1-82.2

(Lo and Mount, 1990)

U1a-82Ec

(Mount and Salz, 2000)

U1snRNA82Ec

snRNA-U1-82.2

snRNA:U1

snRNA:U1:82Ec

Name Synonyms

small nuclear RNA U1 at 82Ec

Secondary FlyBase IDs

FBgn0003917

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 0 )

References (26)

NA

Report Sections