FlyBase Gene Report: Dmel\snRNA:U2:38ABb

General Information

Symbol

Dmel\snRNA:U2:38ABb

Species

D. melanogaster

Name

small nuclear RNA U2 at 38AB b

Annotation Symbol

CR32878

Feature Type

snRNA_gene

FlyBase ID

FBgn0003923

Gene Model Status

Current

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

U2, U2 snRNA, dU2, U2:38ABb , U2-141B

Key Links

Genomic Location

Cytogenetic map

38A4-38A4

Sequence location

2L:19,812,646..19,812,836 [+]

Recombination map

2-54

RefSeq locus

NT_033779 REGION:19812646..19812836

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 (5 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables pre-mRNA branch point binding

inferred from electronic annotation with Rfam:RF00004

(RNAcentral, 2018-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in mRNA branch site recognition

inferred from electronic annotation with Rfam:RF00004

(RNAcentral, 2018-)

involved_in mRNA splicing, via spliceosome

inferred from sequence or structural similarity

(Mount and Salz, 2000)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in Cajal body

inferred from direct assay

(Liu et al., 2006)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of U2 snRNP

inferred from electronic annotation with Rfam:RF00004

(RNAcentral, 2018-)

inferred from sequence or structural similarity

(Mount and Salz, 2000)

Gene Group (FlyBase)

U2 SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE

SPLICEOSOME COMPLEX A

SPLICEOSOME COMPLEX B

SPLICEOSOME COMPLEX C

SPLICEOSOME COMPLEX P

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

U2 SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE -: The U2 small nuclear ribonucleoprotein particle (U2 snRNP) contains U2 snRNA. It is recruited to the spliceosome after U1 snRNP and forms a stable interaction with the branch site and 3' splice site in pre-mRNA. (Adapted from PMID:23829528 and PMID:21441581).
SPLICEOSOME COMPLEX A -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex A, the pre-spliceosome, is composed of U1 and U2 snRNPs and proteins involved in recognition of the 5' splice site and branch point. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX B -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. After the assembly of complex A on pre-mRNA, the U4-U6 and U5 snRNPs are recruited as a preassembled tri-snRNP to form complex B. U5 snRNP binds exons at the 5' site. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX C -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex B undergoes a number of structural rearrangements and U4 and U1 snRNPs dissociate to generate complex C, the catalytic spliceosome. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX P -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex P, the post-spliceosomal complex, is formed after the catalytic removal of the intron by complex C. Complex P contains the lariat intron and spliced exons. (Adapted from PMID:24452469 and PMID:23118483).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\snRNA:U2:38ABb 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 URS00005ED1B2)

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Sequence Ontology: Class of Gene

nuclear_gene

snRNA_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

snRNA:U2:38ABb-RA

FBtr0081293

NR_001672

191

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\snRNA:U2:38ABb 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

located_in Cajal body

inferred from direct assay

(Liu et al., 2006)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\snRNA:U2:38ABb 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:U2:38ABb

View exonic expression by tissue for Dmel\snRNA:U2:38ABb

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

3772048/tissue=All

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

FBgn0003923

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

FBgn0003923

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

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:U2:38ABb

Transgenic constructs containing regulatory region of snRNA:U2:38ABb

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:U2:38ABb. 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

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)

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

MIST Molecular Interaction Search Tool

View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

snRNA:U2:38ABb - SmB

anti tag coimmunoprecipitation, northern blot

(Rajendra et al., 2007)

snRNA:U2:38ABb - SmD1

anti tag coimmunoprecipitation, primer specific pcr

(Xiong et al., 2013)

snRNA:U2:38ABb - Snup

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

snRNA:U2:38ABb - U2A

anti bait coimmunoprecipitation, northern blot

(Nagengast and Salz, 2001)

snRNA:U2:38ABb - msk

anti tag coimmunoprecipitation, northern blot

(Natalizio and Matera, 2013)

snRNA:U2:38ABb - snf

fluorescence technology, anti bait coimmunoprecipitation, northern blot, filter binding, autoradiography, isothermal titration calorimetry, predetermined participant, nuclear magnetic resonance

(Weber et al., 2018, Williams and Hall, 2010, Nagengast and Salz, 2001)

Summary of Genetic Interactions

esyN Network Diagram

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

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Spliceosome

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-54

Cytogenetic map

38A4-38A4

Sequence location

2L:19,812,646..19,812,836 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

38A4-38A4

Limits computationally determined from genome sequence between P{EP}EP623&P{PZ}spi⁰¹⁰⁶⁸ and P{lacW}l(2)k10239^k10239

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

38A-38B

(Mount, 2000.5)

40A-40B

(determined by in situ hybridisation)

(Saluz et al., 1983)

Experimentally Determined Recombination Data

Location

2-54

(FlyBase, 2016)

2-53.9

(Comeron et al., 2012)

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 (15)

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

cDNA Clones (4)

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 (CR32878) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Coordinates (on date of analysis) on AE003664:80609..80821 .

(Mount, 2000.5)

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 (27)

Reported As

Symbol Synonym

141B

(Alonso et al., 1984)

38A U2

(Hu et al., 2013)

CR32878

D.U2-4

(Saba et al., 1986)

Dm U2-141B

(Alonso et al., 1983)

(Wooley et al., 1982)

(Cheng et al., 2020, Li et al., 2020, Bell et al., 2018, Rau et al., 2012, Gonsalvez et al., 2008, Kroiss et al., 2008, Mount et al., 2007, Liu et al., 2006, Dominski et al., 2003, Giribet et al., 2001, Price et al., 1998, Deshpande et al., 1996, Matunis et al., 1993, Myslinski et al., 1984)

U2 141B

(Kejzlarova-Lepesant et al., 1984)

U2 snRNA

(Natalizio and Matera, 2013, Deryusheva and Gall, 2009, Liu et al., 2009, Nakamura et al., 2008, Rajendra et al., 2007, Gonsalvez et al., 2006, Liu et al., 2006, Komonyi et al., 2005, Labourier and Rio, 2001, Nagengast and Salz, 2001, Nagengast et al., 2001, Reim et al., 1999)

U2-141B

(Jensen et al., 1998, Lo and Mount, 1990)

U2-38ABb

(Mount and Salz, 2000)

U2:38ABb

(Hernandez et al., 2007, Lai et al., 2005)

U2:39AB

(Smith et al., 2011)

U2snRNA

U2snRNA40AB

chr2L:19808533..19808709

(Will et al., 2013)

dU2

(Weber et al., 2018, Williams and Hall, 2010, Liu et al., 2006, Richard et al., 2003, Mount and Steitz, 1981)

snRNA-U2-141B

snRNA1

snRNA2

snRNA:U2

snRNA:U2:38ABb

(Pritykin et al., 2017, Xiong et al., 2013)

snRNA:U2:40AB

snRNA₁

(Saluz et al., 1983)

Name Synonyms

U2 snRNA

(Liu et al., 2006)

small nuclear RNA U2

small nuclear RNA U2 at 38AB b

small nuclear RNA U2 at 38ABb

Secondary FlyBase IDs

FBgn0003919

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 13 )

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.

3772048

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.

NR_001672

RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms

URS00005ED1B2_7227

Other crossreferences

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

3772048/tissue=All

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

FBgn0003923

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

FBgn0003923

FlyMine - An integrated database for Drosophila genomics

FBgn0003923

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

dme:Dmel_CR32878

MARRVEL_MODEL - MARRVEL (model organism gene)

3772048

Linkouts

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0003923

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Spliceosome

References (57)

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

NA

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