FlyBase Gene Report: Dmel\Snrnp65

General Information

Symbol

Dmel\Snrnp65

Species

D. melanogaster

Name

Small nuclear ribonucleoprotein U11/U12 subunit 65

Annotation Symbol

CG44249

Feature Type

protein_coding_gene

FlyBase ID

FBgn0265184

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

Dm65K

Key Links

Genomic Location

Cytogenetic map

58B1-58B2

Sequence location

2R:22,066,883..22,068,372 [+]

Recombination map

2-98

RefSeq locus

NT_033778 REGION:22066883..22068372

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 (9 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables nucleic acid binding

inferred from sequence model with InterPro:IPR000504

(FlyBase Curators, 2011-)

enables pre-mRNA intronic binding

inferred from biological aspect of ancestor with PANTHER:PTN000413238

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from electronic annotation with InterPro:IPR000504

(InterPro Project Members, 2004-)

enables U12 snRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000413238

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in alternative mRNA splicing, via spliceosome

inferred from direct assay

(Li et al., 2024, Li et al., 2020)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in alternative mRNA splicing, via spliceosome

inferred by curator from GO:0005693,GO:0034693

(Schneider et al., 2004)

involved_in mRNA splicing, via spliceosome

inferred from biological aspect of ancestor with PANTHER:PTN000413238

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

part_of U11/U12 snRNP

inferred from direct assay

(Li et al., 2024, Li et al., 2020, Schneider et al., 2004)

part_of U12 snRNP

inferred from direct assay

(Schneider et al., 2004)

part_of U12-type spliceosomal complex

inferred from direct assay

(Li et al., 2024, Li et al., 2020)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of U12-type spliceosomal complex

inferred from biological aspect of ancestor with PANTHER:PTN000413238

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with HGNC:18666

(Schneider et al., 2004)

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\Snrnp65 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry A0A0B4LGA2)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Shares 5' UTR with downstream gene.

Gene model reviewed during 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Snrnp65-RA

FBtr0339103

NM_001299774

1490

407

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Snrnp65-PA

FBpp0308248

45.4

407

9.43

A0A0B4LGA2

NP_001286703

AHN56498

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

A0A0B4LGA2

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Snrnp65 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).

-0.96

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of U11/U12 snRNP

inferred from direct assay

(Li et al., 2024, Li et al., 2020, Schneider et al., 2004)

part_of U12 snRNP

inferred from direct assay

(Schneider et al., 2004)

part_of U12-type spliceosomal complex

inferred from direct assay

(Li et al., 2024, Li et al., 2020)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Snrnp65 in JBrowse

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

View exonic expression by developmental stage for Dmel\Snrnp65

View exonic expression by tissue for Dmel\Snrnp65

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

19834761/tissue=All

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

FBgn0265184

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

FBgn0265184

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 ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Snrnp65

Transgenic constructs containing regulatory region of Snrnp65

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 12 )

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

partially lethal

Snrnp65^Δ

viable, with Scer\GAL4^pnr-MD237

Snrnp65^GD10043

Other Phenotypes

Allele

decreased fecundity

Snrnp65^Δ

decreased rate of larval locomotory behavior

Snrnp65^Δ

Phenotype manifest in

Allele

NMJ bouton | decreased number

Snrnp65^Δ

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) (11)

Hsap\RNPC3

9 of 14

Yes

Hsap\RBM41

5 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (8)

Rnor\Rnpc3

9 of 14

Yes

Rnor\Rbm41

4 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (9)

Mmus\Rnpc3

8 of 14

Yes

Mmus\Rbm41

4 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (8)

Xtro\rnpc3

6 of 13

Yes

Xtro\bahd1

5 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (12)

Drer\rnpc3

10 of 14

Yes

Drer\cldn2

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Drer\rbmx

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (8)

Cele\mec-8

1 of 14

Yes

Cele\pab-1

1 of 14

Yes

Cele\R06C1.4

1 of 14

Yes

Cele\rbm-3.1

1 of 14

Yes

Cele\rnp-2

1 of 14

Yes

Cele\rnp-3

1 of 14

Yes

Cele\rnp-7

1 of 14

Yes

Cele\sftb-6

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP005296

9 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (24)

Atha\AT1G09230

9 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\ML3

1 of 13

Yes

Atha\ML5

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\MSL1

1 of 13

Yes

Scer\MUD1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (5)

Spom\msl1

1 of 12

Yes

Spom\sab14

1 of 12

Yes

Spom\SPAC328.05

1 of 12

Yes

Spom\SPBC23E6.01c

1 of 12

Yes

Spom\usp102

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Snrnp65. 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) (4)

Rox8

1 of 13

Sf3b6

1 of 13

snf

1 of 13

Syp

1 of 13

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?

RNPC3; RNA binding region (RNP1, RRM) containing 3

9 of 14

618016

PITUITARY HORMONE DEFICIENCY, COMBINED OR ISOLATED, 7; CPHD7

RBM41; RNA binding motif protein 41

5 of 14

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

Snrnp65 - Actβ

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - BuGZ

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2024, Li et al., 2020)

Snrnp65 - CG16837

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - CG32846

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - CG3982

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - CG4836

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - CG9616

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - Fas3

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - HipHop

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - KaiR1D

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - Kcmf1

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2024, Li et al., 2020)

Snrnp65 - Lasp

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - Pcyt2

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - Phb2

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2024, Li et al., 2020)

Snrnp65 - Taf4

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - Zmynd10

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - pyd

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

Snrnp65 - snRNA:U11

anti tag coimmunoprecipitation, reverse transcription pcr, pull down, anti tag western blot, northern blot

(Li et al., 2024, Li et al., 2020)

Snrnp65 - snRNA:U12

anti tag coimmunoprecipitation, northern blot, reverse transcription pcr

(Li et al., 2024, Li et al., 2020)

Snrnp65 - stas

anti tag coimmunoprecipitation, reverse transcription pcr

(Li et al., 2020)

protein-protein

Physical Interaction

Assay

References

Snrnp65 - Ankrd11

anti tag coimmunoprecipitation, anti tag western blot, western blot

(Li et al., 2024)

Snrnp65 - CG2233

anti tag coimmunoprecipitation, anti tag western blot, western blot

(Li et al., 2024)

Snrnp65 - SmD2

anti bait coimmunoprecipitation, anti tag western blot

(Li et al., 2020)

Snrnp65 - Snrnp48

anti tag coimmunoprecipitation, western blot

(Li et al., 2024)

Snrnp65 - Snrnp59

anti tag coimmunoprecipitation, western blot, anti tag western blot

(Li et al., 2024)

Snrnp65 - bel

anti tag coimmunoprecipitation, western blot, anti tag western blot

(Li et al., 2024)

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

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

mRNA Splicing - Minor Pathway

Class of Gene

nuclear_gene

(FlyBase Genome Annotators, 2012)

protein_coding_gene

(FlyBase Genome Annotators, 2012)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-98

Cytogenetic map

58B1-58B2

Sequence location

2R:22,066,883..22,068,372 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

58B1-58B2

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-98

(FlyBase, 2016)

2-103.6

(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

602394

y¹ w¹; P{TKO-UAS.GS06201}attP40/CyO

21207

y¹ w^67c23; P{EPgy2}Snp^EY16388 Snrnp65^EY16388

FlyORF

F002506

M{UAS-Snrnp65.ORF.3xHA.GW}ZH-86Fb

VDRC

v33705

w¹¹¹⁸; P{GD10043}v33705

v33706

w¹¹¹⁸; P{GD10043}v33706

Genomic Clones (16)

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

cDNA Clones (2)

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

IP10959

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.

FBgn0265184

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

AT21721

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

Identified as a potential ortholog of the 65K subunit of the U12 small nuclear ribonucleoprotein particle (snRNP).

(Schneider et al., 2004)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG30327 CG6393

(FlyBase Genome Annotators, 2008)

Source for merge of: CG30327 CG11478

(FlyBase Genome Annotators, 2002-2003)

Additional comments

Annotation CG42257 split into CG44248 (which corresponds to Snp) and CG44249 in release 5.49 of the genome annotation.

(FlyBase Genome Annotators, 2012)

Split based in part on on data from FBrf0191914.

(FlyBase Genome Annotators, 2012)

Annotations CG30327 and CG6393 merged as CG42257 in release 5.8 of the genome annotation.

(FlyBase Genome Annotators, 2008)

Release 1 annotation CG11478 was eliminated in release 2 of the genome annotation and has been restored in release 3.0 of the genome annotation, where it has been renamed CG30327.

(FlyBase Genome Annotators, 2002-2003)

Nomenclature History

Source for database identify of

Source for identity of: Snrnp65 CG44249

(Li et al., 2024)

Nomenclature comments

FlyBase curator comment: Stated to be the fly homolog of human 'U11/U12-65K' and referred to as 'Dm65K', but named in FlyBase as 'Snrnp65' to provide a more informative symbol/name that is consistent with other small nuclear ribonucleoprotein U11/U12 subunits.

(Li et al., 2024)

Etymology

Synonyms and Secondary IDs (9)

Reported As

Symbol Synonym

65K

(Schneider et al., 2004)

CG11478

CG30327

(Giot et al., 2003)

CG42257

(FlyBase Genome Annotators, 2008)

CG44249

(Li et al., 2024, Li et al., 2020, Transgenic RNAi Project members, 2017-, FlyBase Genome Annotators, 2012, Perkins et al., 2009)

Dm65K

(Li et al., 2024, Li et al., 2020)

Snrnp65

cg11478

(Lasko, 2000)

Name Synonyms

Small nuclear ribonucleoprotein U11/U12 subunit 65

Secondary FlyBase IDs

FBgn0259142
FBgn0034686
FBgn0050327

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 20 )

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.

19834761

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

AHN56498

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

A0A0B4LGA2

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

A0A0B4LGA2

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

A0A0B4LGA2

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

19834761/tissue=All

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

FBgn0265184

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

FBgn0265184

InterPro - A database of protein families, domains and functional sites

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

dme:Dmel_CG44249

MARRVEL_MODEL - MARRVEL (model organism gene)

19834761

Linkouts

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

FBgn0265184

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0265184

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC010372

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

mRNA Splicing - Minor Pathway

References (19)

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

-0.96

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