FB2025_01 , released February 20, 2025
Gene: Dmel\snRNP-U1-C
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General Information
Symbol
Dmel\snRNP-U1-C
Species
D. melanogaster
Name
small ribonucleoprotein particle U1 subunit C
Annotation Symbol
CG5454
Feature Type
protein_coding_gene
FlyBase ID
FBgn0261792
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
small ribonucleoprotein particle U1 subunit C (snRNP-U1-C) encodes a U1 snRNA-containing protein that initiates spliceosome assembly by binding to the 5' splice site in pre-mRNA. [Date last reviewed: 2019-02-28] (FlyBase Gene Snapshot)
All Summaries
Also Known As

snRNP-U1, U1C, snRNPC

Key Links
Genomic Location
Cytogenetic map
91E2-91E2
Sequence location
Recombination map
3-65
RefSeq locus
NT_033777 REGION:18982964..18983650
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables nucleic acid binding
inferred from electronic annotation with InterPro:IPR000690, InterPro:IPR003604
(InterPro Project Members, 2004-)
enables pre-mRNA 5'-splice site binding
inferred from biological aspect of ancestor with PANTHER:PTN001259483
(GO Reference Genome Project, 2011-)
enables zinc ion binding
inferred from electronic annotation with InterPro:IPR000690, InterPro:IPR003604, InterPro:IPR013085
(InterPro Project Members, 2004-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in regulation of alternative mRNA splicing, via spliceosome
inferred from mutant phenotype
(Katzenberger et al., 2009)
inferred from high throughput mutant phenotype
(Park et al., 2004)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in mRNA 5'-splice site recognition
inferred from biological aspect of ancestor with PANTHER:PTN001259483
(GO Reference Genome Project, 2011-)
involved_in mRNA splicing, via spliceosome
inferred from sequence or structural similarity with SGD:S000004289
(Mount and Salz, 2000)
inferred from electronic annotation with InterPro:IPR017340
(InterPro Project Members, 2004-)
involved_in spliceosomal snRNP assembly
inferred from electronic annotation with InterPro:IPR017340
(InterPro Project Members, 2004-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Paterson et al., 1991)
part_of small nuclear ribonucleoprotein complex
inferred from direct assay
(Paterson et al., 1991)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred by curator from GO:0000381
(Park et al., 2004)
inferred from electronic annotation with InterPro:IPR000690
(InterPro Project Members, 2004-)
part_of U1 snRNP
inferred from sequence or structural similarity with SGD:S000004289
(Mount and Salz, 2000)
inferred from biological aspect of ancestor with PANTHER:PTN001259483
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR017340
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the U1 small nuclear ribonucleoprotein C family. (Q9VE17)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
small ribonucleoprotein particle U1 subunit C (snRNP-U1-C) encodes a U1 snRNA-containing protein that initiates spliceosome assembly by binding to the 5' splice site in pre-mRNA. [Date last reviewed: 2019-02-28]
Gene Group (FlyBase)
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE -
The U1 small nuclear ribonucleoprotein particle (U1 snRNP) contains U1 snRNA and initiates spliceosome assembly by binding to the 5' splice site in pre-mRNA. (Adapted from PMID:11206553 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).
Protein Function (UniProtKB)
Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. U1-C is directly involved in initial 5' splice-site recognition for both constitutive and regulated alternative splicing. The interaction with the 5' splice-site seems to precede base-pairing between the pre-mRNA and the U1 snRNA. Stimulates commitment or early (E) complex formation by stabilizing the base pairing of the 5' end of the U1 snRNA and the 5' splice-site region (By similarity). Regulates alternative splicing of a distinct group of target genes.
(UniProt, Q9VE17)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\snRNP-U1-C 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 Q9VE17)

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

Gene model reviewed during 5.43

Gene model reviewed during 5.53

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
snRNP-U1-C-RA
FBtr0083720
NM_142510
687
145
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
snRNP-U1-C-PA
FBpp0083134
15.8
145
9.97
Q9VE17
NP_650767
AAF55616
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
Subunit Structure (UniProtKB)

U1 snRNP is composed of the 7 core Sm proteins B/B', D1, D2, D3, E, F and G that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least 3 U1 snRNP-specific proteins U1-70K, U1-A and U1-C. U1-C interacts with U1 snRNA and the 5' splice-site region of the pre-mRNA.

(UniProt, Q9VE17)
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\snRNP-U1-C using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
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).

1.87

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Paterson et al., 1991)
part_of small nuclear ribonucleoprotein complex
inferred from direct assay
(Paterson et al., 1991)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\snRNP-U1-C in JBrowse
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
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 ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of snRNP-U1-C
Transgenic constructs containing regulatory region of snRNP-U1-C
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)Exel6182
(Ryder, 2004.4.26)
Inferred from location ( 7 )
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
lethal, with Scer\GAL4insc-Mz1407
lethal, with Scer\GAL4nub-AC-62
lethal | female limited, with Scer\GAL4dome-PG14
lethal | pupal stage, with Scer\GAL4pnr-MD237
partially lethal - majority die | pupal stage, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
female sterile, with Scer\GAL4VP16.otu
Other Phenotypes
Allele
abnormal neuroanatomy, with Scer\GAL4insc-Mz1407
abnormal neuroanatomy | larval stage, with Scer\GAL4insc-Mz1407
abnormal neurophysiology | adult stage, with Scer\GAL4ninaE.PU
abnormal size | third instar larval stage, with Scer\GAL4Cg.PA
decreased cell number, with Scer\GAL4insc-Mz1407
flightless, with Scer\GAL4Mef2.PR
visible, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
embryonic/larval fat body | third instar larval stage, with Scer\GAL4Cg.PA
ganglion mother cell | larval stage, with Scer\GAL4insc-Mz1407
larval neuroblast | larval stage, with Scer\GAL4insc-Mz1407
mesonotum, with Scer\GAL4pnr-MD237
mitochondrion | third instar larval stage, with Scer\GAL4Cg.PA
myofibril, with Scer\GAL4Mef2.PR
retina, with Scer\GAL4ninaE.PU
sarcomere, with Scer\GAL4Mef2.PR
type II neuroblast, with Scer\GAL4insc-Mz1407
Z disc, with Scer\GAL4Mef2.PR
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (5)
Hsap\SNRPC
11 of 14
Yes
Yes
Hsap\KIF13B
1 of 14
No
No
Hsap\SPTBN2
1 of 14
No
No
3  
Hsap\WBP4
1 of 14
No
No
1  
Hsap\ZMAT5
1 of 14
No
No
1  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (5)
Rnor\Snrpc
11 of 14
Yes
Yes
Rnor\Asap1
1 of 14
No
No
Rnor\Sfi1
1 of 14
No
Yes
Rnor\Zfp385b
1 of 14
No
No
Rnor\Zmat5
1 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Snrpc
11 of 14
Yes
Yes
Mmus\Wbp4
1 of 14
No
No
Mmus\Zmat5
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\snrpc
9 of 13
Yes
Yes
Xtro\mia3
1 of 13
No
No
Danio rerio (Zebrafish) (4)
Drer\snrpc
11 of 14
Yes
Yes
Drer\itsn2b
1 of 14
No
No
Drer\mia3
1 of 14
No
No
Drer\nup155
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\snrp-3
11 of 14
Yes
Yes
Cele\H05L14.2
1 of 14
No
Yes
Cele\ift-74
1 of 14
No
Yes
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP001584
11 of 12
Yes
Yes
Agam\AgaP_AGAP010248
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT4G03120
10 of 13
Yes
Yes
Atha\AT5G26749
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\YHC1
7 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\usp103
9 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:snRNP-U1-C. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
Snrnp20
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 ( 3 )
    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?
    SNRPC; small nuclear ribonucleoprotein polypeptide C
    11 of 14
    603522
        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:
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        Select Layout:
        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
        snRNP-U1-C - gro
        coimmunoprecipitation, quantitative reverse transcription pcr
        (Kwong et al., 2015)
        protein-protein
        Physical Interaction
        Assay
        References
        snRNP-U1-C - CG32846
        two hybrid
        (Hu et al., 2017.6.13)
        snRNP-U1-C - CG3708
        two hybrid
        (Hu et al., 2017.6.13)
        snRNP-U1-C - SmF
        experimental knowledge based
        (Guruharsha et al., 2011)
        snRNP-U1-C - snRNP-U1-70K
        experimental knowledge based
        (Guruharsha et al., 2011)
        snRNP-U1-C - snf
        experimental knowledge based
        (Guruharsha et al., 2011)
        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
        Subunit Structure (UniProtKB)
        U1 snRNP is composed of the 7 core Sm proteins B/B', D1, D2, D3, E, F and G that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least 3 U1 snRNP-specific proteins U1-70K, U1-A and U1-C. U1-C interacts with U1 snRNA and the 5' splice-site region of the pre-mRNA.
        (UniProt, Q9VE17 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-65
        Cytogenetic map
        91E2-91E2
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        91E2-91E2
        Limits computationally determined from genome sequence between P{PZ}sprd05284 and P{PZ}cdi07013&P{lacW}nosj3B6
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-65

        (FlyBase, 2016)

        3-65.1

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (9)
        Genomic Clones (13)
         

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

        cDNA Clones (30)
         

        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
        DRSC - Results frm RNAi screens
        Antibody Information
        Laboratory Generated Antibodies
         
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            RNAi screen using dsRNA made from templates generated with primers directed against this gene results in a long metaphase spindle with misaligned chromosomes when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.

            (Goshima et al., 2007)

            Identified as a protein specific to U1 small nuclear ribonucleoprotein particles (snRNPs).

            (Paterson et al., 1991)
            Relationship to Other Genes
            Source for database merge of

            Source for merge of: snRNP-U1 snRNPC

            (Labourier and Rio, 2001)

            Source for merge of: CG5454 BcDNA:RH29440

            (FlyBase, 1996-)
            Additional comments

            Source for merge of CG5454 BcDNA:RH29440 was a shared cDNA ( date:030728 ).

            (FlyBase, 1996-)
            Nomenclature History
            Source for database identify of

            Source for identity of: snRNP-U1 CG5454

            (Goshima et al., 2007)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (12)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 35 )
            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.
            GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
            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.
            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.
            UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
            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.
            BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
            DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
            EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            Linkouts
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            References (58)