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Gene Dmel\snRNP-U1-C

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	5 publicly available
Also Known As	U1C
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	91E2-91E2	Sequence location	3R:14,808,686..14,809,370 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene small ribonucleoprotein particle U1 subunit C is referred to in FlyBase by the symbol Dmel\snRNP-U1-C (CG5454, FBgn0261792). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: mRNA binding. There is experimental evidence that it is involved in the biological process: mitotic spindle organization; regulation of alternative nuclear mRNA splicing, via spliceosome; neurogenesis. 5 alleles are reported. The phenotype of these alleles is annotated with: mesothoracic tergum. It has one annotated transcript and one annotated polypeptide. Protein features are: U1 small nuclear ribonucleoprotein C; Zinc finger, C2H2-type matrin; Zinc finger, U1-C type; Zinc finger, U1-type. Gene sequence location is 3R:14808686..14809370.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2012_01	Sequence features HFA15804 BKN21376
FB2011_10
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
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
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse 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
Comments on Gene Model
	Gene model reviewed during 5.43
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) snRNP-U1-C-RA FBtr0083720  NM_142510   685   145
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein snRNP-U1-C-PA   FBpp0083134   15.8   145   9.97     NP_650767   AAF55616
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, C2H2-type matrin (IPR000690) Zinc finger, U1-type (IPR003604) Zinc finger, U1-C type (IPR013085) U1 small nuclear ribonucleoprotein C (IPR017340)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF55616   AI259778   AI946767   BI575114   BI583460   BI586496   BI588287   BI588560   BT003460 AAO39463   CA805478   CO265508   CO268234   CO294636   CO301689   CO317294   CZ470318   EC066617   EC198891   EC201405   EC209069   EC212836   EC223241   EC227797   EC232203   EV580417   EV590936   GH949836   GH962036   GH963376   GH965365   GH965740   GH968617   GH978014
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VE17
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal, with Scer\GAL41407 snRNP-U1-CGD11660 lethal | pupal stage, with Scer\GAL4pnr-MD237 snRNP-U1-CGD11660 semi-lethal | pupal stage, with Scer\GAL4pnr-MD237 snRNP-U1-CGD11660 Other Phenotypes Allele neuroanatomy defective | larval stage, with Scer\GAL41407 snRNP-U1-CGD11660 visible, with Scer\GAL4pnr-MD237 snRNP-U1-CGD11660 Phenotype manifest in Allele embryonic/larval neuroblast | larval stage, with Scer\GAL41407 snRNP-U1-CGD11660 ganglion mother cell | larval stage, with Scer\GAL41407 snRNP-U1-CGD11660 mesothoracic tergum, with Scer\GAL4pnr-MD237 snRNP-U1-CGD11660
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of snRNP-U1-C Class Mutagen Stocks Known lesion snRNP-U1-Cc05870 piggyBac transposase 1 --
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of snRNP-U1-C Class Mutagen Stocks Known lesion snRNP-U1-CGD11660 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes snRNP-U1-CHM04055 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes snRNP-U1-CHMS00137 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes snRNP-U1-CKK101325 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)Exel6182 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{TRiP.HM04055} NA P{TRiP.HMS00137} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{PB}snRNP-U1-Cc05870 NA
Gene Ontology: Function, Process & Cellular Component ( 10 unique terms )
Terms Based on Experimental Evidence ( 5 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
mitotic spindle organization inferred from mutant phenotype (Goshima et al., 2007) neurogenesis inferred from mutant phenotype (Neumüller et al., 2011) regulation of alternative nuclear mRNA splicing, via spliceosome inferred from mutant phenotype (Park et al., 2004, Katzenberger et al., 2009)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Paterson et al., 1991) small nuclear ribonucleoprotein complex inferred from direct assay (Paterson et al., 1991)
Terms Based on Predictions or Assertions ( 6 terms )
Molecular Function
CV term Evidence References
mRNA binding inferred from sequence or structural similarity with UniProtKB:Q03369 (FlyBase, 1992-) zinc ion binding inferred from electronic annotation with InterPro:IPR000690, InterPro:IPR003604, InterPro:IPR013085, InterPro:IPR017340 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
nuclear mRNA splicing, via spliceosome inferred from sequence or structural similarity with NCBI:NP_003084 AND inferred from sequence or structural similarity with Saccharomyces YHC1 (Mount and Salz, 2000) inferred from sequence or structural similarity with UniProtKB:Q03369 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus inferred by curator from GO:0000381 (Park et al., 2004) U1 snRNP inferred from sequence or structural similarity with NCBI:NP_003084 AND inferred from sequence or structural similarity with Saccharomyces YHC1 (Mount and Salz, 2000) U11 snRNP inferred from sequence or structural similarity with UniProtKB:Q03369 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	gene   nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions snRNP-U1-C allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0261792 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 42274
Orthologs
Genome-wide drosophilid orthologs	Dana\GF23008 Dere\GG16240 Dgri\GH22525 Dmoj\GI22226 Dper\GL24104 Dpse\GA18892 Dsec\GM13647 Dsim\GD20140 Dvir\GJ24347 Dwil\GK12970 Dyak\GE25158
Curated drosophilid orthologs	Dpse\GA18892
Linkouts	OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB16825 NV16315 LH24349 ISCW020627 FBgn0242244 FBgn0214979 FBgn0211427 FBgn0191619 FBgn0168578 JGI_V11_40364 FBgn0078892 FBgn0161694 FBgn0144954 FBgn0130826 FBgn0129983 FBgn0108475 FBgn0100002 CPIJ003277 CPIJ019181 BGIBMGA008088 ACYPI001217 GB13746 AGAP001584 AAEL013527 PHUM222080 GLEAN_00509
Stocks & Reagents
Stocks Listed in FlyBase ( 5 )
Bloomington	31745 y1 v1; P{TRiP.HM04055}attP2 34822 y1 sc* v1; P{TRiP.HMS00137}attP2
Harvard	- PBac{PB}snRNP-U1-Cc05870
VDRC	v22132 w1118; P{GD11660}v22132 v22133 w1118; P{GD11660}v22133
Genomic Clones ( 2 )
	BACR07D13 BACR44N12 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 31 )
	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 GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones	RH29440
Other clones	DPiM_RH29440
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	LP03267 RH22077 RH26452 RH27981 RH29923
Other clones	922 952 33095 58983 75488 77471 163419 190869 bs30e01 Dmel_dig_009054_0605_0693 Dmel_neb_011852_0358_3510 EK090702 EK142831 EK181916 EK207336 EK267629 ESG0118b.B21_F03 RP004183193 RP004264522 RP004451819 RP004488247 RP004492102 RP004515404 RP004529375
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0261792 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42274
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: snRNP-U1 CG5454 (Goshima et al., 2007)
Source for database merge of	Source for merge of: CG5454 BcDNA:RH29440 (FlyBase, 1996-) Source for merge of: snRNP-U1 snRNPC (Labourier and Rio, 2001)
Additional comments	Source for merge of CG5454 BcDNA:RH29440 was a shared cDNA (date:030728). (FlyBase, 1996-)
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)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_142510 RefSeq (Proteins) • NP_650767 DDBJ / EMBL / GenBank • AAF55616 AAO39463 AI259778 AI946767 BI588287 BT003460 CZ470318 Entrez Gene - A searchable database of RefSeq genes. • 42274 UniProtKB/TrEMBL • Q9VE17
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, C2H2-type matrin (IPR000690) Zinc finger, U1-type (IPR003604) Zinc finger, U1-C type (IPR013085) U1 small nuclear ribonucleoprotein C (IPR017340)
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0261792 DRSC - Results from RNAi screens. • FBgn0261792 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0261792 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42274 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 42274 modMine - Data generated by the modENCODE project. • FBgn0261792 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB16825 NV16315 LH24349 ISCW020627 FBgn0242244 FBgn0214979 FBgn0211427 FBgn0191619 FBgn0168578 JGI_V11_40364 FBgn0078892 FBgn0161694 FBgn0144954 FBgn0130826 FBgn0129983 FBgn0108475 FBgn0100002 CPIJ003277 CPIJ019181 BGIBMGA008088 ACYPI001217 GB13746 AGAP001584 AAEL013527 PHUM222080 GLEAN_00509
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	BcDNA:RH29440   C (Paterson et al., 1991) CG5454 (Goshima et al., 2007, Katzenberger et al., 2009, Zhou et al., 2008, Keleman et al., 2009.8.5, McIntyre et al., 2006, Ni et al., 2008, Ni et al., 2011.7.19) dU1-C (Labourier and Rio, 2001) snRNPC   snRNP-U1   snRNP-U1-C   U1C (Park et al., 2004, Katzenberger et al., 2009)
Name Synonym	CG5454   small ribonucleoprotein particle U1 subunit C   snRNPC   snRNP-U1
Secondary FlyBase IDs
	FBgn0022969 FBgn0038667 FBgn0064828
References ( 27 )
Generate a list of	All references relating to this gene ( 27 )
List References by type	Research paper  ( 10 ) Supplementary material  ( 4 ) Personal communication to FlyBase  ( 6 ) FlyBase analysis  ( 2 ) Computer file  ( 3 ) Automatic genome annotation  ( 1 ) Curated genome annotation  ( 1 )
Recent research papers ( 1 )
	Blanco et al., 2010, BMC Dev. Biol. 10: 94 Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs. [FBrf0211812] Show all research papers ...