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Gene Dmel\snRNA:U1:95Ca

General Information
Symbol	Dmel\snRNA:U1:95Ca	Species	D. melanogaster
Name	small nuclear RNA U1 at 95Ca	Annotation symbol	CR31341
Feature type	snRNA_gene	FlyBase ID	FBgn0004185
Gene Model Status	Current	Stock availability	1 publicly available
Also Known As	U1, U1 snRNA, DMU1951, U1:95Ca, U1-95.1, U1a, U1snRNA
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	95C5-95C5	Sequence location	3R:19,685,189..19,685,352 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents Beta	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 nuclear RNA U1 at 95Ca is referred to in FlyBase by the symbol Dmel\snRNA:U1:95Ca (CR31341, FBgn0004185). It is a snRNA_gene from Drosophila melanogaster. Its molecular function is unknown. Based on sequence similarity, it is predicted to be involved in the biological process: mRNA splicing, via spliceosome. 2 alleles are reported. No phenotypic data is available. It has one annotated transcript. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of low expression to a trough of no expression detected. Peak expression observed within 00-06 hour embryonic stages, in adult female stages. CAVEAT: These RNA-Seq temporal profiles depend upon RNA-Seq reads that are uniquely placed in the genome. For this reason, genes such as histones, Stellates and many classes of RNA genes that are present in multiple exact or near exact copies in the genome, expression levels may be reported as much lower than their true values. Summary of FlyAtlas Anatomical Expression Data: No FlyAtlas data available because no Affy2 ProbeSet aligns to an exon of snRNA:U1:95Ca. Comments on Affy2 ProbeSet: No relevant information because no Affy2 ProbeSet aligns to an exon of snRNA:U1:95Ca. Gene sequence location is 3R:19685189..19685352.
User Contributed Data
	Beta version, feedback welcome
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.
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FB2013_03
FB2013_02
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 95C5-95C5   Limits computationally determined from genome sequence between P{PZ}l(3)0468404684 and P{PZ}Atg600096
Experimentally Determined Cytological Location
Cytogenetic map Notes References 95C-95C   (determined by in situ hybridisation)   (Lo and Mount, 1990)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\snRNA:U1:95Ca for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt)   snRNA:U1:95Ca-RA FBtr0084528  NR_002078   164
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence   Name AF067911   AF067912   EV587046   EV587581   M17639   X53543
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 protein binding site FBsf0000161107 3R:19,685,383..19,685,420 evidence=experimental (Su et al., 1997, Bergman et al., 2005) regulatory region FBsf0000435327 3R:19,685,320..19,685,733 evidence=Reporter construct (in vitro) (McNamara-Schroeder et al., 2001, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of low expression to a trough of no expression detected. Peak expression observed within 00-06 hour embryonic stages, in adult female stages. CAVEAT: These RNA-Seq temporal profiles depend upon RNA-Seq reads that are uniquely placed in the genome. For this reason, genes such as histones, Stellates and many classes of RNA genes that are present in multiple exact or near exact copies in the genome, expression levels may be reported as much lower than their true values. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    0 larva L3 puffstage 7-9    0 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    1 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    0 adult female 05day    1 adult female 30day    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 2 )
For All Classical Alleles Show
Allele of snRNA:U1:95Ca Class Mutagen Stocks Known lesion snRNA:U1:95CaG14596 P-element activity 1 -- snRNA:U1:95CaDG12112 P-element activity 0 --
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of snRNA:U1:95Ca Class Mutagen Stocks Known lesion
Aneuploid Aberrations
Disrupted in	Df(3R)Exel9014 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data characterization construct P{U1-Neo.M} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions P{wHy}snRNA:U1:95CaDG12112 NA insertion of mobile activating element P{EP}snRNA:U1:95CaG14596 NA
Gene Ontology: Function, Process & Cellular Component ( 2 unique terms )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 2 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
mRNA splicing, via spliceosome inferred from sequence or structural similarity (Mount and Salz, 2000)
Cellular Component
CV term Evidence References
U1 snRNP inferred from sequence or structural similarity (Mount and Salz, 2000)
Sequence Ontology: Class of Gene
	nuclear_gene   snRNA_gene
Interactions & Pathways
Summary of Physical Interactions
RNA-protein
Interacting group Assay References
snRNA:U1:95Ca - snf anti bait coimmunoprecipitation, nothern blot (Nagengast and Salz, 2001)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions snRNA:U1:95Ca allele Gene References
External Data
Linkouts
Orthologs
OrthoDB Orthologs (0) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search No orthologs identified Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (None identified)
No orthologies identified
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (0) based on analysis using Dmel annotation version 4.3
No orthologs identified
Stocks & Reagents
Stocks Listed in FlyBase ( 1 )
Bloomington	30205 w1118; P{EP}snRNA:U1:95CaG14596
Genomic Clones ( 2 )
	BACR05C11 BACR11E07 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 GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	Dmel_neb_007379_0147_1339 Dmel_neb_012921_0173_2641
RNAi & Array Information
Linkouts	GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 3772037
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	New annotation (CR31341) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003) Coordinates (on date of analysis) on AE003745:55799..55636. (Mount, 2000.5) Variation of a microsatellite within the snRNA:U1:95Ca locus has been studied in North American populations of D.melanogaster. (Goldstein and Clark, 1995) Basal snRNA:U1:95Ca transcription in vitro requires DNA sequences upstream of position -32; PSEA, PSEB and the initiation site for transcription in vitro. Spacing between PSEA and PSEB is crucial for efficient expression in vitro. snRNA:U1:95Ca transcription in vitro requires Tbp. (Zamrod et al., 1993) snRNA:U1:95Ca has been cloned and sequenced. (Lo and Mount, 1990)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NR_002078 DDBJ / EMBL / GenBank • AF067911 AF067912 M17639 X53543 Entrez Gene - A searchable database of RefSeq genes. • 3772037
Other Crossreferences
Linkouts
	FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0004185 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 3772037 modMine - Data generated by the modENCODE project. • FBgn0004185
Synonyms & Secondary IDs ( 21 )
Reported As
Symbol Synonym	CR31341   DMU1951 (Fernando Vazquez et al., 2000, Colson and Goldstein, 1999, Schug et al., 1998, Schug et al., 1997, Kennington et al., 2006) K5 (Wooley et al., 1982) snRNA:U1 (Gonzalez et al., 2004, ) snRNA:U1:95Ca   snRNA-U1-95.1   U1 (Dominski et al., 2003, Yuan et al., 2003, Harding et al., 2002, Price et al., 1998, Wang and Stumph, 1998, Wang et al., 1996, Deshpande et al., 1996, Matunis et al., 1993, Saluz et al., 1988, Myslinski et al., 1984, Li et al., 2004, Kroiss et al., 2008, Mount et al., 2007, Gonsalvez et al., 2008, Gonsalvez et al., 2010) U1-95.1 (McNamara-Schroeder et al., 2001, Jensen et al., 1998, Kamakaka et al., 1991, Lo and Mount, 1990) U1-95Ca (Ezzeddine et al., 2011) U1:95C (Smith et al., 2011) U1:95Ca (Lai et al., 2005, Hernandez et al., 2007, Barakat and Stumph, 2008, Lai et al., 2008, Kim et al., 2010) U1a (Colson, 1998.5.26, Colson, 1998.5.26) u1a (Goldstein and Clark, 1995) U1a-95Ca (Mount and Salz, 2000) U1 snRNA (Labourier et al., 2001, Nagengast et al., 2001, Reim et al., 1999, Gonsalvez et al., 2006, Nakamura et al., 2008, Deryusheva and Gall, 2009, Labourier and Rio, 2001, Rajendra et al., 2007, Berg et al., 2012) U1snRNA (Horowitz and Krainer, 1994, Wang and Stumph, 1995, Duckett et al., 1995, ) U1snRNA 95.1 (Zamrod et al., 1993) U1snRNA95Ca   U1951 (Colson and Goldstein, 1999)
Name Synonym	small nuclear RNA U1   small nuclear RNA U1 at 95Ca
Secondary FlyBase IDs
	FBgn0003915 FBgn0003918 FBgn0026851 FBgn0051341
References ( 65 )
Generate a list of	All references relating to this gene ( 65 )
List References by type	Research paper  ( 51 ) Review  ( 1 ) Personal communication to FlyBase  ( 6 ) Abstract  ( 2 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 4 )
Recent research papers ( 5 )
	Berg et al., 2012, Cell 150(1): 53--64 U1 snRNP determines mRNA length and regulates isoform expression. [FBrf0219531] Doherty et al., 2012, J. Biol. Chem. 287(47): 39369--39379 Architectural Arrangement of the Small Nuclear RNA (snRNA)-activating Protein Complex 190 Subunit (SNAP190) on U1 snRNA Gene Promoter DNA. [FBrf0219968] Hung and Stumph, 2012, FEBS Lett. 586(6): 841--846 Localization of residues in a novel DNA-binding domain of DmSNAP43 required for DmSNAPc DNA-binding activity. [FBrf0217869] Ezzeddine et al., 2011, Mol. Cell. Biol. 31(2): 328--341 A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3'-End Formation. [FBrf0212592] Smith et al., 2011, Mol. Cell 44(6): 954--965 The little elongation complex regulates small nuclear RNA transcription. [FBrf0217100] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...