Gene Dmel\snRNA:U1:95Ca

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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

2 publicly available

Also Known As

U1, U1 snRNA, DMU1951, U1:95Ca, U1-95.1, U1a, U1snRNA

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

95C5-95C5

Sequence location

3R:19,685,189..19,685,352 [-]

Genomic Maps

Select View:

modENCODE GBrowse

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: nuclear 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.

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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FB2011_10

FB2012_01

References

Kim et al., 2010, Mol. Cell. Biol. 30(10): 2411--2423

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

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., 2004)

External Data

Linkouts

Crossreferences

Expression Data

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Notes

High-Throughput Expression Data

Untitled Document detailed view

See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.

modENCODE Temporal Expression Data for FBgn0004185

	Styles
	Linear
	Logarithmic
	Heatmap
	Scales
	max expr for FBgn0004185
	Very low expression bin max
	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 expression (0 - 0)
	Extremely low expression (1 - 10)
	Very low expression (11 - 100)
	Low expression (101 - 400)
	Moderate expression (401 - 1400)
	Moderately high expression (1401 - 4000)
	High expression (4001 - 10000)
	Very high expression (10001 - 100000)
	Extremely high expression (100001 - 2000000)

Linear, scaled to maximum FBgn0004185 expression level
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low

Linear, scaled to Very low expression
Developmental Stage		Expression Level
embryo 00-02hr		(148)
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		(210)
Expression Level Scale		None Extremely low Very low Low

Linear, scaled to Moderate expression
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low Moderate Moderately high

Linear, scaled to High expression
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low Moderate Moderately high High Very high

Linear, scaled to Extremely high expression
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low Moderate Moderately high High Very high Extremely high

log, scaled to maximum FBgn0004185 expression level
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low

log, scaled to Very low expression
Developmental Stage		Expression Level
embryo 00-02hr		(148)
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		(210)
Expression Level Scale		None Extremely low Very low Low

log, scaled to Moderate expression
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low Moderate Moderately high

log, scaled to High expression
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low Very low Low Moderate Moderately high High Very high

log, scaled to Extremely high expression
Developmental Stage		Expression Level
embryo 00-02hr		148
embryo 02-04hr		33
embryo 04-06hr		11
embryo 06-08hr		8
embryo 08-10hr		36
embryo 10-12hr		22
embryo 12-14hr		12
embryo 14-16hr		6
embryo 16-18hr		0
embryo 18-20hr		2
embryo 20-22hr		3
embryo 22-24hr		0
larva L1		1
larva L2		0
larva L3 12hr old		0
larva L3 puffstage 1-2		0
larva L3 puffstage 3-6		17
larva L3 puffstage 7-9		0
white prepupae new		1
white prepupae 12hr		0
white prepupae 24hr		39
pupae 2d postWPP		11
pupae 3d postWPP		3
pupae 4d postWPP		0
adult male 01day		3
adult male 05day		29
adult male 30day		0
adult female 01day		9
adult female 05day		79
adult female 30day		210
Expression Level Scale		None Extremely low 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)
FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)

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:U1:95Ca^DG12112		P-element activity	1	--
snRNA:U1:95Ca^G14596		P-element activity	1	--

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}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

P{wHy}snRNA:U1:95Ca^DG12112

insertion of mobile activating element

P{EP}snRNA:U1:95Ca^G14596

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

nuclear 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

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

snRNA:U1:95Ca allele

Gene

References

External Data

Linkouts

Orthologs

Genome-wide drosophilid orthologs

Curated drosophilid orthologs

Dsec\snRNA:U1:95Ca

(Colson, 1998.5.26)

Dsim\snRNA:U1:95Ca

(Colson, 1998.5.26)

Linkouts

Stocks & Reagents

Stocks Listed in FlyBase ( 2 )

Bloomington

30205

w¹¹¹⁸; P{EP}snRNA:U1:95Ca^G14596

20584

y¹ w^67c23; P{wHy}snRNA:U1:95Ca^DG12112

Genomic Clones ( 2 )

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

RNAi & Array Information

Linkouts

GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents

•

49590

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

•

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

•

49590

modMine - Data generated by the modENCODE project.

•

FBgn0004185

Synonyms & Secondary IDs ( 20 )

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)

(Wooley et al., 1982)

snRNA:U1

(Gonzalez et al., 2004, )

snRNA:U1:95Ca

snRNA-U1-95.1

(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)

U1:95Ca

(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)

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 ( 59 )

Generate a list of

All references relating to this gene ( 59 )

List References by type

Recent research papers ( 3 )

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]
Gonsalvez et al., 2010, Development 137(14): 2341--2351: Sm proteins specify germ cell fate by facilitating oskar mRNA localization. [FBrf0211144]
Kim et al., 2010, Mol. Cell. Biol. 30(10): 2411--2423: Identification of SNAPc subunit domains that interact with specific nucleotide positions in the U1 and U6 gene promoters. [FBrf0214992]

Show all research papers ...

Recent reviews (0)

All reviews listed in FlyBase were published before 2010

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