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Gene Dmel\scaRNA:mgU2-41

General Information
Symbol	Dmel\scaRNA:mgU2-41	Species	D. melanogaster
Name		Annotation symbol	CR43570
Feature type	snoRNA_gene	FlyBase ID	FBgn0261453
Gene Model Status	Current	Stock availability	None publicly available
Also Known As	mgU2-41
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	84E5-84E5	Sequence location	3R:3,747,674..3,747,795 [+]
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	This gene is referred to in FlyBase by the symbol Dmel\scaRNA:mgU2-41 (CR43570, FBgn0261453). It is a snoRNA_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: snRNA 2'-O-ribose methylation guide activity. The biological processes in which it is involved are not known. No alleles are reported. It has one annotated transcript. Gene sequence location is 3R:3747674..3747795.
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.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
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 84E5-84E5
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\scaRNA:mgU2-41 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)   scaRNA:mgU2-41-RA FBtr0309754  NR_048342   141
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence   Name BK006791
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
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 (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Cell Line Expression Data (modENCODE_mRNA-Seq_cell.A) (modENCODE_mRNA-Seq_cell.B)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max 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 Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    1 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    1 wing disc ML-DmD8    1 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    2 eye-antennal disc ML-DmD11    3 antennal disc ML-DmD20-c5    1 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    1 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Cell Line   Expression Level Schneider line 2 S2R+     Schneider line 2 Sg4     embryonic 1182-4H     embryonic GM2     embryonic Kc167     embryonic S1     embryonic S3     leg disc CME L1     wing disc CME-W2     wing disc ML-DmD8     wing disc ML-DmD9     wing disc ML-DmD16-c3     wing disc ML-DmD21     wing disc ML-DmD32     haltere disc ML-DmD17-c3     eye-antennal disc ML-DmD11     antennal disc ML-DmD20-c5     mixed discs ML-DmD4-c1     CNS ML-DmBG1-c1     CNS ML-DmBG2-c2     tumorous blood cells mbn2     ovary fGS/OSS     ovary OSC     ovary OSS
modENCODE Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of scaRNA:mgU2-41 Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of scaRNA:mgU2-41 Class Mutagen Stocks Known lesion
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 2 unique terms )
Terms Based on Experimental Evidence ( 2 terms )
Molecular Function
CV term Evidence References
snRNA 2'-O-ribose methylation guide activity inferred from direct assay (Deryusheva and Gall, 2009)
Biological Process ( 0 terms)
Cellular Component
CV term Evidence References
Cajal body inferred from direct assay (Deryusheva and Gall, 2009)
Terms Based on Predictions or Assertions ( 0 terms )
Sequence Ontology: Class of Gene
	nuclear_gene (Tycowski et al., 2009) snoRNA_gene (Tycowski et al., 2009)
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions scaRNA:mgU2-41 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 ( 0 )
Genomic Clones ( 1 )
	BACR11D12 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 0 )
	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 • 12798055
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments	scaRNA:mgU2-41 is encoded in an intron of lds. (Graveley et al., 2011)
Other Comments
	New annotation (CR43570) in release 5.41 of the genome annotation. (FlyBase Genome Annotators, 2011) scaRNA:mgU2-41 is a Cajal body-specific RNA (scaRNA) that is predicted to modify U2 snRNA. (Tycowski et al., 2009)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NR_048342 DDBJ / EMBL / GenBank • BK006791 Entrez Gene - A searchable database of RefSeq genes. • 12798055
Other Crossreferences
Linkouts
	GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 12798055
Synonyms & Secondary IDs ( 3 )
Reported As
Symbol Synonym	mgU2-41 (Tycowski et al., 2009, Deryusheva and Gall, 2009) scaRNA:lds-a (Graveley et al., 2011) scaRNA:mgU2-41 (FlyBase Genome Annotators, 2011)
Name Synonym
Secondary FlyBase IDs
References ( 4 )
Research paper	Deryusheva and Gall, 2009, Mol. Biol. Cell 20(24): 5250--5259 Small Cajal Body-specific RNAs of Drosophila Function in the Absence of Cajal Bodies. [FBrf0209497] Tycowski et al., 2009, Mol. Cell 34(1): 47--57 A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles. [FBrf0207722]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 7. Unannotated Small Non-Coding RNAs. [FBrf0214678]
FlyBase analysis	FlyBase Genome Annotators, 2011, Changes affecting gene model number or type in release 5.41 of the annotated D.melanogaster genome. Changes affecting gene model number or type in release 5.41 of the annotated D.melanogaster genome. [FBrf0214764]