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Gene Dmel\mir-1

General Information
Symbol	Dmel\mir-1	Species	D. melanogaster
Name	mir-1 stem loop	Annotation symbol	CR43027
Feature type	miRNA_gene	FlyBase ID	FBgn0262455
Gene Model Status	Current	Stock availability	1 publicly available
Also Known As	DmiR-1, dme-mir-1, Mir1
Genomic Location
Chromosome (arm)	2L	Recombination map
Cytogenetic map	38C8-38C8	Sequence location	2L:20,487,441..20,487,531 [+]
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 mir-1 stem loop is referred to in FlyBase by the symbol Dmel\mir-1 (CR43027, FBgn0262455). It is a miRNA_gene from Drosophila melanogaster. Its molecular function is unknown. There is experimental evidence that it is involved in the biological process: regulation of Notch signaling pathway; cardiocyte differentiation. 12 alleles are reported. The phenotypes of these alleles are annotated with: abdominal 7 dorsal acute muscle 1; mesothoracic dorsal acute muscle 1; metathoracic dorsal acute muscle 1; wing; cardioblast; embryonic/larval somatic muscle. It has one annotated transcript. Gene sequence location is 2L:20487441..20487531.
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 38C8-38C8   Limits computationally determined from genome sequence between P{EP}CG16798EP401&P{lacW}k07219 and P{lacW}k02501&P{lacW}k14810
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\mir-1 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Locations and structures of miRNA models as mapped by miRBase (FBrf0220601).
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt)   mir-1-RM FBtr0304487  NR_048021   91   mir-1-RA FBtr0304488  NR_048022   22
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences	miRBase - the home of microRNA data • MI0000116
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence   Name AJ421756
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 regulatory region FBsf0000435136 2L:20,475,806..20,477,901 evidence=Reporter construct (in vivo) (Zeitlinger et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000435596 2L:20,480,577..20,481,741 evidence=Reporter construct (in vivo) (Biemar et al., 2005, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 5 -- 11   mesoderm   (Biemar et al., 2005) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage -- adult stage     (Sempere et al., 2003, Aravin et al., 2003)
Additional Descriptive Data
	Expression increases with time to a peak in the first larval instar, then decreases. Expression levels in male and female adults are comparable to that in first instar larvae. (Aravin et al., 2003) Northern analysis of 24 microRNAs showed that a number of them were expressed constituitively throughout development. (Sempere et al., 2003) mir-1 transcript is expressed in embryonic mesoderm and mesoderm-derived tissues. (Biemar et al., 2005)
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 Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal, with Scer\GAL4Act5C.PU mir-1Scer\UAS.cSa lethal, with Scer\GAL4Bx-MS1096 mir-1Scer\UAS.cSa lethal, with Scer\GAL4ey.PU mir-1Scer\UAS.cSa lethal, with Scer\GAL4ptc-559.1 mir-1Scer\UAS.T:Disc\RFP lethal | embryonic stage mir-1Δ31kb lethal | embryonic stage, with Scer\GAL4da.G32 mir-1Scer\UAS.cKa lethal | embryonic stage, with Scer\GAL4how-24B mir-1Scer\UAS.cKa lethal | embryonic stage, with Scer\GAL4ptc-559.1 mir-1Scer\UAS.T:Ppyr\LUC lethal | larval stage mir-1Δ31kb lethal | pharate adult stage, with Scer\GAL4Bx-MS1096 mir-1Scer\UAS.T:Disc\RFP mir-1Scer\UAS.T:Ppyr\LUC lethal | pupal stage, with Scer\GAL4Bx-MS1096 mir-1Scer\UAS.T:Disc\RFP mir-1Scer\UAS.T:Ppyr\LUC lethal | pupal stage, with Scer\GAL4sd-SG29.1 mir-1Scer\UAS.T:Disc\RFP mir-1Scer\UAS.T:Ppyr\LUC lethal | recessive | second instar larval stage mir-1KO Other Phenotypes Allele hypoactive | larval stage | recessive mir-1KO Phenotype manifest in Allele abdominal 7 dorsal acute muscle 1 mir-1Δ31kb cardioblast mir-1Δ31kb cardioblast, with Scer\GAL4da.G32 mir-1Scer\UAS.cKa cardioblast, with Scer\GAL4how-24B mir-1Scer\UAS.cKa embryonic/larval somatic muscle mir-1Δ31kb embryonic/larval somatic muscle, with Scer\GAL4da.G32 mir-1Scer\UAS.cKa embryonic/larval somatic muscle, with Scer\GAL4how-24B mir-1Scer\UAS.cKa embryonic/larval somatic muscle | second instar larval stage mir-1KO mesothoracic dorsal acute muscle 1 mir-1Δ31kb metathoracic dorsal acute muscle 1 mir-1Δ31kb visceral muscle of larval heart & embryonic/larval pericardial cell mir-1Δ31kb wing, with Scer\GAL4Bx-MS1096 mir-1Scer\UAS.T:Ppyr\LUC
Classical Alleles ( 2 )
For All Classical Alleles Show
Allele of mir-1 Class Mutagen Stocks Known lesion mir-1KO FLPase SCEI endonuclease recombination I-CreI endonuclease ends-in gene targeting 0 Yes mir-1Δ31kb FLPase 0 Yes
Alleles Carried on Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Allele of mir-1 Class Mutagen Stocks Known lesion mir-1Scer\UAS.T:Ppyr\LUC in vitro construct 1 Yes mir-1+t8.6 in vitro construct - genomic fragment 0 Yes mir-18.6.XhoI in vitro construct - site directed mutagenesis 0 Yes mir-1KO.Scer\SceI.RS in vitro construct 0 Yes mir-1Scer\UAS.cKa in vitro construct - regulatory fusion in vitro construct - genomic fragment 0 Yes mir-1Scer\UAS.cSa in vitro construct - regulatory fusion 0 Yes mir-1Scer\UAS.cTa in vitro construct - regulatory fusion 0 Yes mir-1Scer\UAS.P\T.cSa in vitro construct - regulatory fusion 0 Yes mir-1Scer\UAS.T:Disc\RFP in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct 0 Yes mir-1αTub84B.PS in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct M{UAS-mir-1.S} NA P{UAS-DsRed-mir-1.L} NA P{UAS-LUC-mir-1.T} NA P{UAS-mir-1.K} NA P{UAS-mir-1.T} NA P{UASp-mir-1.S} NA reporter construct P{mir-1.eve-lacZ} No P{mir-1-lacZ.E1-5} No P{mir-1-lacZ.E1-7} No P{mir-1-lacZ.E2-5} No P{mir-1-lacZ.H-Pelican} No characterization construct P{FRT(w+.mir-1KO.Scer\SceI.RS)} NA P{mir-18.6.XhoI} NA P{mir-1+t8.6} NA
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 ( 0 terms)
Biological Process
CV term Evidence References
cardiocyte differentiation inferred from mutant phenotype (Kwon et al., 2005) regulation of Notch signaling pathway inferred from mutant phenotype (Kwon et al., 2005)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 0 terms )
Sequence Ontology: Class of Gene
	miRNA_gene (Lagos-Quintana et al., 2001, FlyBase Genome Annotators, 2010) nuclear_gene (Lagos-Quintana et al., 2001, FlyBase Genome Annotators, 2010)
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 mir-1 allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0262455
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	41125 w1118; P{UAS-LUC-mir-1.T}attP2/TM3, Sb1
Genomic Clones ( 3 )
	BACR03G24 BACR08D17 BACR34H03 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 • 12798026
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments	The annotation for mir-1 has been changed in release 5.31 of the genome annotation, so that instead of representing a mature miRNA it now represents the precursor stem loop pre-miRNA. The symbol of the annotation has been changed from CR32958 to CR43027 to reflect this change. (FlyBase Genome Annotators, 2010)
Other Comments
	Tiling experiments indicate that the mir-1 gene is 2.9kb in length. mir-1 is directly activated by dl amd twi. (Biemar et al., 2005) mir-1 is not required for the formation or physiological function of the larval musculature, but is required for the dramatic post-mitotic growth of larval muscle. (Sokol and Ambros, 2005) New annotation (CR32958) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NR_048021 NR_048022 DDBJ / EMBL / GenBank • AJ421756 Entrez Gene - A searchable database of RefSeq genes. • 12798026
Other Crossreferences
	miRBase - the home of microRNA data • MI0000116
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0262455 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0262455 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 12798026 modMine - Data generated by the modENCODE project. • FBgn0262455
Synonyms & Secondary IDs ( 14 )
Reported As
Symbol Synonym	CR32958   CR43027 (FlyBase Genome Annotators, 2010, ) dme-mir-1 (Berezikov et al., 2011, Huang and Gu, 2007, Reinhardt et al., 2012) DmiR-1 (Taylor, 2006, Sokol and Ambros, 2005, Taylor, 2006) dmiR-1 (Kwon et al., 2005) miR-1 (Liu et al., 2011, Zekri et al., 2009, Hong et al., 2009, Eulalio et al., 2009, Allawi et al., 2004, Ameres et al., 2010, Leaman, 2005, Taylor, 2006, Carthew, 2006, Kwon et al., 2005, Brennecke, 2005, Sokol and Ambros, 2005, Nakahara and Carthew, 2004, Boutla et al., 2003, Lai et al., 2003, Grosshans and Slack, 2002, Sempere et al., 2003, Lee et al., 2001, Lagos-Quintana et al., 2001, Stark et al., 2003, Stark et al., 2003, Biemar et al., 2006, Saito et al., 2006, Biemar et al., 2006, Nguyen and Frasch, 2006, Stark et al., 2005, Zeitlinger et al., 2007, Behura, 2007, Okamura et al., 2007, Moss, 2002, Taylor, 2006, Nahvi et al., 2009, Easow et al., 2007, Yu et al., 2009, Czech et al., 2009, Kadener et al., 2009, Lau et al., 2001, Ni et al., 2011, Ibáñez-Ventoso et al., 2008, Liu et al., 2012, Tan et al., 2012, Fukunaga et al., 2012) mir-1 (Daneshvar et al., 2013, Schertel et al., 2012, FlyBase Genome Annotators, 2010, Zeitlinger et al., 2007, Sandmann et al., 2007, Neumuller et al., 2008, Sandmann et al., 2006, Liu et al., 2009, Liu et al., 2007, Martin et al., 2009, Ruby et al., 2007, Schnall-Levin et al., 2010, Bejarano et al., 2012) Mir-1 (Robins et al., 2005) Mir1 (Olson, 2006) MiR-1 (Yang et al., 2009) miR1 (Berdnik et al., 2008) mirR-1 (Haley et al., 2008) transfrag 8 (Biemar et al., 2006)
Name Synonym	mir-1   miR-1 (Easow et al., 2007) mir-1 stem loop
Secondary FlyBase IDs
	FBgn0046834 FBgn0262320
References ( 76 )
Generate a list of	All references relating to this gene ( 76 )
List References by type	Research paper  ( 51 ) Supplementary material  ( 8 ) Review  ( 11 ) Personal communication to FlyBase  ( 1 ) Abstract  ( 3 ) FlyBase analysis  ( 2 )
Recent research papers ( 13 )
	Daneshvar et al., 2013, Biol. Open 2(1): 1--9 MicroRNA miR-308 regulates dMyc through a negative feedback loop in Drosophila. [FBrf0220584] Fernandez-Costa et al., 2013, Hum. Mol. Genet. 22(4): 704--716 Expanded CTG repeats trigger miRNA alterations in Drosophila that are conserved in myotonic dystrophy type 1 patients. [FBrf0220611] Fukunaga et al., 2012, Cell 151(3): 533--546 Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. [FBrf0219804] Liu et al., 2012, Nature 482(7386): 519--523 The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. [FBrf0217556] Marrone et al., 2012, BMC Cell Biol. 13: 26 Dg-Dys-Syn1 signaling in Drosophila regulates the microRNA profile. [FBrf0220581] Reinhardt et al., 2012, Front. Genet. 3: 226 Lack of miRNA Misregulation at Early Pathological Stages in Drosophila Neurodegenerative Disease Models. [FBrf0219876] Schertel et al., 2012, Genetics 192(4): 1543--1552 Functional Characterization of Drosophila microRNAs by a Novel in Vivo Library. [FBrf0220194] Tan et al., 2012, PLoS Genet. 8(5): e1002681 MicroRNA-277 Modulates the Neurodegeneration Caused by Fragile X Premutation rCGG Repeats. [FBrf0218227] Wen et al., 2012, Anal. Chem. 84(18): 7664--7669 DNAzyme-Based Rolling-Circle Amplification DNA Machine for Ultrasensitive Analysis of MicroRNA in Drosophila Larva. [FBrf0219442] Berezikov et al., 2011, Genome Res. 21(2): 203--215 Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. [FBrf0213080] Liu et al., 2011, Curr. Biol. 21(22): 1888--1893 The Exoribonuclease Nibbler Controls 3' End Processing of MicroRNAs in Drosophila. [FBrf0216782] Ni et al., 2011, Nat. Methods 8(5): 405--407 A genome-scale shRNA resource for transgenic RNAi in Drosophila. [FBrf0213581] Qian et al., 2011, J. Cell Biol. 193(7): 1181--1196 Tinman/Nkx2-5 acts via miR-1 and upstream of Cdc42 to regulate heart function across species. [FBrf0213988] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...