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Gene Dmel\mir-9a

General Information
Symbol	Dmel\mir-9a	Species	D. melanogaster
Name	mir-9a stem loop	Annotation symbol	CR42891
Feature type	miRNA_gene	FlyBase ID	FBgn0262373
Gene Model Status	Current	Stock availability	None publicly available
Also Known As	miR-9, dme-miR-9a
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	76B7-76B7	Sequence location	3L:19,558,231..19,558,308 [+]
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 mir-9a stem loop is referred to in FlyBase by the symbol Dmel\mir-9a (CR42891, FBgn0262373). 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: sensory organ boundary specification; wing disc development; imaginal disc-derived wing morphogenesis; gene silencing by miRNA. 13 alleles are reported. The phenotypes of these alleles are annotated with: organ system subdivision; adult segment; thoracic segment; organ system; peripheral nervous system; portion of tissue; integumentary plate; abdominal 1 dorsal multidendritic neuron ddaF; cell part; postalar bristle. It has one annotated transcript. Gene sequence location is 3L:19558231..19558308.
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.
FB2011_10
FB2012_01	Sequence features BKN40162
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 76B7-76B7   Limits computationally determined from genome sequence between P{EP}MESR6EP3142 and P{lacW}l(3)L3809L3809
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-9a 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)   mir-9a-RM FBtr0304196     78   mir-9a-RA FBtr0304197     23
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences	Rfam - RNA families database of alignments and covariance models • RF00237 miRBase - the home of microRNA data • MI0000129
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence   Name AJ421769
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
northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage -- adult stage     (Sempere et al., 2003) embryonic stage 5 -- adult stage   organism   (Aravin et al., 2003) Comment:expression starts at 2 hr AEL
Additional Descriptive Data
	Expression is weak, with a broad peak from 6 hours of embryonic development through the first larval instar. (Aravin et al., 2003) Northern analysis of 24 microRNAs showed that a number of them were expressed constituitively throughout development. (Sempere et al., 2003)
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 viable mir-9aE39 mir-9aJ22 Sterility Allele fertile mir-9aE39 mir-9aJ22 Other Phenotypes Allele increased cell death | somatic clone mir-9aE39 increased cell death | third instar larval stage (with mir-9aE39) mir-9aJ22 increased cell death | third instar larval stage (with mir-9aJ22) mir-9aE39 neuroanatomy defective, with Scer\GAL4221 mir-9aScer\UAS.cLa visible mir-9aE39 mir-9aJ22 visible, with Scer\GAL4ap-md544 mir-9aScer\UAS.cLa visible, with Scer\GAL4Bx-MS1096 mir-9aScer\UAS.cBa visible (with mir-9aE39) mir-9aJ22 visible (with mir-9aJ22) mir-9aE39 visible | somatic clone mir-9aE39 Phenotype manifest in Allele abdominal 1 dorsal multidendritic neuron ddaE, with Scer\GAL4221 mir-9aScer\UAS.cLa abdominal 1 dorsal multidendritic neuron ddaF, with Scer\GAL4221 mir-9aScer\UAS.cLa abdominal dorsal multidendritic neuron ddaE | ectopic mir-9aE39 mir-9aJ22 abdominal dorsal multidendritic neuron ddaF | ectopic mir-9aE39 mir-9aJ22 anterior postalar bristle (with mir-9aE39) mir-9aJ22 anterior postalar bristle (with mir-9aJ22) mir-9aE39 anterior wing margin mir-9aE39 mir-9aJ22 anterior wing margin (with mir-9aE39) mir-9aJ22 anterior wing margin (with mir-9aJ22) mir-9aE39 dendrite, with Scer\GAL4221 mir-9aScer\UAS.cLa dendritic arborizing neuron, with Scer\GAL4221 mir-9aScer\UAS.cLa dorsocentral bristle (with mir-9aE39) mir-9aJ22 dorsocentral bristle (with mir-9aJ22) mir-9aE39 eo neuron | ectopic mir-9aJ22 microchaeta mir-9aJ22 microchaeta (with mir-9aE39) mir-9aJ22 microchaeta (with mir-9aJ22) mir-9aE39 posterior wing margin mir-9aE39 mir-9aJ22 posterior wing margin (with mir-9aE39) mir-9aJ22 posterior wing margin (with mir-9aJ22) mir-9aE39 posterior wing margin | somatic clone mir-9aE39 scutellar bristle, with Scer\GAL4ap-md544 mir-9aScer\UAS.cLa scutellar bristle | ectopic mir-9aJ22 sensory mother cell, with Scer\GAL4ap-md544 mir-9aScer\UAS.cLa sensory mother cell | ectopic mir-9aJ22 tormogen cell | ectopic mir-9aJ22 trichogen cell | ectopic mir-9aJ22 wing, with Scer\GAL4Bx-MS1096 mir-9aScer\UAS.cBa wing disc | somatic clone mir-9aE39 wing margin mir-9aJ22 wing margin bristle | ectopic & anterior wing margin mir-9aJ22 wing pouch (with mir-9aE39) mir-9aJ22 wing pouch (with mir-9aJ22) mir-9aE39
Classical Alleles ( 6 )
For All Classical Alleles Show
Allele of mir-9a Class Mutagen Stocks Known lesion mir-9aE39 recombination SCEI endonuclease FLPase 0 Yes mir-9aE44 recombination SCEI endonuclease FLPase 0 Yes mir-9aE45 recombination SCEI endonuclease FLPase 0 Yes mir-9aJ22 recombination SCEI endonuclease FLPase 0 Yes mir-9aJ34 recombination SCEI endonuclease FLPase 0 Yes mir-9aunspecified 0 --
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of mir-9a Class Mutagen Stocks Known lesion mir-9amut.Scer\UAS in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes mir-9aScer\UAS.cBa in vitro construct - regulatory fusion 0 Yes mir-9aScer\UAS.cLa in vitro construct - regulatory fusion 0 Yes mir-9aScer\UAS.cLb in vitro construct - regulatory fusion 0 Yes mir-9aScer\UAS.T:Disc\RFP-DsRed2 in vitro construct - regulatory fusion 0 Yes mir-9at20.1 in vitro construct - genomic fragment 0 Yes mir-9aw.Scer\SceI.RS in vitro construct 0 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{UAS-DsRed-mir-9a} NA P{UAS-mir-9a.B} NA P{UAS-mir-9a.L} NA P{UAS-mir-9a.Lb} NA P{UAS-mir-9a.mut} NA characterization construct P{FRT(w+.mir-9aw.Scer\SceI.RS)} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
Terms Based on Experimental Evidence ( 4 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
gene silencing by miRNA inferred from direct assay (Bejarano et al., 2010) imaginal disc-derived wing morphogenesis inferred from mutant phenotype (Bejarano et al., 2010) sensory organ boundary specification inferred from mutant phenotype (Li et al., 2006) wing disc development inferred from genetic interaction with Bx (Biryukova et al., 2009) inferred from mutant phenotype (Biryukova et al., 2009)
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
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 mir-9a allele Gene References unspecified sens (Li et al., 2006)
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0262373
Orthologs
Genome-wide drosophilid orthologs
Curated drosophilid orthologs	Dpse\mir-9a
Linkouts
Stocks & Reagents
Stocks Listed in FlyBase ( 0 )
Genomic Clones ( 1 )
	BACR01D04 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 • 170854 3772063
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: mir-9a mir-9 (Stark et al., 2003)
Source for database merge of
Additional comments	The annotation for mir-9a 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 CR33063 to CR42891 to reflect this change. (FlyBase Genome Annotators, 2010)
Other Comments
	mir-9a ensures the precise specification of sensory organ precursors by down-regulating the expression of sens through its 3' untranslated region. (Li et al., 2006) New annotation (CR33063) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	DDBJ / EMBL / GenBank • AJ421769 Entrez Gene - A searchable database of RefSeq genes. • 3772063
Other Crossreferences
	Rfam - RNA families database of alignments and covariance models • RF00237 miRBase - the home of microRNA data • MI0000129
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0262373 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0262373 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 170854 3772063 modMine - Data generated by the modENCODE project. • FBgn0262373
Synonyms & Secondary IDs ( 12 )
Reported As
Symbol Synonym	CR33063 (Quinones-Coello, 2007) CR42891 (FlyBase Genome Annotators, 2010, ) dme-miR-9a (O'Farrell et al., 2008) dme-mir-9a (Huang and Gu, 2007) miR-9 (Boutla et al., 2003, Lai et al., 2003, Sempere et al., 2003, Lee et al., 2001, Lagos-Quintana et al., 2001, Behura, 2007, Enright et al., 2003) mir-9 (Asmar et al., 2007) mir-9a (FlyBase Genome Annotators, 2010, Quinones-Coello, 2007, Biryukova et al., 2009, Martin et al., 2009, Bejarano et al., 2010, Ruby et al., 2007, Cooper et al., 2010) miR-9a (Li et al., 2006, Leaman, 2005, Biemar et al., 2006, Venken, 2006, Biemar et al., 2006, Stark et al., 2005, Venken et al., 2006, Cohen et al., 2006, Rehwinkel et al., 2006, Huang et al., 2008, Kuzin et al., 2007, Leaman et al., 2005, Kadener et al., 2009, Xu et al., 2008, Ghildiyal et al., 2010) mir-9A (Kuzin et al., 2007) miR9a (Berdnik et al., 2008) transfrag 22 (Biemar et al., 2006)
Name Synonym	mir-9a   mir-9a stem loop
Secondary FlyBase IDs
	FBgn0046813 FBgn0067680 FBgn0262184
References ( 39 )
Generate a list of	All references relating to this gene ( 39 )
List References by type	Research paper  ( 24 ) Supplementary material  ( 8 ) Review  ( 2 ) Abstract  ( 3 ) FlyBase analysis  ( 2 )
Recent research papers ( 3 )
	Bejarano et al., 2010, Dev. Biol. 338(1): 63--73 miR-9a prevents apoptosis during wing development by repressing Drosophila LIM-only. [FBrf0209786] Cooper et al., 2010, Genetics 185(3): 811--822 Molecular Genetic Analysis of Chd3 and Polytene Chromosome Region 76B-D in Drosophila melanogaster. [FBrf0211329] Ghildiyal et al., 2010, RNA 16(1): 43--56 Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. [FBrf0209572] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...