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Gene Dmel\mir-4

General Information
Symbol	Dmel\mir-4	Species	D. melanogaster
Name	mir-4 stem loop	Annotation symbol	CR42961
Feature type	miRNA_gene	FlyBase ID	FBgn0262414
Gene Model Status	Current	Stock availability	None publicly available
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	56E1-56E1	Sequence location	2R:15,548,794..15,548,874 [-]
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-4 stem loop is referred to in FlyBase by the symbol Dmel\mir-4 (CR42961, FBgn0262414). It is a miRNA_gene from Drosophila melanogaster. Its molecular function is unknown. The biological processes in which it is involved are not known. 5 alleles are reported. The phenotype of these alleles is annotated with: chaeta. It has one annotated transcript. Gene sequence location is 2R:15548794..15548874.
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 56E1-56E1   Limits computationally determined from genome sequence between P{PZ}sm05338&P{PZ}emm1 and P{lacW}l(2)k08002k08002
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-4 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-4-RM FBtr0304347  NR_048160   81   mir-4-RA FBtr0304348  NR_048161   21
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences	miRBase - the home of microRNA data • MI0000122
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence   Name AJ421762
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
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4   organism | ubiquitous   • nucleus (Biemar et al., 2005) Comment:probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018 embryonic stage 5   organism | 10-90% egg length   • nucleus (Biemar et al., 2005) Comment:probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018 embryonic stage 5 -- 7   dorsal ectoderm | striped   • nucleus (Biemar et al., 2005) Comment:probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018 northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Sempere et al., 2003) embryonic stage -- first instar larval stage   organism   (Aravin et al., 2003) first instar larval stage     (Sempere et al., 2003)
Additional Descriptive Data
	mir-4 transcript is ubquitously expressed in precellular embryos. At stage 5, transcript expression is repressed, first at the posterior pole of the embryo, then in a dorsal patch at the anterior of the embryo. Late in stage 5, transcript expression begins to be lost in the mesoderm and neural ectoderm in ventral and lateral regions. By late embryonic stage 5, expression is refined to transient stripes in the dorsal ectoderm These stripes become further refined to a single central band by embryonic stage 7. Expression is essentially lost by the onset of germband elongation, except for residual expression at the anterior tip of the embryo, and in the dorsal ectoderm. mir-4 transcript is localized to the nucleus at all stages. (Biemar et al., 2005) Northern analysis of 24 microRNAs showed that the expression of mir-4, mir-5, mir-124 and mir-6 isoforms (mir-6-1, mir-6-2 and mir-6-3) is restricted to embryogenesis and the first larval instar with levels decreasing during the latter part of the first larval stage. (Sempere et al., 2003) Expression peaks at 2-4 hours of embryonic development. (Aravin et al., 2003)
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
Other Phenotypes Allele visible, with Scer\GAL4Act5C.PU mir-4Scer\UAS.cSa Phenotype manifest in Allele chaeta, with Scer\GAL4Act5C.PU mir-4Scer\UAS.cSa chaeta | ectopic, with Scer\GAL4Act5C.PU mir-4Scer\UAS.cSa
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of mir-4 Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of mir-4 Class Mutagen Stocks Known lesion mir-4+2.6 in vitro construct - genomic fragment 0 Yes mir-4Scer\UAS.cluster.cLc in vitro construct - regulatory fusion 0 Yes mir-4Scer\UAS.cluster.T:Disc\RFP-DsRed2 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes mir-4Scer\UAS.cSa in vitro construct - regulatory fusion 0 Yes mir-4Scer\UAS.T:Disc\RFP in vitro construct 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2R)mir-309-6Δ1 (Bushati et al., 2008)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct M{UAS-mir-4.S} NA P{UAS-DsRed2-mir-286.mir-4.mir-5} NA P{UAS-DsRed-mir-4.L} NA P{UAS-mir-309+mir-3+mir-286+mir-4+mir-5+mir-6-1+mir-6-2+mir-6-3.L} NA characterization construct P{mir-309-6.2.6} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 0 unique terms )
Terms Based on Experimental Evidence ( 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-4 allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0262414
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 )
	BACR02J10 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 • 12798355
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-4 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 CR33038 to CR42961 to reflect this change. (FlyBase Genome Annotators, 2010)
Other Comments
	New annotation (CR33561) in release 4.1 of the genome annotation. (FlyBase Genome Annotators, 2005) mir-3, mir-4, mir-5, mir-6-1, mir-6-2 and mir-6-3 sequences are clustered within 900bp in 56D7-56E3. (Sempere et al., 2003) New annotation (CR33038) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NR_048160 NR_048161 DDBJ / EMBL / GenBank • AJ421762 Entrez Gene - A searchable database of RefSeq genes. • 3772406 12798355
Other Crossreferences
	miRBase - the home of microRNA data • MI0000122
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0262414 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0262414 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 12798355 modMine - Data generated by the modENCODE project. • FBgn0262414
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	CR33038   CR33561 (FlyBase Genome Annotators, 2005) CR42961 (FlyBase Genome Annotators, 2010, ) mir-4 (Daneshvar et al., 2013, Bejarano et al., 2012, Okamura et al., 2008, FlyBase Genome Annotators, 2010, Moss, 2002, Tyler et al., 2008, Ruby et al., 2007, Schertel et al., 2012) miR-4 (Bejarano et al., 2012, Lai et al., 2004, Leaman, 2005, Alvarez-Garcia and Miska, 2005, Biemar et al., 2005, Miska, 2005, Brennecke et al., 2005, Boutla et al., 2003, Lai et al., 2003, Schwarz et al., 2003, Sempere et al., 2003, Lai, 2002, Lee et al., 2001, Lagos-Quintana et al., 2001, Ruvkun, 2001, Stark et al., 2003, Stark et al., 2003, Venken, 2006, Stark et al., 2005, Venken et al., 2006, Bushati et al., 2008, Behura et al., 2011, Thomsen et al., 2010, Ibáñez-Ventoso et al., 2008, Westholm et al., 2012) mir-4* (Aravin et al., 2003) mir-4S
Name Synonym	mir-4   mir-4S   mir-4 stem loop
Secondary FlyBase IDs
	FBgn0046821 FBgn0082173 FBgn0262254
References ( 41 )
Generate a list of	All references relating to this gene ( 41 )
List References by type	Research paper  ( 26 ) Supplementary material  ( 7 ) Review  ( 4 ) Erratum  ( 1 ) FlyBase analysis  ( 3 )
Recent research papers ( 6 )
	Daneshvar et al., 2013, Biol. Open 2(1): 1--9 MicroRNA miR-308 regulates dMyc through a negative feedback loop in Drosophila. [FBrf0220584] Marrone et al., 2012, BMC Cell Biol. 13: 26 Dg-Dys-Syn1 signaling in Drosophila regulates the microRNA profile. [FBrf0220581] Schertel et al., 2012, Genetics 192(4): 1543--1552 Functional Characterization of Drosophila microRNAs by a Novel in Vivo Library. [FBrf0220194] Szuplewski et al., 2012, Genetics 190(2): 617--626 MicroRNA Transgene Overexpression Complements Deficiency-Based Modifier Screens in Drosophila. [FBrf0217517] Westholm et al., 2012, RNA 18(2): 177--192 Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. [FBrf0217201] Behura et al., 2011, PLoS ONE 6(7): e21504 Comparative Genomic Analysis of Drosophila melanogaster and Vector Mosquito Developmental Genes. [FBrf0214308] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...