FB2022_03, released June 9, 2022

Gene: Dmel\mir-34

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General Information
Symbol
Dmel\mir-34
Species
D. melanogaster
Name
mir-34 stem loop
Annotation Symbol
CR43033
Feature Type
miRNA_gene
FlyBase ID
FBgn0262459
Gene Model Status
Current
Stock Availability
4 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

dme-mir-34, miR-34-5p

Key Links
Genomic Location
Cytogenetic map
85F10-85F10
Sequence location
Recombination map
3-49
RefSeq locus
NT_033777 REGION:10100936..10101034
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (5 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables mRNA 3'-UTR binding
inferred from direct assay
(Xiong et al., 2016, Liu et al., 2012, Burgler and Macdonald, 2005, Robins et al., 2005)
enables mRNA base-pairing post-transcriptional repressor activity
inferred from direct assay
(Xiong et al., 2016, Liu et al., 2012, Burgler and Macdonald, 2005, Robins et al., 2005)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in miRNA-mediated gene silencing
inferred from mutant phenotype
(Liu et al., 2012)
inferred from direct assay
(Xiong et al., 2016, Kuzin et al., 2007, Burgler and Macdonald, 2005, Robins et al., 2005)
involved_in negative regulation of neuron death
inferred from mutant phenotype
(Liu et al., 2012)
acts_upstream_of negative regulation of peptidoglycan recognition protein signaling pathway
inferred from mutant phenotype
(Xiong et al., 2016)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\mir-34 for information on other features

    To submit a correction to a gene model please use the Contact FlyBase form

    Protein Domains (via Pfam)
    Isoform displayed:
    Pfam protein domains
    InterPro name
    classification
    start
    end
    Protein Domains (via SMART)
    Isoform displayed:
    SMART protein domains
    InterPro name
    classification
    start
    end
    Structure New Section
    Comments on Gene Model

    Annotation as per FBrf0155442.

    Locations and structures of miRNA models as mapped by miRBase (FBrf0220601).

    Conserved: found throughout the Drosophila genus (FBrf0230987).

    Sequence Ontology: Class of Gene
    miRNA_gene
    (FlyBase Genome Annotators, 2010, Sokol and Ambros, 2003)
    nuclear_gene
    (FlyBase Genome Annotators, 2010, Sokol and Ambros, 2003)
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    mir-34-RA
    FBtr0304500
    NR_048363
    24
    mir-34-RB
    FBtr0472729
    23
    mir-34-RM
    FBtr0304499
    NR_048362
    99
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    miRBase - A searchable database of published miRNA sequences and annotation.
    Sequences Consistent with the Gene Model
    Nucleotide / Polypeptide Records
      Mapped Features

      Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\mir-34 using the Feature Mapper tool.

      External Data
      Crossreferences
      Linkouts
      Expression Data
      Expression Summary Ribbons
      Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
       low
      high 
      Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
      Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
      Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
       low
      high 
      as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
      Transcript Expression
      northern blot
      Stage
      Tissue/Position (including subcellular localization)
      Reference
      larval stage -- prepupal stage
      (Sempere et al., 2003)
      adult stage
      (Sempere et al., 2003)
      day 3 of adulthood
      adult head

      Comment: Transcripts encoding the mature isoforms a,b and c

      (Liu et al., 2012)
      adult brain

      Comment: Transcripts encoding the mature isoforms a,b and c

      (Liu et al., 2012)
      adult thorax | faint

      Comment: Thorax and abdomen assayed together. Transcripts encoding the mature isoforms a,b and c

      (Liu et al., 2012)
      adult abdomen | faint

      Comment: Thorax and abdomen assayed together. Transcripts encoding the mature isoforms a,b and c

      (Liu et al., 2012)
      day 5 of adulthood
      adult head

      Comment: Transcripts encoding the mature isoforms a,b and c

      (Liu et al., 2012)
      day 30 of adulthood
      adult head

      Comment: Assay detects mature isoforms a,b and c. Stronger expression of isoform c.

      (Liu et al., 2012)
      adult brain | intense

      Comment: Transcripts encoding the mature isoforms a,b and c. Stronger expression of isoform c.

      (Liu et al., 2012)
      adult thorax | faint

      Comment: Thorax and abdomen assayed together. Transcripts encoding the mature isoforms a,b and c. Stronger expression of isoform c.

      (Liu et al., 2012)
      adult abdomen | faint

      Comment: Thorax and abdomen assayed together. Transcripts encoding the mature isoforms a,b and c. Stronger expression of isoform c.

      (Liu et al., 2012)
      Additional Descriptive Data

      The three mature mir-34 transcripts (a, b and c) are first detected in the brain of 3 day old adults. Expression of isoform c, but not of isoforms a and b, is stronger on 30 day old adults. Expression in the rest of the fly body at either age is very weak.

      (Liu et al., 2012)

      Northern analysis of 24 microRNAs showed that mir-34 transcript can be detected in larvae but that expression is downregulated at pupation and remains low until expression resumes sometime during adulthood.

      (Sempere et al., 2003)
      Marker for
       
      Subcellular Localization
      CV Term
      Polypeptide Expression
      Additional Descriptive Data
      Marker for
       
      Subcellular Localization
      CV Term
      Evidence
      References
      Expression Deduced from Reporters
      High-Throughput Expression Data
      Associated Tools

      GBrowse - Visual display of RNA-Seq signals

      View Dmel\mir-34 in GBrowse 2
      RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
      Bulk Downloads
      RNA-Seq RPKM values for all genes
      Reference
      See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
      Developmental Proteome: Life Cycle
      Developmental Proteome: Embryogenesis
      External Data and Images
      Linkouts
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      Images
      FlyBase Wiki
      Image Based Resources
      Alleles, Insertions, Transgenic Constructs, and Aberrations
      Classical and Insertion Alleles ( 3 )
      For All Classical and Insertion Alleles Show
       
      Other relevant insertions
      Transgenic Constructs ( 11 )
      For All Alleles Carried on Transgenic Constructs Show
      Transgenic constructs containing/affecting coding region of mir-34
      Transgenic constructs containing regulatory region of mir-34
      Aberrations (Deficiencies and Duplications) ( 2 )
      Inferred from experimentation ( 2 )
      Gene disrupted in
      Df(3R)mir-34
      (Liu et al., 2012)
      Df(3R)mir-277-34-KO
      (Chen et al., 2014)
      Inferred from location ( 0 )
      Alleles Representing Disease-Implicated Variants
      Phenotypes
      Orthologs
      Downloads
      Download All DIOPT Orthologs
      Human Orthologs (via DIOPT v8.0)
      Homo sapiens (Human) (3)
      Species\Gene Symbol
      Score
      Best Score
      Best Reverse Score
      Source
      Compara
      eggNOG
      Hieranoid
      Homologene
      Inparanoid
      Isobase
      OMA
      OrthoDB
      OrthoFinder
      OrthoInspector
      orthoMCL
      Panther
      Phylome
      RoundUp
      TreeFam
      ZFIN
      Alignment
      Complementation?
      Transgene?
      Hsap\MIR34A
      1 of 15
      Yes
      Yes
      Hsap\MIR34B
      1 of 15
      Yes
      Yes
      Hsap\MIR34C
      1 of 15
      Yes
      Yes
      Model Organism Orthologs (via DIOPT v8.0)
      Mus musculus (laboratory mouse) (3)
      Species\Gene Symbol
      Score
      Best Score
      Best Reverse Score
      Source
      Compara
      eggNOG
      Hieranoid
      Homologene
      Inparanoid
      Isobase
      OMA
      OrthoDB
      OrthoFinder
      OrthoInspector
      orthoMCL
      Panther
      Phylome
      RoundUp
      TreeFam
      ZFIN
      Alignment
      Complementation?
      Transgene?
      Mmus\Mir34a
      1 of 15
      Yes
      Yes
      Mmus\Mir34b
      1 of 15
      Yes
      Yes
      Mmus\Mir34c
      1 of 15
      Yes
      Yes
      Rattus norvegicus (Norway rat) (3)
      Rnor\Mir34a
      1 of 13
      Yes
      Yes
      Rnor\Mir34b
      1 of 13
      Yes
      Yes
      Rnor\Mir34c
      1 of 13
      Yes
      Yes
      Xenopus tropicalis (Western clawed frog) (0)
      No records found.
      Danio rerio (Zebrafish) (3)
      Drer\mir34b
      1 of 15
      Yes
      Yes
      Drer\mir34c
      1 of 15
      Yes
      Yes
      Drer\mir34
      1 of 15
      Yes
      Yes
      Caenorhabditis elegans (Nematode, roundworm) (1)
      Cele\mir-34
      1 of 15
      Yes
      Yes
      Arabidopsis thaliana (thale-cress) (0)
      No records found.
      Saccharomyces cerevisiae (Brewer's yeast) (0)
      No records found.
      Schizosaccharomyces pombe (Fission yeast) (0)
      No records found.
      Other Organism Orthologs (via OrthoDB)
      Paralogs
      Downloads
      Download All DIOPT Paralogs
      Paralogs (via DIOPT v8.0)
      Drosophila melanogaster (Fruit fly) (0)
      No records found.
      Human Disease Associations
      FlyBase Human Disease Model Reports
        Disease Model Summary Ribbon
        Disease Ontology (DO) Annotations
        Models Based on Experimental Evidence ( 0 )
        Allele
        Disease
        Evidence
        References
        Potential Models Based on Orthology ( 0 )
        Human Ortholog
        Disease
        Evidence
        References
        Modifiers Based on Experimental Evidence ( 0 )
        Allele
        Disease
        Interaction
        References
        Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
        Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
        Homo sapiens (Human)
        Gene name
        Score
        OMIM
        OMIM Phenotype
        DO term
        Complementation?
        Transgene?
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        Summary of Genetic Interactions
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Fmr1|mir-277|mir-34
        suppressible
        Eip74EF
        (Liu et al., 2012)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-49
        Cytogenetic map
        85F10-85F10
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        85F10-85F10
        Limits computationally determined from genome sequence between P{lacW}s2681 and P{EP}Fmr1EP3517&P{PZ}tws02414 85F10
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        85F10-85F12
        (Sempere et al., 2003)
        Experimentally Determined Recombination Data
        Location

        3-49

        (FlyBase, 2016)

        3-46.6

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (4)
        Genomic Clones (19)
        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
            Drosophila Genomics Resource Center cDNA clones

            For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

              cDNA Clones, End Sequenced (ESTs)
              BDGP DGC clones
                Other clones
                  RNAi and Array Information
                  Linkouts
                  GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                  Antibody Information
                  Laboratory Generated Antibodies
                   
                  Commercially Available Antibodies
                   
                  Other Information
                  Relationship to Other Genes
                  Source for database identify of
                  Source for database merge of
                  Additional comments

                  The annotation for mir-34 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 CR33326 to CR43033 to reflect this change.

                  (FlyBase Genome Annotators, 2010)
                  Other Comments

                  New annotation (CR33326) in release 3.2 of the genome annotation.

                  (FlyBase Genome Annotators, 2004)
                  Origin and Etymology
                  Discoverer
                  Etymology
                  Identification
                  External Crossreferences and Linkouts ( 16 )
                  Sequence Crossreferences
                  NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
                  RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
                  RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms
                  Other crossreferences
                  DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                  EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                  FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                  FlyMine - An integrated database for Drosophila genomics
                  GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                  KEGG Genes - Molecular building blocks of life in the genomic space.
                  MARRVEL_MODEL - MARRVEL (model organism gene)
                  miRBase - A searchable database of published miRNA sequences and annotation.
                  modMine - A data warehouse for the modENCODE project
                  Linkouts
                  DroID - A comprehensive database of gene and protein interactions.
                  Synonyms and Secondary IDs (13)
                  Reported As
                  Symbol Synonym
                  34
                  (Han et al., 2011)
                  CR33326
                  CR43033
                  (FlyBase Genome Annotators, 2010)
                  MIR-34
                  (Ylla et al., 2016)
                  Mir-34
                  (Robins et al., 2005)
                  Mir34
                  (Nakamura and Yoshimori, 2018)
                  dme-miR-34
                  (Alberti et al., 2018, Volin et al., 2018, Dhahbi et al., 2016, Towler et al., 2015, Esslinger et al., 2013, O'Farrell et al., 2008)
                  dme-miR-34-5p
                  (Chandra et al., 2015)
                  dme-mir-34
                  (Mohammed et al., 2014, miRBase, 2013, Reinhardt et al., 2012, Berezikov et al., 2011, Wang and Liu, 2011, Huang and Gu, 2007, Gesellchen and Boutros, 2004)
                  miR-34
                  (Srinivasan et al., 2022, Furusawa and Emoto, 2021, Jin et al., 2020, Kinser and Pincus, 2020, Kitatani et al., 2020, McNeill et al., 2020, Song and Zhou, 2020, Xia et al., 2020, Liu et al., 2019, Reichholf et al., 2019, Ma et al., 2018, Ueda et al., 2018, Atilano et al., 2017, Church et al., 2017, Picao-Osorio et al., 2017, Rainey et al., 2016, Wang et al., 2016, Xiong et al., 2016, Fulga et al., 2015, Lucas et al., 2015, Mugat et al., 2015, Suh et al., 2015, Xiong et al., 2015, Abe et al., 2014, Chen et al., 2014, Kozomara et al., 2014, Xia and Zhang, 2014, Lucas and Raikhel, 2013, Mezan et al., 2013, Nesler et al., 2013, Smibert et al., 2013, Soni et al., 2013, Bejarano et al., 2012, Chan and Kocerha, 2012, Behura et al., 2011, Han et al., 2011, Lawlor et al., 2011, Liu et al., 2011, Ameres et al., 2010, Czech et al., 2009, Kadener et al., 2009, Yu et al., 2009, Ibáñez-Ventoso et al., 2008, Kuzin et al., 2007, Rehwinkel et al., 2006, Leaman, 2005, Nakahara and Carthew, 2004, Lai et al., 2003, Sempere et al., 2003, Stark et al., 2003, Stark et al., 2003, Grosshans and Slack, 2002, Lau et al., 2001)
                  miR-34-5p
                  (Xie et al., 2020, Feltzin et al., 2015, Abe et al., 2014)
                  mir-34
                  (Bejarano and Lai, 2021, Bejarano et al., 2021, Takemura et al., 2021, Lai et al., 2020, Goh and Okamura, 2019, Hanyu-Nakamura et al., 2019, Kennerdell et al., 2018, Lai et al., 2016, Mohammed and Lai, 2016.2.8, Shlyueva et al., 2014, Wang et al., 2014, Yeh et al., 2014, Zhou et al., 2014, Kato and Slack, 2013, Okamura et al., 2013, Bejarano et al., 2012, Bejarano et al., 2012, Liu et al., 2012, Schertel et al., 2012, Szuplewski et al., 2012, Westholm et al., 2012, FlyBase Genome Annotators, 2010, Okamura et al., 2009, Neumuller et al., 2008, Okamura et al., 2008, Ruby et al., 2007, Burgler and Macdonald, 2005)
                  Name Synonyms
                  mir-34
                  mir-34 stem loop
                  Secondary FlyBase IDs
                  • FBgn0064158
                  • FBgn0053326
                  • FBgn0262326
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (0)
                  Result
                  Result Type
                  Title
                  References (116)