miRBase entry: cel-mir-239b

Stem-loop cel-mir-239b

Caenorhabditis elegans cel-mir-239b precursor miRNA
Gene family
MIPF0000135; mir-239

Caution, this is an AI generated summary based on literature. This may have errors. ?

Cel-mir-239b is a microRNA (miRNA) that is used as a negative control in various experiments. It has minimal sequence identity with miRNAs in human, mouse, and rat [PMC2699527]. In different studies, cel-mir-239b has been used as a control miRNA in experiments involving the inhibition of miRNAs function [PMC7253519]. It has been co-transfected with different vectors and synthetic miRNAs to assess the effects on gene expression [PMC7253519]. Cel-mir-239b has also been used as a negative control in studies involving the transfection of microRNA mimics and inhibitors [PMC7708977] [PMC9617134] [PMC4260481] [PMC4546478] [PMC3743786]. Additionally, cel-mir-239b has been employed as a negative control in experiments using siRNAs to minimize off-target effects and equalize the total amount of small RNA [PMC8019740] [PMC3572043]. It has also been used as a negative control in studies investigating microRNA expression and gene regulation using mimics or inhibitors of specific miRNAs [PMC6502783] [PMC4308918] [PMC5460990]  [ [ [ [ [ [ . In summary, cel-mir-239b is commonly used as a negative control in various experimental settings to assess the specific effects of other miRNAs or RNAi molecules.

Literature search
4 open access papers mention cel-mir-239b
(45 sentences)


16083 reads, 130 reads per million, 14 experiments

--------     aga   a          UA         A   -   a  ua 
        gcgac   ugc auuUUUGUAC  CACAAAAGU CUG guc uu  a
        |||||   ||| ||||||||||  ||||||||| ||| ||| ||   
        cguug   acg uAAAAACGUG  GUGUUUUCA Gac cgg ag  g
ucuauuuu     --a   g          UG         C   u   -  uu 

Annotation confidence High
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miR-239b was predicted by computational analysis and conservation in C. elegans and C. briggsae, and the microRNA confirmed by PCR amplification, cloning and sequencing [1]. A large scale cloning and sequencing study finds two dominant mature miRNA products: the second is 1 nt shorter at the 5' end [3].

Genome context
chrX: 11791302-11791399 [-]
Clustered miRNAs
1 other miRNA is < 10 kb from cel-mir-239b
Name Accession Chromosome Start End Strand Confidence

Database links

Mature cel-miR-239b-5p

Accession MIMAT0000295
Description Caenorhabditis elegans cel-miR-239b-5p mature miRNA
Evidence experimental
cloned [3], Illumina [4], CLIPseq [5]
Database links
Predicted targets

Mature cel-miR-239b-3p

Accession MIMAT0015115
Description Caenorhabditis elegans cel-miR-239b-3p mature miRNA
Evidence experimental
CLIPseq [5]
Database links


  1. PubMed ID: 12672692
    The microRNAs of Caenorhabditis elegans
    "Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP"
    "Genes Dev (2003) 17:991-1008

  2. PubMed ID: 17174894
    Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    "Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP"
    "Cell (2006) 127:1193-1207

  3. PubMed ID: 19460142
    Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development
    Kato M, de Lencastre A, Pincus Z, Slack FJ
    Genome Biol (2009) 10:R54

  4. PubMed ID: 20062054
    Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans
    "Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW"
    "Nat Struct Mol Biol (2010) 17:173-179

  5. PubMed ID: 15317971
    Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
    "Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB"
    "RNA (2004) 10:1309-1322