miRBase entry: cel-mir-254

Stem-loop cel-mir-254

Caenorhabditis elegans cel-mir-254 precursor miRNA
Gene family
MIPF0000310; mir-254

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

Cel-mir-254 is a spike-in control used for normalization and as an indicator of extraction efficiency in miRNA expression studies [PMC9263206] [PMC7868066] [PMC7708817] [PMC5908279] [PMC9571479] [PMC8005714] [PMC8317413]. It is a non-mammalian synthetic miRNA probe that is added to samples to assess RNA extraction efficiency and control for technical variation during the RNA extraction process [PMC7708817] [PMC8005714]. Cel-mir-254 is used in conjunction with other spike-in controls such as ath-miR-159a, cel-miR-248, osa-miR-414, and osa-miR-442 for normalization purposes in miRNA expression analysis using the nCounter® Human v.3 miRNA expression platform [PMC5908279] [PMC8317413]. It is added to each sample before lysis and denaturation to allow for normalization of technical variation that may occur during RNA extraction, reverse transcription, and other steps of the assay process. Cel-mir-254 has been used in various studies to assess miRNA expression patterns in different biological samples such as plasma and worms, providing valuable insights into gene regulation mechanisms and disease processes. For example, cel-mir-254 has been shown to exhibit differential expression patterns between wild-type worms and eat-2(ad1116) worms, indicating its potential role in modulating gene expression during aging processes in C. elegans [PMC4247386].

Literature search
3 open access papers mention cel-mir-254
(12 sentences)


8266 reads, 75 reads per million, 16 experiments

--acua     -a             AA  -AU      C       - au 
      ugcau  uugccgccUACAG  GC   AGAUUU CACAaac c  u
      |||||  |||||||||||||  ||   |||||| ||||||| |  c
      acgua  agcggcggauguC  CG   UCUAAA GUguuug g  g
uuuuug     ca             AG  CUU      C       u ga 

Annotation confidence High
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Genome context
chrX: 11333531-11333630 [-]

Database links

Mature cel-miR-254-3p

Accession MIMAT0000310
Description Caenorhabditis elegans cel-miR-254-3p mature miRNA
Sequence 59 - UGCAAAUCUUUCGCGAC - 75
Evidence experimental
Northern [1-2], PCR [1], Illumina [3]
Database links
Predicted targets

Mature cel-miR-254-5p

Accession MIMAT0031891
Description Caenorhabditis elegans cel-miR-254-5p mature miRNA
Evidence experimental
454 [2]
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