Stem-loop sequence cel-mir-246

Accession

MI0000322 (change log)

Description

Caenorhabditis elegans miR-246 stem-loop

Gene family

MIPF0000260; mir-246

Literature search

6 open access papers mention cel-mir-246
(37 sentences)

Stem-loop

   a  ug  uuauaa    u g    a   uugu           uccca 
5'  uc  aa      aaca c ccua ccg    cauguaauauu     g
    ||  ||      |||| | |||| |||    |||||||||||     a
3'  ag  uu      uugu g ggau ggc    guacauuauag     g
   c  gu  -caaac    c a    g   -uuu           uaaaa 

Deep sequencing

53138 reads, 346 reads per million, 13 experiments

Confidence

Annotation confidence: high

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Comments

The extents of the dominant mature miRNA species are adjusted here in accordance with a large scale cloning and sequencing study [2].

Genome context

• Coordinates (WBcel235; GCA_000002985.3): chrIV: 10940134-10940230 [+]
• Overlapping transcripts:

  intergenic

Database links

• RNAcentral:URS000057CDE2_6239
• miRBase Tracker:MI0000322

Mature sequence cel-miR-246-5p

• Accession: MIMAT0020337
• Previous IDs: cel-miR-246*
• Sequence: 19 - cgccuaaccguugucauguaaua - 41
• Deep sequencing: 163 reads, 10 experiments
• Evidence: experimental; Illumina [5]
• Database links:
  • RNAcentral:URS00003FEF66_6239

Mature sequence cel-miR-246-3p

• Accession: MIMAT0000302
• Previous IDs: cel-miR-246
• Sequence: 61 - uuacauguuucggguaggagc - 81
• Deep sequencing: 52972 reads, 13 experiments
• Evidence: experimental; cloned [1-2], Northern [1], Illumina [3,5], CLIPseq [4]
• Database links:
  • RNAcentral:URS00005641F3_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-246
  • microrna.org:cel-miR-246-3p

References

1. PMID:12672692 "The microRNAs of Caenorhabditis elegans" Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP Genes Dev. 17:991-1008(2003).
2. PMID: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. 127:1193-1207(2006).
3. PMID: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. 10:R54(2009).
4. PMID: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. 17:173-179(2010).
5. PMID:21307183 "Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer" Warf MB, Johnson WE, Bass BL RNA. 17:563-577(2011).