Stem-loop sequence cel-mir-252

Accession

MI0000328 (change log)

Description

Caenorhabditis elegans miR-252 stem-loop

Gene family

MIPF0000285; mir-252

Literature search

2 open access papers mention cel-mir-252
(47 sentences)

Stem-loop

   uccaggg   --uc        a       u  u  c c      cc   agu 
5'        guc    uuucaguu uaaguag ag gc g agguaa  gcc   c
          |||    |||||||| ||||||| || || | ||||||  |||   u
3'        uag    aaaguuaa auucguc uc cg c uccauu  cgg   a
   ------g   uuau        a       u  -  u a      --   aaa 

Deep sequencing

96764 reads, 394 reads per million, 17 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): chrII: 11446863-11446960 [-]
• Overlapping transcripts:

  antisense

  W02B12.17 ; W02B12.17; exon 1

  W02B12.13a ; W02B12.13a; intron 4

  W02B12.13b ; W02B12.13b; intron 4

Database links

• RNAcentral:URS000033AD3A_6239
• miRBase Tracker:MI0000328

Mature sequence cel-miR-252-5p

• Accession: MIMAT0000308
• Previous IDs: cel-miR-252
• Sequence: 21 - auaaguaguagugccgcagguaa - 43
• Deep sequencing: 96624 reads, 17 experiments
• Evidence: experimental; Northern [1-2], PCR [1], Illumina [3,5], CLIPseq [4]
• Database links:
  • RNAcentral:URS0000184C12_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-252
  • microrna.org:cel-miR-252-5p

Mature sequence cel-miR-252-3p

• Accession: MIMAT0020340
• Previous IDs: cel-miR-252*
• Sequence: 60 - cuuaccuacugccuucugc - 78
• Deep sequencing: 134 reads, 13 experiments
• Evidence: experimental; Illumina [5]
• Database links:
  • RNAcentral:URS00005914E5_6239

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).