Stem-loop sequence cel-mir-57

Accession

MI0000028 (change log)

Description

Caenorhabditis elegans miR-57 stem-loop

Gene family

MIPF0000271; mir-57

Literature search

6 open access papers mention cel-mir-57
(226 sentences)

Stem-loop

   ----------a   aca  c    c    c     a  g    g     u   a 
5'            ucg   ug ucgu uacc uguag uc agcu ugugu uga a
              |||   || |||| |||| ||||| || |||| ||||| ||| c
3'            agc   ac agca gugg acauc ag ucga gcaca acu a
   aaguauuuaga   caa  a    c    a     -  a    -     u   a 

Deep sequencing

282903 reads, 1.6e+03 reads per million, 17 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (WBcel235; GCA_000002985.3): chrII: 7850499-7850597 [-]
• Overlapping transcripts:

  antisense

  T09A5.19 ; T09A5.19; exon 1

Database links

• RNAcentral:URS00001F3FDF_6239
• Rfam:mir-10
• miRBase Tracker:MI0000028

Mature sequence cel-miR-57-5p

• Accession: MIMAT0000029
• Previous IDs: cel-miR-57
• Sequence: 16 - uacccuguagaucgagcugugugu - 39
• Deep sequencing: 281690 reads, 17 experiments
• Evidence: experimental; cloned [1-2], 454 [3], Illumina [4,6], CLIPseq [5]
• Database links:
  • RNAcentral:URS00001FCAC5_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-57
  • microrna.org:cel-miR-57-5p

Mature sequence cel-miR-57-3p

• Accession: MIMAT0020314
• Previous IDs: cel-miR-57*
• Sequence: 55 - acgagcuagacuacaaggugca - 76
• Deep sequencing: 1212 reads, 16 experiments
• Evidence: experimental; Illumina [6]
• Database links:
  • RNAcentral:URS00003C68FF_6239

References

1. PMID:11679671 "An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans" Lau NC, Lim LP, Weinstein EG, Bartel DP Science. 294:858-862(2001).
2. 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).
3. 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).
4. 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).
5. 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).
6. 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).