Stem-loop sequence cel-mir-56

Accession

MI0000027 (change log)

Description

Caenorhabditis elegans miR-56 stem-loop

Gene family

MIPF0001735; mir-56

Literature search

5 open access papers mention cel-mir-56
(7 sentences)

Stem-loop

   -ga  -  gu   u     ug     uc    u     ugu   -   ucc 
5'    gc ca  guc guucu  gcgga  cauu ugggu   acc uca   u
      || ||  ||| |||||  |||||  |||| |||||   ||| |||   a
3'    cg gu  cag caaga  cgccu  guaa gccca   ugg agu   a
   cca  u  --   c     gu     uu    u     ---   c   uua 

Deep sequencing

555551 reads, 2.57e+03 reads per million, 17 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (WBcel235; GCA_000002985.3): chrX: 13144691-13144787 [-]
• Overlapping transcripts:

  antisense

  F09A5.3b ; F09A5.3b; intron 1

Clustered miRNAs

< 10kb from cel-mir-56

• cel-mir-54: chrX: 13144996-13145094 [-]
• cel-mir-55b: chrX: 13144830-13144919 [+]
• cel-mir-55: chrX: 13144827-13144924 [-]
• cel-mir-56: chrX: 13144691-13144787 [-]

Database links

• RNAcentral:URS00002575E8_6239
• miRBase Tracker:MI0000027

Mature sequence cel-miR-56-5p

• Accession: MIMAT0000027
• Previous IDs: cel-miR-56*
• Sequence: 18 - uggcggauccauuuuggguuguacc - 42
• Deep sequencing: 1438 reads, 14 experiments
• Evidence: experimental; cloned [1], CLIPseq [7]
• Database links:
  • RNAcentral:URS0000784E40_6239
• Predicted targets:
  • microrna.org:cel-miR-56-5p

Mature sequence cel-miR-56-3p

• Accession: MIMAT0000028
• Previous IDs: cel-miR-56
• Sequence: 61 - uacccguaauguuuccgcugag - 82
• Deep sequencing: 553388 reads, 17 experiments
• Evidence: experimental; cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]
• Database links:
  • RNAcentral:URS0000374B7C_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-56
  • microrna.org:cel-miR-56-3p

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:12747828 "MicroRNAs and other tiny endogenous RNAs in C. elegans" Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D Curr Biol. 13:807-818(2003).
4. PMID:12769849 "Computational and experimental identification of C. elegans microRNAs" Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J Mol Cell. 11:1253-1263(2003).
5. 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).
6. 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).
7. 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).