Stem-loop sequence cel-mir-54

Accession

MI0000025 (change log)

Description

Caenorhabditis elegans miR-54 stem-loop

Gene family

MIPF0000874; mir-54

Literature search

1 open access papers mention cel-mir-54
(9 sentences)

Stem-loop

     g   cgc         a    -    -  cg   a a   uug    u 
5' gu agu   gcucugacu ggau auga ga  acg g aca   cuuu u
   || |||   ||||||||| |||| |||| ||  ||| | |||   ||||  
3' ca ucg   cgggacuga ccua uacu cu  ugc c ugu   gaaa u
     g   -au         g    a    u  aa   c a   uca    a 

Deep sequencing

241628 reads, 3.14e+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: 13144996-13145094 [-]
• Overlapping transcripts:

  antisense

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

Clustered miRNAs

< 10kb from cel-mir-54

• 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:URS00001D3EF3_6239
• miRBase Tracker:MI0000025

Mature sequence cel-miR-54-5p

• Accession: MIMAT0020773
• Sequence: 19 - aggauaugagacgacgagaaca - 40
• Deep sequencing: 142657 reads, 17 experiments
• Evidence: experimental; Illumina [7]
• Database links:
  • RNAcentral:URS000043FDBE_6239

Mature sequence cel-miR-54-3p

• Accession: MIMAT0000025
• Previous IDs: cel-miR-54
• Sequence: 61 - uacccguaaucuucauaauccgag - 84
• Deep sequencing: 98962 reads, 17 experiments
• Evidence: experimental; cloned [1-3], 454 [4], Illumina [5,7], CLIPseq [6]
• Database links:
  • RNAcentral:URS000028E50A_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-54
  • microrna.org:cel-miR-54-3p

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: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).
5. 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).
6. 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).
7. 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).