Stem-loop sequence cel-mir-55

Accession

MI0000026 (change log)

Description

Caenorhabditis elegans miR-55 stem-loop

Gene family

MIPF0000270; mir-55

Literature search

3 open access papers mention cel-mir-55
(8 sentences)

Stem-loop

   agauuu    cu   u   a            c   -   u    - uuuu 
5'       ggaa  uaa ggg cucggcagaaac uau cgg uaua c    u
         ||||  ||| ||| |||||||||||| ||| ||| |||| |    g
3'       ccuu  auu ccc gagucgucuuug aua gcc auau g    g
   --uugu    --   c   -            a   u   c    c uaua 

Deep sequencing

485428 reads, 3.1e+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: 13144827-13144924 [-]
• Overlapping transcripts:

  antisense

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

Clustered miRNAs

< 10kb from cel-mir-55

• 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:URS000058CC12_6239
• miRBase Tracker:MI0000026

Mature sequence cel-miR-55-5p

• Accession: MIMAT0020313
• Previous IDs: cel-miR-55*
• Sequence: 23 - cggcagaaaccuaucgguuaua - 44
• Deep sequencing: 8699 reads, 17 experiments
• Evidence: experimental; Illumina [6]
• Database links:
  • RNAcentral:URS0000226147_6239

Mature sequence cel-miR-55-3p

• Accession: MIMAT0000026
• Previous IDs: cel-miR-55
• Sequence: 61 - uacccguauaaguuucugcugag - 83
• Deep sequencing: 476715 reads, 17 experiments
• Evidence: experimental; cloned [1-3], 454 [4], Illumina [5-6]
• Database links:
  • RNAcentral:URS00002DF027_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-55
  • microrna.org:cel-miR-55-3p

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: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).