Stem-loop sequence cel-mir-49

Accession

MI0000020 (change log)

Description

Caenorhabditis elegans miR-49 stem-loop

Gene family

MIPF0000237; mir-49

Literature search

3 open access papers mention cel-mir-49
(6 sentences)

Stem-loop

   uuuugaaaaa    a     c       g     au     c  ag aau 
5'           gacc ccguc gcaguuu uugug  gugcu ca  c   c
             |||| ||||| ||||||| |||||  ||||| ||  |    
3'           uugg gguag cgucgaa agcac  cacga gu  g   a
   ---uuuaguc    a     a       g     --     a  cu agu 

Deep sequencing

51177 reads, 418 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: 9989282-9989378 [+]
• Overlapping transcripts:

  intergenic

Database links

• RNAcentral:URS000023E371_6239
• miRBase Tracker:MI0000020

Mature sequence cel-miR-49-5p

• Accession: MIMAT0020309
• Previous IDs: cel-miR-49*
• Sequence: 21 - cgcaguuuguugugaugugcucc - 43
• Deep sequencing: 3089 reads, 15 experiments
• Evidence: experimental; Illumina [6]
• Database links:
  • RNAcentral:URS00003A2D13_6239

Mature sequence cel-miR-49-3p

• Accession: MIMAT0000020
• Previous IDs: cel-miR-49
• Sequence: 61 - aagcaccacgagaagcugcaga - 82
• Deep sequencing: 48078 reads, 17 experiments
• Evidence: experimental; cloned [1-2], 454 [3], Illumina [4,6], CLIPseq [5]
• Database links:
  • RNAcentral:URS00003E7140_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-49
  • microrna.org:cel-miR-49-3p

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: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).