Stem-loop sequence cel-mir-42

Accession

MI0000013 (change log)

Description

Caenorhabditis elegans miR-42 stem-loop

Gene family

MIPF0000233; mir-42

Literature search

7 open access papers mention cel-mir-42
(16 sentences)

Stem-loop

   ----uucgc                 u   uuuu        ---uu  cuu 
5'          ggaccuuuguggguguu gcu    cggugaag     gu   c
            ||||||||||||||||| |||    ||||||||     ||    
3'          ccuggagacaucuacaa ugg    gccacuuc     cg   c
   ggggaaaaa                 u   ----        uucuu  aug 

Deep sequencing

70468 reads, 600 reads per million, 17 experiments

Confidence

Annotation confidence: high

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Comments

The extents of the dominant mature miRNA species are adjusted here in accordance with a large scale cloning and sequencing study [5].

Genome context

• Coordinates (WBcel235; GCA_000002985.3): chrII: 11889811-11889905 [+]
• Overlapping transcripts:

  antisense

  ZK930.12 ; ZK930.12; exon 1

Clustered miRNAs

< 10kb from cel-mir-42

• cel-mir-45: chrII: 11880944-11881039 [-]
• cel-mir-42: chrII: 11889811-11889905 [+]
• cel-mir-43: chrII: 11889910-11890007 [+]
• cel-mir-44: chrII: 11890023-11890118 [+]

Database links

• RNAcentral:URS00000D1CA7_6239
• miRBase Tracker:MI0000013

Mature sequence cel-miR-42-5p

• Accession: MIMAT0015095
• Previous IDs: cel-miR-42*
• Sequence: 14 - guggguguuugcuuuuucggugaag - 38
• Deep sequencing: 2455 reads, 16 experiments
• Evidence: experimental; CLIPseq [7]
• Database links:
  • RNAcentral:URS00002A1423_6239
• Predicted targets:
  • microrna.org:cel-miR-42-5p

Mature sequence cel-miR-42-3p

• Accession: MIMAT0000013
• Previous IDs: cel-miR-42
• Sequence: 60 - ucaccggguuaacaucuacaga - 81
• Deep sequencing: 68005 reads, 17 experiments
• Evidence: experimental; cloned [1-4], Northern [1], 454 [5], Illumina [6], CLIPseq [7]
• Database links:
  • RNAcentral:URS00001ED05D_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-42
  • microrna.org:cel-miR-42-3p

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:11679672 "An extensive class of small RNAs in Caenorhabditis elegans" Lee RC, Ambros V Science. 294:862-864(2001).
3. 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).
4. 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).
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).