Stem-loop sequence cel-mir-250

Accession

MI0000326 (change log)

Description

Caenorhabditis elegans miR-250 stem-loop

Gene family

MIPF0000283; mir-250

Literature search

1 open access papers mention cel-mir-250
(1 sentences)

Stem-loop

   ----a    cuuc g    c   uu      c  c     c  -   aaca 
5'      gggu    g acca gcc  caguug cu gugau cg cca    c
        ||||    | |||| |||  |||||| || ||||| || |||    a
3'      ccca    c uggu cgg  gucaac ga cacua gc ggu    a
   uuuua    ugcu g    a   uu      u  -     a  a   aaau 

Deep sequencing

498312 reads, 3.24e+03 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 [2].

Genome context

• Coordinates (WBcel235; GCA_000002985.3): chrV: 11769917-11770015 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from cel-mir-250

• cel-mir-61: chrV: 11770060-11770156 [-]
• cel-mir-250: chrV: 11769917-11770015 [-]

Database links

• RNAcentral:URS00004A6A16_6239
• miRBase Tracker:MI0000326

Mature sequence cel-miR-250-5p

• Accession: MIMAT0020339
• Previous IDs: cel-miR-250*
• Sequence: 18 - ccuucaguugccucgugauccg - 39
• Deep sequencing: 1610 reads, 16 experiments
• Evidence: experimental; Illumina [5]
• Database links:
  • RNAcentral:URS00001AD372_6239

Mature sequence cel-miR-250-3p

• Accession: MIMAT0000306
• Previous IDs: cel-miR-250
• Sequence: 60 - aaucacagucaacuguuggc - 79
• Deep sequencing: 496648 reads, 17 experiments
• Evidence: experimental; Northern [1-2], PCR [1], Illumina [3,5], CLIPseq [4]
• Database links:
  • RNAcentral:URS0000562C41_6239
• Predicted targets:
  • TargetScanWorm:cel-miR-250
  • microrna.org:cel-miR-250-3p

References

1. 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).
2. 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).
3. 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).
4. 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).
5. 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).