ABOUT THIS RECORDspecies: Caenorhabditis elegans
miRNA family: mir-239
source: miRBase, original name: cel-mir-239b (MI0000315)
Taxonomy by NCBI:
Caenorhabditis elegans Caenorhabditis Peloderinae Rhabditidae Rhabditoidea Rhabditida Chromadorea Nematoda Pseudocoelomata Bilateria Eumetazoa Metazoa Fungi/Metazoa group Eukaryota cellular organisms
SEQUENCE & STRUCTURE| miRNA TTTGTACTACACAAAAGTACTG miRNA* GCACTTTTGTGGTGTGCAAAAA mismatches: 3 bulges: 0 |
pre-miRNA
GCGACAGATGCAATTTTTGTACTACACAAAAGTACTGGTCATTTAAGTTGAGGCTCAGCACTTTTGTGGTGTGCAAAAATGGCAAGTTGCTTTTATCT
dot-bracket secondary structure
(((((...(((.((((((((((..(((((((((.((((((.((......))))).))).)))))))))..)))))))))).))).)))))........
SIMILARITIES
MORE
miRNEST target predictions: none
non-miRNEST targets: none
HuntMi prediction: true miRNA
additional data
download this record
evidence: cloned, Solexa, CLIPseq
deep sequencing data evidence
references
[1] Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB, RNA. 10:1309-1322(2004)., "Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification"
[2] Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP, Genes Dev. 17:991-1008(2003)., "The microRNAs of Caenorhabditis elegans"
[3] Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP, Cell. 127:1193-1207(2006)., "Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans"
[4] Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW, Nat Struct Mol Biol. 17:173-179(2010)., "Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans"
[5] Kato M, de Lencastre A, Pincus Z, Slack FJ, Genome Biol. 10:R54(2009)., "Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development"
GCGACAGATGCAATTTTTGTACTACACAAAAGTACTGGTCATTTAAGTTGAGGCTCAGCACTTTTGTGGTGTGCAAAAATGGCAAGTTGCTTTTATCT
dot-bracket secondary structure
(((((...(((.((((((((((..(((((((((.((((((.((......))))).))).)))))))))..)))))))))).))).)))))........
SIMILARITIES| miRBase cbr-mir-239b: 0.00000008 PMRD no hits microPC no hits | UniProt no hits RFAM mir-239: 1e-49 |
MOREmiRNEST target predictions: none
non-miRNEST targets: none
HuntMi prediction: true miRNA
additional data
download this record
evidence: cloned, Solexa, CLIPseq
deep sequencing data evidence
references
[1] Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB, RNA. 10:1309-1322(2004)., "Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification"
[2] Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP, Genes Dev. 17:991-1008(2003)., "The microRNAs of Caenorhabditis elegans"
[3] Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP, Cell. 127:1193-1207(2006)., "Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans"
[4] Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW, Nat Struct Mol Biol. 17:173-179(2010)., "Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans"
[5] Kato M, de Lencastre A, Pincus Z, Slack FJ, Genome Biol. 10:R54(2009)., "Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development"
