Stem-loop sequence dre-mir-196a-1

AccessionMI0001372
Previous IDsdre-mir-196a
DescriptionDanio rerio miR-196a-1 stem-loop
Gene family MIPF0000031; mir-196
Community annotation

This text is a summary paragraph taken from the Wikipedia entry entitled mir-196_microRNA_precursor_family. miRBase and Rfam are facilitating community annotation of microRNA families and entries in Wikipedia. Read more ...

miR-196 is a non-coding RNA called a microRNA that has been shown to be expressed in human (MI0000238, MI0000279) and mouse (MI0000552, MI0000553). miR-196 appears to be a vertebrate specific microRNA and has now been predicted or experimentally confirmed in a wide range of vertebrate species (MIPF0000031). In many species the miRNA appears to be expressed from intergenic regions in HOX gene clusters. The hairpin precursors are predicted based on base pairing and cross-species conservation—their extents are not known. In this case the mature sequence is excised from the 5' arm of the hairpin. It has been suggested that a rare SNP (rs11614913) that overlaps hsa-mir-196a2 has been found to be associated with non-small cell lung carcinoma.

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Stem-loop
   ------------c   c     gu        u          a          auu    
5'              gcg ggcug  gcgugguu agguaguuuc uguuguuggg   ggc 
                ||| |||||  |||||||| |||||||||| ||||||||||   || u
3'              ugc uugac  ugcauuag uccgucaaag acaacagcuc   ccu 
   cgggaacuacuuc   -     --        u          a          ggu    
Get sequence
Deep sequencing
4063 reads, 537 reads per million, 4 experiments
Confidence
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Genome context
Coordinates (Zv9) Overlapping transcripts
23: 36139635-36139740 [+]
sense
OTTDART00000059220 ; hoxc3a-004; intron 1
ENSDART00000154825 ; hoxc3a-004; intron 1
ENSDART00000053295 ; hoxc10a-201; intron 2
antisense
OTTDART00000059827 ; hoxc10a-001; exon 1
ENSDART00000153674 ; mir196a-1-001; exon 1
Database links

Mature sequence dre-miR-196a-5p

Accession MIMAT0001276
Previous IDsdre-miR-196a
Sequence

21 - 

uagguaguuucauguuguuggg

 - 42

Get sequence
Deep sequencing3632 reads, 4 experiments
Evidence experimental; cloned [1]

References

1
PMID:12624257 "Vertebrate microRNA genes" Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP Science. 299:1540(2003).
2
PMID:15937218 "The developmental miRNA profiles of zebrafish as determined by small RNA cloning" Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T Genes Dev. 19:1288-1293(2005).