Stem-loop rno-mir-196b-1

Accession

MI0001152

Description

Rattus norvegicus rno-mir-196b-1 precursor miRNA

Literature search

9 open access papers mention rno-mir-196b-1
(40 sentences)

Sequence

108648 reads, 242 reads per million, 327 experiments

aacuggucggugauuUAGGUAGUUUCCUGUUGUUGGGauccaccuuucucUCGACAGCACGACACUGCCUUCAuuacuucaguug
((((((..((((((..(((((((.((.(((((((((((..........))))))))))).)).)))))))..)))))))))))).

Structure

-      uc      uU       U  C           ucca 
 aacugg  ggugau  AGGUAGU UC UGUUGUUGGGa    c
 ||||||  ||||||  ||||||| || |||||||||||     
 uugacu  ucauuA  UCCGUCA AG ACGACAGCUcu    c
g      --      CU       C  C           cuuu 

Annotation confidence High

Comments

miR-196b is predicted based on sequence homology to miR-196a [1]. Yekta et al. report that miR-196 miRNAs are expressed from HOX gene clusters in mammals, and that HOX genes in these clusters are targets of miR-196. Indeed, HOXB8 mRNA was shown to be a natural target for miR-196-directed cleavage through a perfectly complementary miR-target site. Other HOX genes have imperfect miR-196 complementary sites indicative of regulation by translational repression [1]. The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies [2]. The ends of the miRNA may be offset with respect to previous annotations.

Genome context

chr4: 82199056-82199140 [-]

Mature rno-miR-196b-5p

• Accession: MIMAT0001082
• Description: Rattus norvegicus rno-miR-196b-5p mature miRNA
• Sequence: 16 - UAGGUAGUUUCCUGUUGUUGGG - 37
• Evidence: experimental ; cloned [2], SOLiD [3]

Mature rno-miR-196b-3p

• Accession: MIMAT0017171
• Description: Rattus norvegicus rno-miR-196b-3p mature miRNA
• Sequence: 51 - UCGACAGCACGACACUGCCUUCA - 73
• Evidence: experimental ; SOLiD [3]

References

1. PubMed ID: 17604727
   A mammalian microRNA expression atlas based on small RNA library sequencing
   "Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M"
   "Cell (2007) 129:1401-1414


2. PubMed ID: 15105502
   MicroRNA-directed cleavage of HOXB8 mRNA
   "Yekta S, Shih IH, Bartel DP"
   "Science (2004) 304:594-596


3. PubMed ID: 20403161
   Small RNA expression and strain specificity in the rat
   Linsen SE, de Wit E, de Bruijn E, Cuppen E
   BMC Genomics (2010) 11:249