miRBase entry: rno-mir-196b-1

Stem-loop rno-mir-196b-1


Accession
MI0001152
Description
Rattus norvegicus rno-mir-196b-1 precursor miRNA
Gene family
MIPF0000031; mir-196

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
Do you think this miRNA is real?
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 [-]

Database links

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