Stem-loop sequence ath-MIR156f

AccessionMI0000183
DescriptionArabidopsis thaliana miR156f stem-loop
Gene family MIPF0000008; MIR156
Community annotation

This text is a summary paragraph taken from the Wikipedia entry entitled mir-156_microRNA_precursor. miRBase and Rfam are facilitating community annotation of microRNA families and entries in Wikipedia. Read more ...

MicroRNA (miRNA) precursor mir-156 is a family of plant non-coding RNA. This microRNA has now been predicted or experimentally confirmed in a range of plant species (MIPF0000008). Animal miRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. In plants the precursor sequences may be longer, and the carpel factory (caf) enzyme appears to be involved in processing. In this case the mature sequence comes from the 5' arm of the precursor, and both Arabidopsis thaliana and rice genomes contain a number of related miRNA precursors which give rise to almost identical mature sequences. The extents of the hairpin precursors are not generally known and are estimated based on hairpin prediction. The products are thought to have regulatory roles through complementarity to mRNA.

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Stem-loop
      u  u    aauu  ---u      a  -                    ggcu   uu    auuug 
5' gag gg gagg    ga    ggugac ga agagagugagcacacauggu    uuc  gcau     a
   ||| || ||||    ||    |||||| || ||||||||||||||||||||    |||  ||||     a
3' cuc cc cucc    cu    ccacug cu ucucucacucguguguaucg    aag  cgua     g
      -  u    cucu  uccc      c  a                    ----   uu    ccuug 
Get sequence
Deep sequencing
12514 reads, 2.17e+04 reads per million, 8 experiments
Confidence Annotation confidence: high
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Comments

MIR156f is thought to target 10 mRNAs coding for proteins containing the Squamosa-promoter Binding Protein (SBP) box [1]. The complementary sites are downstream of this conserved domain, within a poorly conserved protein-coding context or the 3' UTR [2].

Genome context
Coordinates (TAIR10) Overlapping transcripts
chr5: 9136106-9136237 [+]
intergenic
Database links

Mature sequence ath-miR156f-5p

Accession MIMAT0000171
Previous IDsath-miR156f
Sequence

21 - 

ugacagaagagagugagcac

 - 40

Get sequence
Deep sequencing10392 reads, 8 experiments
Evidence experimental; cloned [1,3], Northern [1], 5'RACE [3], 454 [4-5], MPSS [4], Illumina [6]
Validated targets

Mature sequence ath-miR156f-3p

Accession MIMAT0031869
Sequence

92 - 

gcucacucucuauccgucacc

 - 112

Get sequence
Deep sequencing26 reads, 2 experiments
Evidence not experimental

References

1
PMID:12101121 "MicroRNAs in plants" Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP Genes Dev. 16:1616-1626(2002).
2
PMID:12202040 "Prediction of plant microRNA targets" Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP Cell. 110:513-520(2002).
3
PMID:16040653 "Expression of Arabidopsis MIRNA genes" Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC Plant Physiol. 138:2145-2154(2005).
4
PMID:16954541 "MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant" Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC Genome Res. 16:1276-1288(2006).
5
PMID:17182867 "A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana" Rajagopalan R, Vaucheret H, Trejo J, Bartel DP Genes Dev. 20:3407-3425(2006).
6
PMID:19815687 "Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis" Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson IW J Exp Bot. 61:165-177(2010).