Stem-loop ath-MIR169j

Accession

MI0000984

Description

Arabidopsis thaliana ath-MIR169j precursor miRNA

Literature search

35 open access papers mention ath-MIR169j
(160 sentences)

Sequence

95850 reads, 1385.0 reads per million, 166 experiments

gaguauaaugaggaagagaggucuaacauggcgaaaagagucauguuuagUAGCCAAGGAUGACUUGCCUGAucuuuuucaccuccaugauucaauuuguaauucauggguuuuggauuauuauacauucaaaaguauaauaauuugaaaucauguugaaucuugcggguuagguuucAGGCAGUCUCCUUGGCUAUCUugacaugcuuuuuucauucacg
....................(((......)))((((((((.((((((.((((((((((((.((((.((((((....(((.((((.((.((((((((............((((((((((((((((((........))))))))))))))))))..)))))))).)).)))).)))..)))))))))))))))))))).)).)))))))))))))).......

Structure

gaguauaaugaggaagagaggucuaacauggc        u      u  -          U    U      ucuu   c    c  u        uuguaauucaug                  auu 
                                gaaaagag cauguu ag UAGCCAAGGA GACU GCCUGA    uuu accu ca gauucaau            gguuuuggauuauuauac   c
                                |||||||| |||||| || |||||||||| |||| ||||||    ||| |||| || ||||||||            ||||||||||||||||||    
                                cuuuuuuc guacag UC AUCGGUUCCU CUGA CGGAcu    gga uggg gu cuaaguug            cuaaaguuuaauaauaug   a
-------------------------gcacuua        -      u  U          -    -      --uu   u    c  u        ----------ua                  aaa 

Annotation confidence High

Comments

This sequence is a predicted paralogue of the previously identified miR169 family [1], later experimentally verified [2]. It is predicted to target mRNAs coding for the CCAAT Binding Factor (CBF) and HAP2-like transcription factors.

Genome context

chr3: 9872333-9872553 [-]

Clustered miRNAs

5 other miRNAs are < 10 kb from ath-MIR169j

Mature ath-miR169j-5p

• Accession: MIMAT0000915
• Description: Arabidopsis thaliana ath-miR169j-5p mature miRNA
• Sequence: 51 - UAGCCAAGGAUGACUUGCCUGA - 72
• Evidence: experimental ; cloned [2], 454 [3-4], MPSS [3], Illumina [5]

Mature ath-miR169j-3p

• Accession: MIMAT0053813
• Description: Arabidopsis thaliana ath-miR169j-3p mature miRNA
• Sequence: 179 - AGGCAGUCUCCUUGGCUAUCU - 199
• Evidence: experimental ; unknown

References

1. PubMed ID: 16040653
   Expression of Arabidopsis MIRNA genes
   "Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC"
   "Plant Physiol (2005) 138:2145-2154


2. PubMed ID: 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 (2006) 16:1276-1288


3. PubMed ID: 17182867
   A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
   "Rajagopalan R, Vaucheret H, Trejo J, Bartel DP"
   "Genes Dev (2006) 20:3407-3425


4. PubMed ID: 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 (2010) 61:165-177


5. PubMed ID: 15200956
   Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
   "Jones-Rhoades MW, Bartel DP"
   "Mol Cell (2004) 14:787-799