miRBase entry: ath-MIR169e

Stem-loop ath-MIR169e


Accession
MI0000979
Description
Arabidopsis thaliana ath-MIR169e precursor miRNA
Gene family
MIPF0000037; MIR169_2

Literature search
34 open access papers mention ath-MIR169e
(156 sentences)

Sequence

ugaugaugaugaugagucacuaauuaauuguaucauagagucuugcauggaaaaauagaaaaugagauUGAGCCAAGGAUGACUUGCCGauuuucucaacgaaucuuacugauuaugguauccggcaaguugacuuuggcucuguuuccuucccuucuuuucgaugucaaacucuagauaccuaaccacauaucauauauaucaucaucauucauca
(((((((((((((((..............(((((.((((((.((((((.(((((..((..((.(((((.(((((((((..(((((((((..(...(((...((((.....)))).))).)..)))))))))..))))))))).))))).))..))..))))).))).))))))))))))))........((((...)))).))))))))).))))))

Structure
      -         ------gucacuaauuaauu     a      c   -   g     au  aa  u     U         AU         au uuc   acg    u 
ugauga ugaugauga                    guauc uagagu uug cau gaaaa  ag  aa gagau GAGCCAAGG  GACUUGCCG  u   uca   aauc u
|||||| |||||||||                    ||||| |||||| ||| ||| |||||  ||  || ||||| |||||||||  |||||||||  |   |||   |||| a
acuacu acuacuacu                    cauag aucuca aac gua cuuuu  uc  uu cuuug cucgguuuc  uugaacggc  a   ggu   uuag c
      u         auauauacuauacaccaauc     -      -   u   g     cu  cc  c     u         ag         cu --u   --a    u 


Annotation confidence Not enough data
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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
chr1: 20041518-20041734 [+]
Clustered miRNAs
1 other miRNA is < 10 kb from ath-MIR169e
Name Accession Chromosome Start End Strand Confidence




Database links

Mature ath-miR169e

Accession MIMAT0000909
Description Arabidopsis thaliana ath-miR169e mature miRNA
Sequence 69 - UGAGCCAAGGAUGACUUGCCG - 89
Evidence experimental
cloned [2], 454 [3-4], MPSS [3], Illumina [5]

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