miRBase entry: aly-MIR162a

Stem-loop aly-MIR162a


Accession
MI0014525
Description
Arabidopsis lyrata aly-MIR162a precursor miRNA
Gene family
MIPF0000127; MIR162_1


Sequence

81 reads, 2824 reads per million, 1 experiments
gauucgggaaauuuuauguuucuuugccauuuuuuuuggaguuuaguuggaaaaagagugagagucgcuGGAGGCAGCGGUUCAUCGAUCucuuccugggaacgaauauauaaauauugaaaaagcaugaauagaUCGAUAAACCUCUGCAUCCAGcguuugccucuuuaucuuuguuauuggcuucaauuuuuuugguuuuugaaaaaagugagggaaaacagaguc
(((((......((((((.((((...((((......((((((((.....(((.((((((.(.(((.(((((((.((((.((((.((((((((.(((.((......(((((....))))).......)).))).)))))))).)))).)))).)))))))))).))))))).)))........))))))))......))))....))))...)))))).......)))))

Structure
     -gggaaa      --g    -uuu    uuuuuu        ---uaguu   a      u a   u       G    C    C        c   c  -ggaacg     a 
gauuc       uuuuau   uuuc    gcca      uuggaguu        gga aaagag g gag cgcuGGA GCAG GGUU AUCGAUCu uuc ug       aauau u
|||||       ||||||   ||||    ||||      ||||||||        ||| |||||| | ||| ||||||| |||| |||| |||||||| ||| ||       |||||  
cugag       ggagug   aaag    uggu      aacuucgg        ucu uuucuc c uuu gcGACCU CGUC CCAA UAGCUaga aag ac       uuaua a
     acaaaag      aaa    uuuu    uuuuuu        uuauuguu   a      - g   -       A    U    A        u   u  gaaaaag     a 


Annotation confidence Not enough data
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Genome context
GL348718.1: 3221153-3221380 [-]
Clustered miRNAs
1 other miRNA is < 10 kb from aly-MIR162a
Name Accession Chromosome Start End Strand Confidence




Database links

Mature aly-miR162a-5p

Accession MIMAT0017445
Description Arabidopsis lyrata aly-miR162a-5p mature miRNA
Sequence 70 - GGAGGCAGCGGUUCAUCGAUC - 90
Evidence experimental
Illumina [1], SOLiD [2]

Mature aly-miR162a-3p

Accession MIMAT0017446
Description Arabidopsis lyrata aly-miR162a-3p mature miRNA
Sequence 136 - UCGAUAAACCUCUGCAUCCAG - 156
Evidence experimental
Illumina [1], SOLiD [2]
Database links

References

  1. PubMed ID: 20407027
    MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
    "Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC"
    "Plant Cell (2010) 22:1074-1089

  2. PubMed ID: 20407023
    Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus
    "Ma Z, Coruh C, Axtell MJ"
    "Plant Cell (2010) 22:1090-1103