miRBase entry: aly-MIR399e

Stem-loop aly-MIR399e


Accession
MI0014592
Description
Arabidopsis lyrata aly-MIR399e precursor miRNA
Gene family
MIPF0000015; MIR399


Sequence

agugagagaggaaaacagagauuauguuuugguagaaagcauuacaGGGCGAAUCCUCUAUUGGCAGGggaaguugaugaguguugaucacucuuauauuuucucaucauuuuccucUGCCAAAGGAGAUUUGCCUCGcaaugcuucccuaccguuauggcguuauucauuucuccaauguccaaucuacu
(((.(((..(((.....((((..(((((.((((((.(((((((.(.(((((((((.(((.(((((((((((((.(((((((.....................))))))).))))))))))))).)))))))))))).).)))))))..))))))....)))))........)))).....)))..))))))

Structure
   g   ga   aaaca    ------uu     ---u      -a       a a         C   A             u       uguugauca 
agu aga  gga     gaga        auguu    ugguag  aagcauu c GGGCGAAUC UCU UUGGCAGGggaag ugaugag         c
||| |||  |||     ||||        |||||    ||||||  ||||||| | ||||||||| ||| ||||||||||||| |||||||         u
uca ucu  ccu     cucu        ugcgg    gccauc  uucguaa G UCCGUUUAG AGG AACCGUcuccuuu acuacuc         c
   -   aa   guaac    uuacuuau     uauu      cc       c C         -   A             u       uuuuauauu 


Annotation confidence Not enough data
Do you think this miRNA is real?

Genome context
GL348716.1: 16218063-16218253 [+]
Clustered miRNAs
2 other miRNAs are < 10 kb from aly-MIR399e
Name Accession Chromosome Start End Strand Confidence




Database links

Mature aly-miR399e-5p

Accession MIMAT0017579
Description Arabidopsis lyrata aly-miR399e-5p mature miRNA
Sequence 47 - GGGCGAAUCCUCUAUUGGCAGG - 68
Evidence experimental
Illumina [1], SOLiD [2]

Mature aly-miR399e-3p

Accession MIMAT0017580
Description Arabidopsis lyrata aly-miR399e-3p mature miRNA
Sequence 118 - UGCCAAAGGAGAUUUGCCUCG - 138
Evidence experimental
Illumina [1], SOLiD [2]

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