TarDB: A miRNA Target Database in Plants.


TarDB employs cross-species conservation filter, degradome and sRNA-seq data to identify high-confidence miRNA targets in plants.



miRNA ID

bdi-miR160a-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

GCGUGCGAGGAGCCAAGCAUG

miRBase

Precursor miRNA Sequence(5'-3')

UGCGGAAGGAGGUGAAAAAAAAAAUGGGAUAUGCCUGGCUCCCUGUAUGCCACUCGCGUAGCUGCCAACAACUCAGUUUGAGCUCCCCCGGCCCAAACGCAAACGUUGGCUCUACCGCGGAUGGCGUGCGAGGAGCCAAGCAUGACCGUCUCUCCCCCUCCCUCCCUCUCUCCCU

miRBase

Precursor miRNA Structure(5'-3') 

---UGC   A     U  -AAAAAAAA    GA     C       C         C     -   CU      AACUCA     A   C 
      GGA GGAGG GA         AUGG  UAUGC UGGCUCC UGUAUGCCA UCGCG UAG  GCCAAC      GUUUG GCU C
      ||| ||||| ||         ||||  ||||| ||||||| ||||||||| ||||| |||  ||||||      ||||| ||| C
      UCU CCUCC CU         UGCC  GUACG ACCGAGG GCGUGCGGU GGCGC AUC  CGGUUG      CAAAC CGG G
UCCCUC   C     -  CCCCCUCUC    -A     A       A         A     C   -U      CAAACG     C   C

Homologous Mature miRNAs   miRNAs are clustered by CD-HIT with sequence identity of >85% and word size of 5.

osa-miR160e-3p      GCGUGCGAGGUGCCAAGCAUG
zma-miR160f-3p      GCGUGCGAGGUGCCAGGCAUG
bdi-miR160a-3p      GCGUGCGAGGAGCCAAGCAUG
zma-miR160d-3p      GCGUGCGUGGAGCCAAGCAUG
csi-miR160c-3p      GCGUGCGAGGAGCCAUGCAUG
zma-miR160a-3p      GCGUGCAAGGGGCCAAGCAUG
                    ******  ** **** *****