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

ptc-miR171l-5p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UGUGAUAUUGGUCCGGCUCAUC

miRBase

Precursor miRNA Sequence(5'-3')

GGAGAAGUAGACACGGUGUGAUAUUGGUCCGGCUCAUCUUCUGUGCAUAAGCAUCUGAAGUUCUUCACUCAUGAAGACGAGCCGAAUCAAUAUCACUCUUGUAUGCUUCUUC

miRBase

Precursor miRNA Structure(5'-3') 

         G   C  U           C      AUCUUCUGUGCAUAAGCAUC 
GGAGAAGUA ACA GG GUGAUAUUGGU CGGCUC                    U
||||||||| ||| || ||||||||||| ||||||                    G
CUUCUUCGU UGU UC CACUAUAACUA GCCGAG                    G
         A   -  U           A      CAGAAGUACUCACUUCUUGA

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

zma-miR171k-5p      --UGGUAUUGUUUCGGCUCAUGU
zma-miR171h-5p      --UGGUAUUGUUUCGGCUCAUGU
vvi-miR479          UGUGGUAUUGGUUCGGCUCAUC-
csi-miR171b-5p      UGUGAUAUUGGUUCGGCUCAUC-
ppe-miR171d-5p      UGUGAUAUUGGUUCGGUUCAUA-
ptc-miR171l-5p      UGUGAUAUUGGUCCGGCUCAUC-
sbi-miR171f         -AUGAGCCGAACCAAUAUCACU-
lus-miR171h         -AUGAGCCGAACCAAUAUCACU-
vvi-miR171g         -UUGAGCCGAACCAAUAUCACC-
                      **             ***