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

csi-miR171b-5p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

UGUGAUAUUGGUUCGGCUCAUC

miRBase

Precursor miRNA Sequence(5'-3')

CAUGGAGAGCAAAAGCACCUUCUUGGCGAUUGGAGAAGUAGACAUGGUGUGAUAUUGGUUCGGCUCAUCUUAAUUAAUAGAUUAAUAUUUCAGCCCUUAAGGUUCUUACAUGUAUAUAUCUAGACGAGCCGAAUCAAUAUCACUCUUGUAUGCUUCUUUCUUUUGAUU

miRBase

Precursor miRNA Structure(5'-3') 

CAUGGAGAGCAAAAGCACCUUCUUGG   UU   -      G   U  U                  A   UAAUUAAU    UA    ----UUC    C 
                          CGA  GGA GAAGUA ACA GG GUGAUAUUGGUUCGGCUC UCU        AGAU  AUAU       AGCC U
                          |||  ||| |||||| ||| || |||||||||||||||||| |||        ||||  ||||       |||| U
                          GUU  CUU CUUCGU UGU UC CACUAUAACUAAGCCGAG AGA        UCUA  UAUG       UUGG G
-----------------------UUA   UU   U      A   -  U                  C   --------    UA    UACAUUC    A

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-
                      **             ***