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-miR164d-3p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

CACGCGCUCCCCUUCUCCAAC

miRBase

Precursor miRNA Sequence(5'-3')

UAUUGUUCUAUUGGGUGAGUAGCUCCUUGCUGGAGAAGCAGGGCACGUGCAAACACCACUUUGGCUCCUUUCGGUUUCAGAAUUGCCACUAAAUCCUUUGCACGCGCUCCCCUUCUCCAACAUGGGUUCCUCACCUUUCCUGAUCUCUCAC

miRBase

Precursor miRNA Structure(5'-3') 

--UAUU U  -UAUU       U   U  U  C        CA    A        CACCACUU    UCCU   GG 
      G UC     GGGUGAG AGC CC UG UGGAGAAG  GGGC CGUGCAAA        UGGC    UUC  U
      | ||     ||||||| ||| || || ||||||||  |||| ||||||||        ||||    |||  U
      C AG     UCCACUC UUG GG AC ACCUCUUC  CUCG GCACGUUU        ACCG    AAG  A
CACUCU U  UCCUU       C   -  U  A        CC    C        CCUAAAUC    --UU   AC

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

csi-miR164c-3p      CACGCGCUCCCCUUCUCCAAC
csi-miR164d-3p      CACGCGCUCCCCUUCUCCAAC
csi-miR164b-3p      CACGCGCUCCCCUUCUCCAAC
aly-miR164a-3p      CACGUACUCCCCUUCUCCAAC
fve-miR164a-3p      CACGUGCUCCCCUUCUCCAAC
zma-miR164g-3p      CACGUGCUCCCCUUCUCCACC
zma-miR164f-3p      CACGUGCGCUCCUUCUCCAAC
bdi-miR164c-3p      CAUGUGCGCUCCUUCUCCAGC
zma-miR164d-3p      CACGUGGUCUCCUUCUCCAU-
                    ** *    * *********