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

mdm-miR399d

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

UGCCAAAGGAGAGUUGCCCUA

miRBase

Precursor miRNA Sequence(5'-3')

UGAGCGAAUUAGUUGUAGGGCUUCUCUCCGAUGGCAGGAAAUAUUAAUGGUCAUGAAUCAUGGAAGCAUGGAUUUUUGUGUUCUCUCAUGAGUUAUGACCUGCCAAAGGAGAGUUGCCCUACGACUGCUUUUGCUUA

miRBase

Precursor miRNA Structure(5'-3') 

        -U            UU      GA     GGAAAUAUUAAU        A     -  -       A 
UGAGCGAA  UAGUUGUAGGGC  CUCUCC  UGGCA            GGUCAUGA UCAUG GA AGCAUGG U
||||||||  ||||||||||||  ||||||  |||||            |||||||| ||||| || |||||||  
AUUCGUUU  GUCAGCAUCCCG  GAGAGG  ACCGU            CCAGUAUU AGUAC CU UUGUGUU U
        UC            UU      AA     ------------        G     U  C       U

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

ppe-miR399k         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399l         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399j         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399i         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399h         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399g         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399f         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399e         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399d         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399c         UGCCAAAGAAGAGUUGCCCUA
stu-miR399i-3p      UGCCAAAGGAGAGUUGCCCUA
mdm-miR399d         UGCCAAAGGAGAGUUGCCCUA
csi-miR399b-3p      UGCCAAAGGAGAGUUGCCCUA
sly-miR399          UGCCAAAGGAGAGUUGCCCUA
bra-miR399h         UGCCAAAGGAGAGUUGCCCU-
mdm-miR399k         UGCCAAAGGAGAGUUGCCCUU
mac-miR399a         -GCCAAAGGAGACUUGCCCUA
ptc-miR399e         CGCCAAAGGAGAGUUGCCCUC
ppe-miR399a         CGCCAAAGGAGAGUUGCCCUU
vvi-miR399i         CGCCAAAGGAGAGUUGCCCUG
tcc-miR399a         CGCCAAAGGAGAGUUGCCCUG
tcc-miR399e         CGCCAAAGGAGAAUUGCCCUG
csi-miR399f-3p      CGCCAAAGGAGAAUUGCCCUG
stu-miR399j-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399k-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399l-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399m-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399n-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399o-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399g-3p      CGCCAAAGGGGAGCUGCCCUA
                     *******  **  ******