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

zma-miR156j-5p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

UGACAGAAGAGAGAGAGCACA

miRBase

Precursor miRNA Sequence(5'-3')

CGAGUGGACCUCGGGAGCGAUGACAGAAGAGAGAGAGCACAACCCAGCACCAGCGAGGAAAAGCCUCGCUUCUGCGAGGGCCGUGUGCUCUCUGCUCUCACUGUCAUCGCCCACAGGCCACCGAA

miRBase

Precursor miRNA Structure(5'-3') 

--  A    A   CG  A          -A    -          --A   -A   CC       A 
  CG GUGG CCU  GG GCGAUGACAG  AGAG AGAGAGCACA   CCC  GCA  AGCGAGG A
  || |||| |||  || ||||||||||  |||| ||||||||||   |||  |||  ||||||| A
  GC CACC GGA  CC CGCUACUGUC  UCUC UCUCUCGUGU   GGG  CGU  UCGCUCC C
AA  -    -   CA  -          AC    G          GCC   AG   CU       G

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

rco-miR156e         ----UGACAGAAGAGAGAGAGCACA
tcc-miR156a         ----UGACAGAAGAGAGAGAGCACA
bdi-miR156a         ----UGACAGAAGAGAGAGAGCACA
zma-miR156j-5p      ----UGACAGAAGAGAGAGAGCACA
gma-miR156b         ----UGACAGAAGAGAGAGAGCACA
mtr-miR156a         ----UGACAGAAGAGAGAGAGCACA
sbi-miR156d         ----UGACAGAAGAGAGAGAGCACA
osa-miR156k         ----UGACAGAAGAGAGAGAGCACA
bdi-miR156j         ----UGACAGAAGAGAGAGAGCAC-
ath-miR156j         ----UGACAGAAGAGAGAGAGCAC-
sit-miR156e         ----UGACAGAAGAGAGAGAGCAC-
mdm-miR156t         ---UUGACAGAAGAGAGAGAGCAC-
mdm-miR156u         ---UUGACAGAAGAGAGAGAGCAC-
mdm-miR156v         ---UUGACAGAAGAGAGAGAGCAC-
mdm-miR156w         ---UUGACAGAAGAGAGAGAGCAC-
mes-miR156k         ---UUGACAGAAGAGAGAGAGCAC-
gma-miR156f         ---UUGACAGAAGAGAGAGAGCACA
esa-miR156b         ----UGACAGAAGAGAGAGAGCAC-
esa-miR156c         ----UGACAGAAGAGAGAGAGCAC-
pvi-miR156p         ---AUGACAGAAGAGAGAGAGCAC-
pvi-miR156r         ---AUGACAGAAGAGAGAGAGCAC-
bra-miR156n         ----UGACAGAAGAGAGAGAGCAC-
bra-miR156p         ----UGACAGAAGAGAGAGAGCAC-
csi-miR3946         UUGUAGAGAAAGAGAAGAGAGCAC-
                         ** * *    *********