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

aly-miR403a-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

UUAGAUUCACGCACAAACUCG

miRBase

Precursor miRNA Sequence(5'-3')

GAAGAGUCGUAUUACAUGUUUUGUGCGUGACUCUAAUUUAACAGGCUUAUGUUUGAGAUUUUUUUGACAAAUCCGGAUUUUGCUGUUGGAUUAGAUUCACGCACAAACUCGUAAUCUGUCUUUUC

miRBase

Precursor miRNA Structure(5'-3') 

      U  U     AU    U        C             G UUAU     A     UU 
GAAGAG CG AUUAC  GUUU GUGCGUGA UCUAAUUUAACAG C    GUUUG GAUUU  U
|||||| || |||||  |||| |||||||| ||||||||||||| |    ||||| |||||  U
CUUUUC GU UAAUG  CAAA CACGCACU AGAUUAGGUUGUC G    UAGGC CUAAA  C
      U  C     CU    -        U             - -UUU     -     CA

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

gma-miR403a         UUAGAUUCACGCACAAACUUG---
gma-miR403b         UUAGAUUCACGCACAAACUUG---
bra-miR403          UUAGAUUCACGCACAAACUCG---
cru-miR403          UUAGAUUCACGCACAAACUCG---
esa-miR403          UUAGAUUCACGCACAAACUCG---
ath-miR403-3p       UUAGAUUCACGCACAAACUCG---
ptc-miR403a         UUAGAUUCACGCACAAACUCG---
ptc-miR403b         UUAGAUUCACGCACAAACUCG---
ptc-miR403c-3p      UUAGAUUCACGCACAAACUCG---
vvi-miR403a         UUAGAUUCACGCACAAACUCG---
vvi-miR403b         UUAGAUUCACGCACAAACUCG---
vvi-miR403c         UUAGAUUCACGCACAAACUCG---
vvi-miR403d         UUAGAUUCACGCACAAACUCG---
vvi-miR403e         UUAGAUUCACGCACAAACUCG---
vvi-miR403f         UUAGAUUCACGCACAAACUCG---
rco-miR403a         UUAGAUUCACGCACAAACUCG---
rco-miR403b         UUAGAUUCACGCACAAACUCG---
aly-miR403a-3p      UUAGAUUCACGCACAAACUCG---
csi-miR403a-3p      UUAGAUUCACGCACAAACUCG---
tcc-miR403a         UUAGAUUCACGCACAAACUCG---
tcc-miR403b         UUAGAUUCACGCACAAACUCG---
mdm-miR403a         UUAGAUUCACGCACAAACUCG---
mdm-miR403b         UUAGAUUCACGCACAAACUCG---
mes-miR403a         UUAGAUUCACGCACAAACUCG---
mes-miR403b         UUAGAUUCACGCACAAACUCG---
ptc-miR403d         UUAGAUUCACGCACAAACUCG---
aly-miR403b-3p      UUAGAUUCACGCACAAACUCG---
ppe-miR403          UUAGAUUCACGCACAAACUCG---
csi-miR403b-3p      UUAGAUUCACGCACAAACUCG---
sly-miR403-3p       CUAGAUUCACGCACAAGCUCG---
csi-miR403b-5p      ---AGUUUGUGCGUGAAUCUAACC
sly-miR403-5p       ---CGUUUGUGCGUGAAUCUAACA
                         **   **   *