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

vvi-miR2111-5p

Organism

Vitis vinifera

Species

Mature miRNA Sequence(5'-3')

UAAUCUGCAUCCUGAGGUCUA

miRBase

Precursor miRNA Sequence(5'-3')

GCAAUAUUGGGUCAGGAUCGGGUAAUCUGCAUCCUGAGGUCUAGAUAAGUAUAUCUCCGUUGCAGCUAGUCCUCUGGUUGCAGAUUACUUCUUCCUCACUGCCAAUGC

miRBase

Precursor miRNA Structure(5'-3') 

GCAA      --  C    UC            U  U    U    AUAA   UAU 
    UAUUGG  GU AGGA  GGGUAAUCUGCA CC GAGG CUAG    GUA   C
    ||||||  || ||||  |||||||||||| || |||| ||||    |||   U
    GUAACC  CA UCCU  UUCAUUAGACGU GG CUCC GAUC    CGU   G
---C      GU  C    UC            U  U    U    --GA   UGC

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

fve-miR2111a         UAAUCUGCAUCCUGAGGUUU-
fve-miR2111b-5p      UAAUCUGCAUCCUGAGGUUU-
fve-miR2111c         UAAUCUGCAUCCUGAGGUUU-
ppe-miR2111d         UAAUCUGCAUCCUGAGGUUUA
ppe-miR2111c         UAAUCUGCAUCCUGAGGUUUA
ppe-miR2111b         UAAUCUGCAUCCUGAGGUUUA
ppe-miR2111a         UAAUCUGCAUCCUGAGGUUUA
aly-miR2111c-5p      UAAUCUGCAUCCUGAGGUUUA
mes-miR2111b         UAAUCUGCAUCCUGAGGUUUA
mes-miR2111a         UAAUCUGCAUCCUGAGGUUUA
mdm-miR2111b         UAAUCUGCAUCCUGAGGUUUA
mdm-miR2111a         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111f         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111e         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111c         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111b         UAAUCUGCAUCCUGAGGUUUA
mtr-miR2111a-5p      UAAUCUGCAUCCUGAGGUUUA
mtr-miR2111f         UAAUCUGCAUCCUGAGGUUUA
tcc-miR2111          UAAUCUGCAUCCUGAGGUUUA
vvi-miR2111-5p       UAAUCUGCAUCCUGAGGUCUA
                     ****************** *