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-miR403b-3p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

UUAGAUUCACGCACAAACUCG

miRBase

Precursor miRNA Sequence(5'-3')

GGGGCACAUCUCAAGUUUGUGCGUGAAUCUAACCCCAUCACAGCCGUCCGUUUUCCCGCUCUCAUCUGAUGGCGUUAGAUUCACGCACAAACUCGCGAUCUGUCC

miRBase

Precursor miRNA Structure(5'-3') 

G     C   U A                    C      CAGCC UC  UU 
 GGGCA AUC C AGUUUGUGCGUGAAUCUAAC CCAUCA     G  CG  U
 ||||| ||| | |||||||||||||||||||| ||||||     |  ||   
 CCUGU UAG G UCAAACACGCACUUAGAUUG GGUAGU     C  GC  C
-     C   C C                    C      CUACU UC  CC

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
                         **   **   *