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-miR3954b-5p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

UUGGACAGAGAAAUCACGGUCA

miRBase

Precursor miRNA Sequence(5'-3')

UAUUAUUUUGCUUUGGUUUGGUCUGUUUACAAAGUGAGAAAAUCACUUUCGUUGUUCGUUGUUAGAAAAAAAUAUGAUCAAUUAUAUUUGUUUGGACAGAGAAAUCACGGUCAUGAGAUGAGUUUUCUAAUCUGUACUGUAAUCUGUAUACGGUGAUGGUGAAUAUUGACGAUGGAUUCUCUUUCUACCGUGUUUCUCUGCCCAAUCAGAUAUAUUUGAUCUUCAUUCCAUUUCUGU

miRBase

Precursor miRNA Structure(5'-3') 

UAUUAUUUUGCUUUGGUUUGGUCUGUUUACAAAGUGAGAAAAUCACUUUCGUUGUUCGUUGUUAGAAAAAAAUAU      U        U    A        U      CAU    U   UU   -----------UA   UG       AU 
                                                                           GAUCAA UAUAUUUG UUGG CAGAGAAA CACGGU   GAGA GAG  UUC             AUC  UACUGUA  C
                                                                           |||||| |||||||| |||| |||||||| ||||||   |||| |||  |||             |||  |||||||  U
                                                                           CUAGUU AUAUAGAC AACC GUCUCUUU GUGCCA   CUUU CUC  AGG             UGG  GUGGCAU  A
-----------------------------------------------------------UGUCUUUACCUUACUU      U        U    C        -      --U    -   UU   UAGCAGUUAUAAG   UA       AU

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

ppe-miR7122b-5p      UUAUACAAUGAAAUCACGGUCG
ppe-miR7122a-5p      UUAUACAAUGAAAUCACGGCCG
stu-miR7122-5p       UUAUACAGAGAAACCGCUGUCG
mdm-miR7122b         UUAUACAGAGAAAUCACGGUCG
mdm-miR7122a         UUAUACAGAGAAAUCACGGUCG
csi-miR3954b-5p      UUGGACAGAGAAAUCACGGUCA
csi-miR3954          -UGGACAGAGAAAUCACGGUCA
                      *  ***  **** * * * *