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

atr-miR2111

Organism

Amborella trichopoda

Species

Mature miRNA Sequence(5'-3')

UAAUCUGUAUCUUGAGGUUUGG

miRBase

Precursor miRNA Sequence(5'-3')

UGCGCUAACUGGCAUGAGAGUGGAUAAUCUGUAUCUUGAGGUUUGGGUUUAGCCCACAACUAUACUUCAUUAUCAAGUGUCGGAGUCUAGUUAACCCAAAACCAGACCUCAGGAUACAGGUUACCUCCUCUACAAUGGUCAGUUUACCUCAGCCA

miRBase

Precursor miRNA Structure(5'-3') 

UGC   ------       --A  -    -U  A                      GUUUAGCCCAC     U     -  UAU 
   GCU      AACUGGC   UG AGAG  GG UAAUCUGUAUCUUGAGGUUUGG           AACUA ACUUC AU   C
   |||      |||||||   || ||||  || ||||||||||||||||||||||           ||||| ||||| ||    
   CGA      UUGACUG   AC UCUC  CC AUUGGACAUAGGACUCCAGACC           UUGAU UGAGG UG   G
-AC   CUCCAU       GUA  A    CU  -                      --AAAACCCAA     C     C  UGA

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

aly-miR2111a-5p      UAAUCUGCAUCCUGAGGUUUA-
aly-miR2111b-5p      UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111k         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111j         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111b         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111o         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111n         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111m-5p      UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111i         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111h         UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111g-5p      UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111e-5p      UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111d-5p      UAAUCUGCAUCCUGAGGUUUA-
mtr-miR2111c         UAAUCUGCAUCCUGAGGUUUA-
ath-miR2111b-5p      UAAUCUGCAUCCUGAGGUUUA-
ath-miR2111a-5p      UAAUCUGCAUCCUGAGGUUUA-
bra-miR2111e         UAAUCUGCAUCCUGAGGUUUA-
bra-miR2111b         UAAUCUGCAUCCUGAGGUUUA-
bra-miR2111a         UAAUCUGCAUCCUGAGGUUUA-
csi-miR2111-5p       UAAUCUGCAUCCUGAGGUUUG-
ptc-miR2111b         UAAUCUGCAUCCUGAGGUUUG-
ptc-miR2111a         UAAUCUGCAUCCUGAGGUUUG-
atr-miR2111          UAAUCUGUAUCUUGAGGUUUGG
                     ******* *** ********