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

osa-miR2118i

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

UUCCUAGUGCCUCCCAUUCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GCAAGUAAGGAAGAGGAAGAAAUUGAGUGUCUAAGGGCAAUCGGAAUGGGAACAUUGAGGAAAGCCUACAGCGUCUUUCUCGUCCACUAGAAGUGGGGGGUAAAGAUAAUGUUUUUGUGUUUUCCUAGUGCCUCCCAUUCCUAUUGUCCUUAGAUACUCCUUCCUCUUCCUUUCAGCUUGC

miRBase

Precursor miRNA Structure(5'-3') 

      ---             AAAUU                 C         -A    G        ----CU   GC      C  G        
GCAAGU   AAGGAAGAGGAAG     GAGUGUCUAAGGGCAAU GGAAUGGGA  CAUU AGGAAAGC      ACA  GUCUUU UC UCCACUA 
||||||   |||||||||||||     ||||||||||||||||| |||||||||  |||| ||||||||      |||  |||||| || |||||| G
CGUUCG   UUCCUUCUCCUUC     CUCAUAGAUUCCUGUUA CCUUACCCU  GUGA UCCUUUUG      UGU  UAGAAA GG GGGUGAG 
      ACU             -----                 U         CC    -        UGUUUU   AA      U  G

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

zma-miR2118c         UUCCUAAUGCCUCCCAUUCCUA-
osa-miR2118l         UUCCUAAUGCUUCCCAUUCCUA-
osa-miR2118i         UUCCUAGUGCCUCCCAUUCCUA-
vvi-miR3633a-3p      UUCCUA-UACCACCCAUUCCCUA
                     ****** * *  ********