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

ptc-miR169b-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

GGCAGGUUGUUCUUGGCUAC

miRBase

Precursor miRNA Sequence(5'-3')

AAGAUUGAUGCAGCCAAGGAUGACUUGCCGACGACUCGUUUUUGCUUCCAUCAAUAUACGCAUAAUUAAGAAGAGAUGAAUCCGUUGGCAGGUUGUUCUUGGCUACAUUUUUC

miRBase

Precursor miRNA Structure(5'-3') 

AA  UU    C                      - C        G   CCAUCAAUA 
  GA  GAUG AGCCAAGGAUGACUUGCCGACG A UCGUUUUU CUU         U
  ||  |||| |||||||||||||||||||||| | |||||||| |||          
  CU  UUAC UCGGUUCUUGUUGGACGGUUGC U AGUAGAGA GAA         G
--  UU    A                      C A        A   UUAAUACGC

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

zma-miR169a-3p      --GGCAAGU-UGUUCUU-GGCUACA
zma-miR169b-3p      --GGCAAGU-UGUUCUU-GGCUACA
bdi-miR169a-3p      --GGCGAGU-UGUUCUU-GGCUACA
bdi-miR169c-3p      --GGCAGGU-UGUCCUU-GGCUAC-
ptc-miR169b-3p      --GGCAGGU-UGUUCUU-GGCUAC-
ath-miR169b-3p      --GGCAAGU-UGUCCUUCGGCUACA
aly-miR169b-3p      --GGCAAGU-UGUCCUUCGGCUACA
zma-miR169r-3p      --GGCAAGU-UGUCCUU-GGCUACA
zma-miR169c-3p      --GGCAAGUCUGUCCUU-GGCUACA
aly-miR169a-3p      --GGCAAGU-UGUCCUU-GGCUACA
ath-miR169a-3p      --GGCAAGU-UGUCCUU-GGCUAC-
csi-miR169n-3p      --GGCAAGU-UGCCCUU-GGCUACA
osa-miR169p         UAGCCAAGGACAAACUU--GCCGG-
                      * *  *      ***  **