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

ppt-miR1030i

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

CCUGCAUCUGCACCUGCACCG

miRBase

Precursor miRNA Sequence(5'-3')

AAUUCUCCUCUUCAUCGCUGUAAUGCCAUGUUCCUGCAUCUGCACCUGCACCGCACUGCCUCACGAGAAUGUGCACGAAUGGAUCAGAGCGGUGUUGUGCAAAUCCUGCUUUCAGUCAAUCACUGAGCUUGAGUUUUAGCAAUUCUUAUUUCCUCUGAACUUUCUUCUGGCAUUAUAGUGGUGGAGGUGCUUAUGCAGAAAUAUUGCAUUGCGGCUGAGAGCCACUAAUG

miRBase

Precursor miRNA Structure(5'-3') 

--AAUUCUC    U  UC          C     C      CU      G      ---AC    UCAC     U  G  C  AU   UCAGAGCGGUGUUGUGCAAAUCCUGCUUUCAG 
         CUCU CA  GCUGUAAUGC AUGUU CUGCAU  GCACCU CACCGC     UGCC    GAGAA GU CA GA  GGA                                U
         |||| ||  |||||||||| ||||| ||||||  |||||| ||||||     ||||    ||||| || || ||  |||                                C
         GAGA GU  CGGCGUUACG UAUAA GACGUA  CGUGGA GUGGUG     ACGG    UUCUU CA GU CU  CCU                                U
GUAAUCACC    -  --          U     A      UU      G      AUAUU    --UC     U  A  -  --   UUAUUCUUAACGAUUUUGAGUUCGAGUCACUA

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

mpo-miR1030-b3.0r1-10150      UCUGCAUCUGCACCUGCACC-
ppt-miR1030h                  UCUGCAUCUGCACCUGCACCG
ppt-miR1030f                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030g                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030e                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030d                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030c                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030b                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030a                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030j                  CCUGCAUCUGCACCUGCACCA
ppt-miR1030i                  CCUGCAUCUGCACCUGCACCG
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