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-miR1030c

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UCUGCAUCUGCACCUGCACCA

miRBase

Precursor miRNA Sequence(5'-3')

UACUCCUUGCUCUGCUGCAUCGUAAUGCAUCUGCAUCUGCACCUGCACCACGUUGUGAUAGGAACAAAACUCUGUCUUGCUGAUUCCCUGCACACAUGCCUUUGUUACCCAGCAUUCUCGAAUACGGCGUCGGUGCUAUCCUCAGAUAAGUAGAGUUGUCCUCACUAGGUUGGUGAGGUGCAUAUGCAGAGGCGUUACAUUGCAGCUGCUUAAUAUUG

miRBase

Precursor miRNA Structure(5'-3') 

-UACUCCUU  UCU      UC       A       C       G     - G U    UA   A  AA      U    -    UUCCCU    AC     ---    UUACCC 
         GC   GCUGCA  GUAAUGC UCUGCAU UGCACCU CACCA C U GUGA  GGA CA  ACUCUG CUUG CUGA      GCAC  AUGCC   UUUG      A
         ||   ||||||  ||||||| ||||||| ||||||| ||||| | | ||||  ||| ||  |||||| |||| ||||      ||||  |||||   ||||       
         CG   CGACGU  CAUUGCG AGACGUA ACGUGGA GUGGU G A CACU  CCU GU  UGAGAU GAAU GACU      CGUG  UGCGG   AAGC      A
GUUAUAAUU  --U      UA       G       U       -     U G U    --   -  --      -    A    -CCUAU    GC     CAU    UCUUAC

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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