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-miR1030h

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UCUGCAUCUGCACCUGCACCG

miRBase

Precursor miRNA Sequence(5'-3')

GCUACGUUACCUAUCUGCAUCUGCACCUGCACCGAGAUUCGAAGAGUAAUGAAGAAUCAUAUACGCAGUUGCAGUCAUUUCCAGUUCAUCACUGGACCUGACAAAUUGAAGCAAUGAUGCAAUUCUCAUUCUCGCUUAUCGGUGCAGUGCUUAUGCAGAUAUGUGGCGUUG

miRBase

Precursor miRNA Structure(5'-3') 

GCU       C         CU    C        GAUU   A    AAU   --GA     AUACG     GCA    UU      U 
   ACGUUAC UAUCUGCAU  GCAC UGCACCGA    CGA GAGU   GAA    AUCAU     CAGUU   GUCA  UCCAGU C
   ||||||| |||||||||  |||| ||||||||    ||| ||||   |||    |||||     |||||   ||||  |||||| A
   UGCGGUG AUAGACGUA  CGUG ACGUGGCU    GCU CUUA   CUU    UAGUA     GUUAA   CAGU  AGGUCA A
-GU       U         UU    -        AUUC   -    -CU   AACG     ACGAA     --A    CC      C

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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