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-miR1030b

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UCUGCAUCUGCACCUGCACCA

miRBase

Precursor miRNA Sequence(5'-3')

UGUCAUGCAUCUGCAUCUGCACCUGCACCACAAUGUGAUCGCGGCGAUCUCUGUUCCGGAGGUUCAGCCCGGUAGUUUUACAUGCGGCCCUGCAUUCAGCGCUGGCAUCUUCCGUGGACAAGUUUCGUAGCUCACAUUCCGAUGGUGCAGUGCUUAUGCAGAAGCGUUGC

miRBase

Precursor miRNA Structure(5'-3') 

U  C    A       CU    C       - --       UC  G    -U  C     -      UUCA   C   A   UUAC     G 
 GU AUGC UCUGCAU  GCAC UGCACCA C  AAUGUGA  GC GCGA  CU UGUUC CGGAGG    GCC GGU GUU    AUGCG C
 || |||| |||||||  |||| ||||||| |  |||||||  || ||||  || ||||| ||||||    ||| ||| |||    |||||  
 CG UGCG AGACGUA  CGUG ACGUGGU G  UUACACU  CG UGCU  GA ACAGG GCCUUC    CGG UCG CGA    UACGU U
-  U    A       UU    -       A CC       --  A    UU  -     U      --UA   -   -   --CU     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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