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-miR169ag

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

AAGCCAAGGGUGACUUGCCUGA

miRBase

Precursor miRNA Sequence(5'-3')

UGAGAGAAGAGAGGUCUAAUAUGAGGAUCAGAGCCUUGUGUGGAAGCCAAGGGUGACUUGCCUGAGCAUUUCAGGAAGGUUUCUAUAUGAAAGCUUUUUGUUAGUUUUGCAGGAAGUCAACCUCGGCUUUCCUGUAGUCUCUUCUUUCUCAUGCUAUGCCUUUCUCUUCUUCCA

miRBase

Precursor miRNA Structure(5'-3') 

--U     A        C  A        -UC    C  UGU U       A   G      G    ---   A UU       G    U 
   GAGAG AGAGAGGU UA UAUGAGGA   AGAG CU   G GGAAGCC AGG UGACUU CCUG   AGC U  CAGGAAG UUUC A
   ||||| |||||||| || ||||||||   |||| ||   | ||||||| ||| |||||| ||||   ||| |  ||||||| |||| U
   UUCUU UCUUUCCG AU GUACUCUU   UCUC GA   C CUUUCGG UCC ACUGAA GGAC   UUG A  GUUUUUC AAAG G
ACC     C        U  C        UCU    U  UGU -       C   A      -    GUU   - UU       G    U

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

hvu-miR169        AAGCCAAGGAUGAGUUGCCUG-
mtr-miR169f       AAGCCAAGGAUGACUUGCCUA-
ptc-miR169o       AAGCCAAGGAUGACUUGCCUG-
ptc-miR169ag      AAGCCAAGGGUGACUUGCCUGA
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