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-miR482c-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UCUUUCCGAGUCCUCCCAUACC

miRBase

Precursor miRNA Sequence(5'-3')

UCCUCCGCCGUGUUGGAAAGGAAAGGGAGACUGCUUUACUGGAAGCUUCCGGUAUGGGAGAGGCGGGAAUGACUCUGAAAGAACUUAGAAGAGUCUUUCCGAGUCCUCCCAUACCGCAGAUUUCCAGUAGUUCCUCCCUUUACUUAUCUUCACUAUUCCAGCAGCUCUGGA

miRBase

Precursor miRNA Structure(5'-3') 

   UCC  CG        -----------  GA       ACU   UU        -  UC           A   -G    U      GAAAG 
UCC   GC  UGUUGGAA           AG  AAGGGAG   GCU  ACUGGAAG CU  CGGUAUGGGAG GGC  GGAA GACUCU     A
|||   ||  ||||||||           ||  |||||||   |||  |||||||| ||  ||||||||||| |||  |||| ||||||     A
AGG   CG  ACGACCUU           UC  UUCCCUC   UGA  UGACCUUU GA  GCCAUACCCUC CUG  CCUU CUGAGA     U
   UCU  --        AUCACUUCUAU  AU       -CU   --        A  -C           -   AG    U      AGAUU

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

gma-miR482b-3p       --UCUUCCCUACACCUCCCAUACC
gma-miR482d-3p       --UCUUCCCUACACCUCCCAUACC
vvi-miR482           --UCUUUCCUACUCCUCCCAUUCC
ptc-miR482a.1        -------CCUACUCCUCCCAUUCC
ppe-miR482f          --UCUUUCCUACUCCACCCAUUCC
ptc-miR482a.2        --UCUUGCCUACUCCUCCCAUU--
csi-miR482b-3p       --UCUUGCCCACCCCUCCCAUUCC
mdm-miR482b          --UCUUUCCUAUCCCUCCCAUUCC
mdm-miR482c          --UCUUUCCUAACCCUCCCAUUCC
fve-miR482c          --UCUUUCCUAUUCCUCCCAUCCC
fve-miR482b          --UCUUUCCUAGUCCUGCCAUUCC
sly-miR482e-3p       --UCUUUCCUACUCCUCCCAUACC
ptc-miR482c-3p       --UCUUUCCGAGUCCUCCCAUACC
gma-miR2118a-5p      GGAGAUGGGAGGGUCGGUAAAG--
gma-miR2118b-5p      GGAGAUGGGAGGGUCGGUAAAG--
mtr-miR482-5p        -GGCAUGGGAUAGUAGGGAAGA--
mdm-miR482d          ---AAUGGAAGGGUAGGAAAGAAG
                                        *