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-miR530a

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UGCAUUUGCACCUGCACCUU

miRBase

Precursor miRNA Sequence(5'-3')

GCCAACAUGUUGCCUUUAUCUGCAUUUGCACCUGCACCUUACUUGUUUCUUUCUUUUGUUUUUGACUCCAAAACCAAAAGUAAGUUUGAAACAUUAAAACAAGCUUGAGGUGCAGGUGCAGGUGCAGGUGAAUGCCAUGUUGGU

miRBase

Precursor miRNA Structure(5'-3') 

         UU  C                           --       ------------   U      U     A 
GCCAACAUG  GC UUUAUCUGCAUUUGCACCUGCACCUUA  CUUGUUU            CUU CUUUUG UUUUG C
|||||||||  || |||||||||||||||||||||||||||  |||||||            ||| |||||| |||||  
UGGUUGUAC  CG AAGUGGACGUGGACGUGGACGUGGAGU  GAACAAA            GAA GAAAAC AAAAC C
         --  U                           UC       AUUACAAAGUUU   U      C     C

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

gma-miR530b         --UGCAUUUGCACCUGCACUUUA
gma-miR530c         --UGCAUUUGCACCUGCACUUUA
gma-miR530d         --UGCAUUUGCACCUGCACUUUA
gma-miR530e         --UGCAUUUGCACCUGCACUUUA
gma-miR530a         --UGCAUUUGCACCUGCACUUU-
mtr-miR530          --UGCAUUUGCACCUGCACUUUC
bdi-miR530a         --UGCAUUUGCACCUGCACCUAC
bdi-miR530b         --UGCAUUUGCACCUGCACCUAC
osa-miR530-5p       --UGCAUUUGCACCUGCACCUA-
mac-miR530          --UGCAUUUGCACCUGCACCUAA
tcc-miR530a         --UGCAUUUGCACCUGCACCUC-
fve-miR530          --UGCAUUUGCACCUGCACCUCU
stu-miR530          UCUGCAUUUGCACCUGCACCU--
ppe-miR530          UCUGCAUUUGCACCUGCACCU--
ptc-miR530b         --UGCAUUUGCACCUGCAUCUU-
csi-miR530b-5p      --UGCAUUUGCACCUGCAUCUUG
csi-miR530a-5p      --UGCAUUUGCACCUGCACCUUG
tcc-miR530b         --UGCAUUUGCACCUGCACCUU-
mes-miR530a         --UGCAUUUGCACCUGCACCUU-
mes-miR530b         --UGCAUUUGCACCUGCACCUUA
ptc-miR530a         --UGCAUUUGCACCUGCACCUU-
lus-miR530b         --UGCAUUUGCACCUGCACCUU-
lus-miR530a         --UGCAUUUGCACCUGCACCUU-
mdm-miR530a         --UGCAUUUGCACCUGCACUUGU
mdm-miR530b         --UGCAUUUGCACCUGCACUUGU
mdm-miR530c         --UGCAUUUGCACCUGCACUUGU
                      ****************  *