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

mtr-miR530

Organism

Medicago truncatula

Species

Mature miRNA Sequence(5'-3')

UGCAUUUGCACCUGCACUUUC

miRBase

Precursor miRNA Sequence(5'-3')

AGCUUUUAUCUGCAUUUGCACCUGCACUUUCCCUGGCUGCGUCUGUAACAUAUAAACAUGUGAAUUAAUUUGUUUUAUAUAUAAAAUAAAAUAAAUUUAUAAUAUUUAGUAUGAGGAAGGACCAAGGGCUAGGUGCAGAUGCAUAUGCAGAUGAAUGCC

miRBase

Precursor miRNA Structure(5'-3') 

A  U           U    C        -U    GGC  C    -GUAA     A  C    GAAUU            AU 
 GC UUUAUCUGCAU UGCA CUGCACUU  CCCU   UG GUCU     CAUAU AA AUGU     AAUUUGUUUUAU  A
 || ||||||||||| |||| ||||||||  ||||   || ||||     ||||| || ||||     ||||||||||||  U
 CG AAGUAGACGUA ACGU GACGUGGA  GGGA   AC CAGG     GUAUG UU UAUA     UUAAAUAAAAUA  A
C  U           U    A        UC    ---  -    AAGGA     A  -    -AUAU            AA

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
                      ****************  *