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

tcc-miR530a

Organism

Theobroma cacao

Species

Mature miRNA Sequence(5'-3')

UGCAUUUGCACCUGCACCUC

miRBase

Precursor miRNA Sequence(5'-3')

CCAACAAGUCUCCAUUUAUCUGCAUUUGCACCUGCACCUCUUUCUCUACACUUCCAGCAGCCAGGGAGAUGAACAACAUUCUCCAUGGACGGUUGCCGAAAUCUUGUUGGUUGGACGGGGAGAGGUGCAGAUGCAGGUGCAGACAAAUGGCCUCUUGGUUUUA

miRBase

Precursor miRNA Structure(5'-3') 

--CCAA    UCU      A            C              CUA  CUU       CCAGGGAGAUGAACAACAUU 
      CAAG   CCAUUU UCUGCAUUUGCA CUGCACCUCUUUCU   CA   CCAGCAG                    C
      ||||   |||||| |||||||||||| ||||||||||||||   ||   |||||||                    U
      GUUC   GGUAAA AGACGUGGACGU GACGUGGAGAGGGG   GU   GGUUGUU                    A
AUUUUG    UCC      C            A              CAG  --U       CUAAAGCCGUUGGCAGGUAC

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
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