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

csi-miR171b-3p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

CGAGCCGAAUCAAUAUCACUC

miRBase

Precursor miRNA Sequence(5'-3')

CAUGGAGAGCAAAAGCACCUUCUUGGCGAUUGGAGAAGUAGACAUGGUGUGAUAUUGGUUCGGCUCAUCUUAAUUAAUAGAUUAAUAUUUCAGCCCUUAAGGUUCUUACAUGUAUAUAUCUAGACGAGCCGAAUCAAUAUCACUCUUGUAUGCUUCUUUCUUUUGAUU

miRBase

Precursor miRNA Structure(5'-3') 

CAUGGAGAGCAAAAGCACCUUCUUGG   UU   -      G   U  U                  A   UAAUUAAU    UA    ----UUC    C 
                          CGA  GGA GAAGUA ACA GG GUGAUAUUGGUUCGGCUC UCU        AGAU  AUAU       AGCC U
                          |||  ||| |||||| ||| || |||||||||||||||||| |||        ||||  ||||       |||| U
                          GUU  CUU CUUCGU UGU UC CACUAUAACUAAGCCGAG AGA        UCUA  UAUG       UUGG G
-----------------------UUA   UU   U      A   -  U                  C   --------    UA    UACAUUC    A

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

dca-miR171-b2.0r1-12556      -UGAGCCGAACCAAUAUUACUC-
pha-miR171f                  -UGAGCCGAACCAAUAUCACUC-
sit-miR171f                  -UGAGCCGAACCAAUAUCACUC-
osa-miR171h                  GUGAGCCGAACCAAUAUCACU--
sbi-miR171e                  GUGAGCCGAACCAAUAUCACU--
zma-miR171k-3p               GUGAGCCGAACCAAUAUCACU--
zma-miR171h-3p               GUGAGCCGAACCAAUAUCACU--
pha-miR171g                  -UGAGCCGAACCAAUAUCACUC-
mdm-miR171i                  -UGAGCCGAACCAAUAUCACUC-
pvi-miR171k                  -UGAGCCGAACCAAUAUCACUC-
bdi-miR171f                  -UGAGCCGAACCAAUAUCACCC-
stu-miR479                   -UGAGCCGAACCAAUAUCACUC-
pvi-miR171m                  -UGAGCCGAACCAAUAUCACUC-
sit-miR171g                  --GAGCCGAACCAAUAUCACUCA
gma-miR171b-3p               -CGAGCCGAAUCAAUAUCACUC-
csi-miR171b-3p               -CGAGCCGAAUCAAUAUCACUC-
mtr-miR171h                  -CGAGCCGAAUCAAUAUCACUC-
mtr-miR171g                  -CGAGCCGAAUCAAUAUCACUC-
mac-miR171k                  -CGAGCCGAACCAAUAUCACUC-
mac-miR171l                  -CGAGCCGAACCAAUAUCACUC-
fve-miR171b                  -CGAGCCGAACCAAUAUCACUC-
mes-miR171l                  -CGAGCCGAACCAAUAUCACUC-
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