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

pvi-miR159b

Organism

Panicum virgatum

Species

Mature miRNA Sequence(5'-3')

UUUGGAUUGAAGGGAGCUCUG

PmiREN

Precursor miRNA Sequence(5'-3')

GCTGCTTGGATTTGAAGCGGAGCTCCCTTCCTTCCAATGAAGGGTCGTTCTGAAGGGTGGTACAGCTGCTCGTTCATGGTTCCCACTATCCTATCTCATCGGCTTTGAGAGCGCGAGAGATTGTGAGGTCCGGTGAGATGGTTTGGCTTGAGATAGGCTTGTGGTTTGCATGGCCGAGGAGCTGCATCGTCCCCTCGTTGACCGCTGTTTGGATTGAAGGGAGCTCTGCATCTCCATCCTCCCGTATAT

PmiREN

Precursor miRNA Structure(5'-3') 

---GCUGCUU    -UU  A              CU     UGA  -     UUC   A   -    A     G    U     GUUC    UAUCCUAUCUCAUCGGCUUUGAGAGCGCGAGAGAUU 
          GGAU   GA GCGGAGCUCCCUUC  UCCAA   AG GGUCG   UGA GGG UGGU CAGCU CUCG UCAUG    CCAC                                    G
          ||||   || ||||||||||||||  |||||   || |||||   ||| ||| |||| ||||| |||| |||||    ||||                                     
          CCUA   CU CGUCUCGAGGGAAG  AGGUU   UC CCAGU   GCU CCC GCUA GUCGA GAGC GGUAC    GGUG                                    A
UAUAUGCCCU    CCU  A              UU     -UG  G     --U   C   U    C     G    C     GUUU    UUCGGAUAGAGUUCGGUUUGGUAGAGUGGCCUGGAG

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

osa-miR159f           CUUGGAUUGAAGGGAGCUCUA-
bdi-miR159a-3p        CUUGGAUUGAAGGGAGCUCU--
cru-miR159a           UUUGGAUUGAAGGGAGCUCUU-
ath-miR159b-3p        UUUGGAUUGAAGGGAGCUCUU-
aly-miR159b-3p        UUUGGAUUGAAGGGAGCUCUU-
lus-miR159c           UUUGGAUUGAAGGGAGCUCUU-
bol-miR159a           UUUGGAUUGAAGGGAGCUCU--
pha-miR159c           UUUGGAUUGAAGGGAGCUCUG-
bdi-miR159c           UUUGGUUUGAAGGGGGCUCUG-
pvi-miR159b           UUUGGAUUGAAGGGAGCUCUG-
pvi-miR159d           UUUGGAUUGAAGGGAGCUCUG-
pvi-miR159e           UUUGGAUUGAAGGGAGCUCUG-
pvi-miR159f           UUUGGAUUGAAGGGAGCUCUG-
tae-miR159a           UUUGGAUUGAAGGGAGCUCUG-
tae-miR159b           UUUGGAUUGAAGGGAGCUCUG-
hvu-miR159a           UUUGGAUUGAAGGGAGCUCUG-
hvu-miR159b           UUUGGAUUGAAGGGAGCUCUG-
osa-miR159a.1         UUUGGAUUGAAGGGAGCUCUG-
osa-miR159b           UUUGGAUUGAAGGGAGCUCUG-
sbi-miR159a           UUUGGAUUGAAGGGAGCUCUG-
zma-miR159a-3p        UUUGGAUUGAAGGGAGCUCUG-
zma-miR159b-3p        UUUGGAUUGAAGGGAGCUCUG-
zma-miR159f-3p        UUUGGAUUGAAGGGAGCUCUG-
zma-miR159j-3p        UUUGGAUUGAAGGGAGCUCUG-
zma-miR159k-3p        UUUGGAUUGAAGGGAGCUCUG-
bdi-miR159b-3p.1      UUUGGAUUGAAGGGAGCUCUG-
bol-miR159b           UUUGGAUUGAAGGGAGCUCU--
mdm-miR159f           UUUGGAUUGAAGGGAGCUCUA-
fve-miR159a-3p        UUUGGAUUGAAGGGAGCUCUA-
mdm-miR159e           UUUGGAUUGAAGGGAGCUCUA-
mdm-miR159d           UUUGGAUUGAAGGGAGCUCUA-
atr-miR159            UUUGGAUUGAAGGGAGCUCUA-
cpa-miR159a           UUUGGAUUGAAGGGAGCUCUA-
ppe-miR159            UUUGGAUUGAAGGGAGCUCUA-
mes-miR159b           UUUGGAUUGAAGGGAGCUCUA-
mes-miR159a-3p        UUUGGAUUGAAGGGAGCUCUA-
gma-miR159e-3p        UUUGGAUUGAAGGGAGCUCUA-
csi-miR159a-3p        UUUGGAUUGAAGGGAGCUCUA-
aly-miR159a-3p        UUUGGAUUGAAGGGAGCUCUA-
rco-miR159            UUUGGAUUGAAGGGAGCUCUA-
pvu-miR159a.1         UUUGGAUUGAAGGGAGCUCUA-
mtr-miR159a           UUUGGAUUGAAGGGAGCUCUA-
sly-miR159            UUUGGAUUGAAGGGAGCUCUA-
vvi-miR159c           UUUGGAUUGAAGGGAGCUCUA-
ptc-miR159b           UUUGGAUUGAAGGGAGCUCUA-
ptc-miR159a           UUUGGAUUGAAGGGAGCUCUA-
gma-miR159a-3p        UUUGGAUUGAAGGGAGCUCUA-
ath-miR159a           UUUGGAUUGAAGGGAGCUCUA-
zos-miR159            UUUGGAUUGAAGGGAGCUCUA-
mac-miR159e           UUUGGAUUGAAGGGAGCUCUA-
mac-miR159d           UUUGGAUUGAAGGGAGCUCUA-
mac-miR159b           UUUGGAUUGAAGGGAGCUCUA-
mac-miR159a           UUUGGAUUGAAGGGAGCUCUA-
esa-miR159b           UUUGGAUUGAAGGGAGCUCUA-
cru-miR159b           UUUGGAUUGAAGGGAGCUCUA-
bra-miR159d           UUUGGAUUGAAGGGAGCUCUA-
bra-miR159b           UUUGGAUUGAAGGGAGCUCUA-
bra-miR159a           UUUGGAUUGAAGGGAGCUCUA-
bol-miR159c           UUUGGAUUGAAGGGAGCUCU--
osa-miR159c           AUUGGAUUGAAGGGAGCUCCA-
zma-miR159e-3p        AUUGGUUUGAAGGGAGCUCCA-
bra-miR159c           UUUGGAUUGAAGGGAGCUCC--
esa-miR159a           UUUGGAUUGAAGGGAGCUCC--
lus-miR159b           UUUGGAUUGAAGGGAGCUCUC-
fve-miR159b           AUUGGAUUGAAGGGAGCUCUC-
sly-miR159b           -UUGGAAAGAAGGGAGCUCUAC
zma-miR159h-3p        UUUGGAGUGAAGGGAGCUCUG-
zma-miR159g-3p        UUUGGAGUGAAGGGAGUUCUG-
zma-miR159i-3p        UUUGGAGUGAAGGGAGCUCUG-
ptc-miR159c           AUUGGAGUGAAGGGAGCUCGA-
lus-miR159a           AUUGGAGUGAAGGGAGCUCGA-
mes-miR159c           AUUGGAGUGAAGGGAGCUCUG-
mes-miR159d           AUUGGAGUGAAGGGAGCUCUG-
vvi-miR159a           CUUGGAGUGAAGGGAGCUCUC-
vvi-miR159b           CUUGGAGUGAAGGGAGCUCUC-
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