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

mdm-miR398b

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

UGUGUUCUCAGGUCGCCCCUG

miRBase

Precursor miRNA Sequence(5'-3')

GGUAGAGGGGUUCCACAGGAGUGACCUGAGAUCACAUGUAGCAUUUAUGUAUUGCGCUUGAUGUGUUCUCAGGUCGCCCCUGCGGUACCUUCUCUACC

miRBase

Precursor miRNA Structure(5'-3') 

        -   U  A    A           U     GU   AUUUA 
GGUAGAGG GGU CC CAGG GUGACCUGAGA CACAU  AGC     U
|||||||| ||| || |||| ||||||||||| |||||  |||     G
CCAUCUCU CCA GG GUCC CGCUGGACUCU GUGUA  UCG     U
        U   U  C    C           U     GU   CGUUA

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

stu-miR398a-3p              ----UAUGUU--CUCAGGUCGCCCCUG-
sly-miR398a                 ----UAUGUU--CUCAGGUCGCCCCUG-
ppe-miR398a-3p              ----UGUGUU--CUCAGGUCGCCCCUG-
csi-miR398b-3p              ----UGUGUU--CUCAGGUCGCCCCUG-
mes-miR398                  ----UGUGUU--CUCAGGUCGCCCCUG-
gma-miR398d                 ----UGUGUU--CUCAGGUCGCCCCUG-
mdm-miR398c                 ----UGUGUU--CUCAGGUCGCCCCUG-
mdm-miR398b                 ----UGUGUU--CUCAGGUCGCCCCUG-
lus-miR398a                 ----UGUGUU--CUCAGGUCGCCCCUG-
bdi-miR398a                 ----UGUGUU--CUCAGGUCGCCCCUG-
gma-miR398c                 ----UGUGUU--CUCAGGUCGCCCCUG-
tcc-miR398a                 ----UGUGUU--CUCAGGUCGCCCCUG-
rco-miR398b                 ----UGUGUU--CUCAGGUCGCCCCUG-
vvi-miR398c                 ----UGUGUU--CUCAGGUCGCCCCUG-
vvi-miR398b                 ----UGUGUU--CUCAGGUCGCCCCUG-
mtr-miR398c                 ----UGUGUU--CUCAGGUCGCCCCUG-
mtr-miR398b                 ----UGUGUU--CUCAGGUCGCCCCUG-
ptc-miR398c-3p              ----UGUGUU--CUCAGGUCGCCCCUG-
ptc-miR398b                 ----UGUGUU--CUCAGGUCGCCCCUG-
osa-miR398b                 ----UGUGUU--CUCAGGUCGCCCCUG-
mac-miR398                  ----UGUGUU--CUCAGGUCGCCCCUG-
dca-miR398-b2.0r1-1847      ----UGUGUU--CUCAGGUCGCCCCUG-
atr-miR398                  ----UGUGUU--CCCAGGUCGCCCCUG-
pha-miR398                  ----UGUGUU--CUCAGGUCGCCCCCG-
pvi-miR398a                 ----UGUGUU--CUCAGGUCGCCCCCG-
sit-miR398                  ----UGUGUU--CUCAGGUCGCCCCCG-
tae-miR398                  ----UGUGUU--CUCAGGUCGCCCCCG-
zma-miR398a-3p              ----UGUGUU--CUCAGGUCGCCCCCG-
zma-miR398b-3p              ----UGUGUU--CUCAGGUCGCCCCCG-
sbi-miR398                  ----UGUGUU--CUCAGGUCGCCCCCG-
pvi-miR398b                 -----GUGUU--CUCAGGUCGCCCCCGC
ppe-miR398b                 ----CGUGUU--CUCAGGUCGCCCCUG-
lus-miR398f                 ----GGUGUU--CUCAGGUCGCCCCUG-
aly-miR398b-3p              ----UGUGUU--CUCAGGUCACCCCUG-
ath-miR398c-3p              ----UGUGUU--CUCAGGUCACCCCUG-
ath-miR398b-3p              ----UGUGUU--CUCAGGUCACCCCUG-
esa-miR398b                 ----UGUGUU--CUCAGGUCACCCCUG-
bra-miR398b                 ----UGUGUU--CUCAGGUCACCCCUG-
bra-miR398a                 ----UGUGUU--CUCAGGUCACCCCUG-
bra-miR398c                 ----UGUGUU--CUCAGGUCACCCCUU-
bra-miR398d                 ----UGUGUU--CUCAGGUCACCCCUU-
ath-miR398a-3p              ----UGUGUU--CUCAGGUCACCCCUU-
osa-miR398a                 ----UGUGUU--CUCAGGUCACCCCUU-
gma-miR398a                 ----UGUGUU--CUCAGGUCACCCCUU-
gma-miR398b-3p              ----UGUGUU--CUCAGGUCACCCCUU-
ptc-miR398a                 ----UGUGUU--CUCAGGUCACCCCUU-
mtr-miR398a-3p              ----UGUGUU--CUCAGGUCACCCCUU-
vvi-miR398a                 ----UGUGUU--CUCAGGUCACCCCUU-
csi-miR398a-3p              ----UGUGUU--CUCAGGUCACCCCUU-
rco-miR398a                 ----UGUGUU--CUCAGGUCACCCCUU-
gra-miR398                  ----UGUGUU--CUCAGGUCACCCCUU-
aly-miR398a-3p              ----UGUGUU--CUCAGGUCACCCCUU-
tcc-miR398b                 ----UGUGUU--CUCAGGUCACCCCUU-
mdm-miR398a                 ----UGUGUU--CUCAGGUCACCCCUU-
bol-miR398                  ----UGUGUU--CUCAGGUCACCCCU--
cru-miR398a                 ----UGUGUU--CUCAGGUCACCCCU--
stu-miR398b-3p              ---UUGUGUU--CUCAGGUCACCCCU--
lus-miR398d                 ----UGUGUU--CUCAGGUCACCCCUC-
lus-miR398e                 ----UGUGUU--CUCAGGUCACCCCUC-
esa-miR398a                 ----UGUGUU--CUCAGGUCACCCCU--
lus-miR398b                 ----UGUGUU--CUCAGGUCACCCCU--
lus-miR398c                 ----UGUGUU--CUCAGGUCACCCCU--
cru-miR398b                 -----GUGUU--CUCAGGUCACCCCUGC
cru-miR398c                 -----GUGUU--CUCAGGUCACCCCUGC
aly-miR398c-3p              ----UGUGUUAACUCAGGUCACCCCUG-
bdi-miR398b                 CAGGAGUGUCA-CUGAGAACACA-----
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