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

aly-miR162a-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

UCGAUAAACCUCUGCAUCCAG

miRBase

Precursor miRNA Sequence(5'-3')

GAUUCGGGAAAUUUUAUGUUUCUUUGCCAUUUUUUUUGGAGUUUAGUUGGAAAAAGAGUGAGAGUCGCUGGAGGCAGCGGUUCAUCGAUCUCUUCCUGGGAACGAAUAUAUAAAUAUUGAAAAAGCAUGAAUAGAUCGAUAAACCUCUGCAUCCAGCGUUUGCCUCUUUAUCUUUGUUAUUGGCUUCAAUUUUUUUGGUUUUUGAAAAAAGUGAGGGAAAACAGAGUC

miRBase

Precursor miRNA Structure(5'-3') 

     -GGGAAA      --G    -UUU    UUUUUU        ---UAGUU   A      U A   U       G    C    C        C   C  -GGAACG     A 
GAUUC       UUUUAU   UUUC    GCCA      UUGGAGUU        GGA AAAGAG G GAG CGCUGGA GCAG GGUU AUCGAUCU UUC UG       AAUAU U
|||||       ||||||   ||||    ||||      ||||||||        ||| |||||| | ||| ||||||| |||| |||| |||||||| ||| ||       |||||  
CUGAG       GGAGUG   AAAG    UGGU      AACUUCGG        UCU UUUCUC C UUU GCGACCU CGUC CCAA UAGCUAGA AAG AC       UUAUA A
     ACAAAAG      AAA    UUUU    UUUUUU        UUAUUGUU   A      - G   -       A    U    A        U   U  GAAAAAG     A

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

bol-miR162          UCGAUAAACCUCUGCAUCCA-
zma-miR162-3p       UCGAUAAACCUCUGCAUCCA-
gma-miR162a         UCGAUAAACCUCUGCAUCCA-
bra-miR162a         UCGAUAAACCUCUGCAUCCAG
bra-miR162c         UCGAUAAACCUCUGCAUCCAG
esa-miR162a         UCGAUAAACCUCUGCAUCCAG
esa-miR162b         UCGAUAAACCUCUGCAUCCAG
mac-miR162a         UCGAUAAACCUCUGCAUCCAG
pha-miR162          UCGAUAAACCUCUGCAUCCAG
pvi-miR162a         UCGAUAAACCUCUGCAUCCAG
pvi-miR162b         UCGAUAAACCUCUGCAUCCAG
sit-miR162          UCGAUAAACCUCUGCAUCCAG
ath-miR162a-3p      UCGAUAAACCUCUGCAUCCAG
ath-miR162b-3p      UCGAUAAACCUCUGCAUCCAG
osa-miR162a         UCGAUAAACCUCUGCAUCCAG
mtr-miR162          UCGAUAAACCUCUGCAUCCAG
ptc-miR162a         UCGAUAAACCUCUGCAUCCAG
ptc-miR162b         UCGAUAAACCUCUGCAUCCAG
sbi-miR162          UCGAUAAACCUCUGCAUCCAG
aly-miR162b-3p      UCGAUAAACCUCUGCAUCCAG
lus-miR162a         UCGAUAAACCUCUGCAUCCAG
mes-miR162          UCGAUAAACCUCUGCAUCCAG
fve-miR162-3p       UCGAUAAACCUCUGCAUCCAG
sly-miR162          UCGAUAAACCUCUGCAUCCAG
osa-miR162b         UCGAUAAGCCUCUGCAUCCAG
aly-miR162a-3p      UCGAUAAACCUCUGCAUCCAG
gma-miR162c         UCGAUAAACCUCUGCAUCCAG
mdm-miR162b         UCGAUAAACCUCUGCAUCCAG
ppe-miR162          UCGAUAAACCUCUGCAUCCAG
mac-miR162b         UCGAUAAACCUCUGCAUCCGG
mac-miR162c         UCGAUAAACCUCUGCAUCCGG
mac-miR162d         UCGAUAAACCUCUGCAUCCGG
mac-miR162e         UCGAUAAACCUCUGCAUCCGG
mac-miR162f         UCGAUAAACCUCUGCAUCCGG
mac-miR162g         UCGAUAAACCUCUGCAUCCGG
bdi-miR162          UCGAUAAACCUCUGCAUCCGG
vvi-miR162          UCGAUAAACCUCUGCAUCCAG
rco-miR162          UCGAUAAACCUCUGCAUCCAG
gma-miR162b         UCGAUAAACCUCUGCAUCCAG
mdm-miR162a         UCGAUAAACCUCUGCAUCCAG
stu-miR162b-3p      UCGAUAAACCUCUGCAUCCAG
stu-miR162a-3p      UCGAUAAACCUCUGCAUCCAG
lus-miR162b         UCGAUAAACCUCUGCAUCCAG
tcc-miR162          UCGAUAAACCUCUGCAUCCAG
csi-miR162-3p       UCGAUAAACCUCUGCAUCCAG
cpa-miR162a         UCGAUAAACCUCUGCAUCCAG
bra-miR162b         UCGAUAAACCUGUGCAUCCAG
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