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

ppt-miR408b

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UGCACUGCCUCUUCCCUGGCU

miRBase

Precursor miRNA Sequence(5'-3')

GUGGAAGAGAGAGAGUGGUGGAAGGGAGGGAAGCCAGCGUGAGGCAAUGCAUGACAACAGCAUGCCCAGGAGGUCCUGAGGGUGUUGUCCUCAUGCACUGCCUCUUCCCUGGCUUCCCUACAUAGCUCGCCAUUCUUGUGCUCU

miRBase

Precursor miRNA Structure(5'-3') 

GUGGA    --A          - AAGG -           C -U      A       CA       G C    A 
     AGAG   GAGAGUGGUG G    G AGGGAAGCCAG G  GAGGCA UGCAUGA  ACAGCAU C CAGG G
     ||||   |||||||||| |    | ||||||||||| |  |||||| |||||||  ||||||| | ||||  
     UCUC   UUCUUACCGC C    C UCCCUUCGGUC C  CUCCGU ACGUACU  UGUUGUG G GUCC C
-----    GUG          U GAUA A           C UU      C       CC       G A    U

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

lus-miR408a                  AUGCACUGCCUCUUCCCUGGC--
mdm-miR408a                  AUGCACUGCCUCUUCCCUGGC--
mes-miR408                   AUGCACUGCCUCUUCCCUGGC--
mtr-miR408-3p                AUGCACUGCCUCUUCCCUGGC--
gma-miR408c-3p               AUGCACUGCCUCUUCCCUGGC--
gma-miR408b-3p               AUGCACUGCCUCUUCCCUGGC--
gma-miR408a-3p               AUGCACUGCCUCUUCCCUGGC--
csi-miR408-3p                AUGCACUGCCUCUUCCCUGGC--
aly-miR408-3p                AUGCACUGCCUCUUCCCUGGC--
vvi-miR408                   AUGCACUGCCUCUUCCCUGGC--
ptc-miR408-3p                AUGCACUGCCUCUUCCCUGGC--
ath-miR408-3p                AUGCACUGCCUCUUCCCUGGC--
esa-miR408                   AUGCACUGCCUCUUCCCUGGC--
cru-miR408                   AUGCACUGCCUCUUCCCUGGC--
gma-miR408d                  -UGCACUGCCUCUUCCCUGGC--
pha-miR408                   CUGCACUGCCUCUUCCCUGGC--
sit-miR408                   CUGCACUGCCUCUUCCCUGGC--
tae-miR408                   CUGCACUGCCUCUUCCCUGGC--
osa-miR408-3p                CUGCACUGCCUCUUCCCUGGC--
zma-miR408a                  CUGCACUGCCUCUUCCCUGGC--
sbi-miR408                   CUGCACUGCCUCUUCCCUGGC--
zma-miR408b-3p               CUGCACUGCCUCUUCCCUGGC--
rco-miR408                   CUGCACUGCCUCUUCCCUGGC--
bdi-miR408-3p                CUGCACUGCCUCUUCCCUGGC--
cpa-miR408                   CUGCACUGCCUCUUCCCUGGC--
fve-miR408                   -UGCACUGCCUCUUCCCUGGCU-
stu-miR408b-3p               -UGCACUGCCUCUUCCCUGGCU-
ppt-miR408b                  -UGCACUGCCUCUUCCCUGGCU-
spo-miR408                   -UGCACUGCCUCUUCCCUGGCU-
pvi-miR408c                  -UGCACUGCCUCUUCCCUGGCU-
pvi-miR408b                  -UGCACUGCCUCUUCCCUGGCU-
pvi-miR408a                  -UGCACUGCCUCUUCCCUGGCU-
mac-miR408                   -UGCACUGCCUCUUCCCUGGCU-
bra-miR408                   -UGCACUGCCUCUUCCCUGGCU-
mpo-miR408-b3.0r1-15745      -UGCACUGCCUCUUCCCUGGCU-
smo-miR408                   -UGCACUGCCUCUUCCCUGGCUG
stu-miR408a-3p               -UGCACAGCCUCUUCCCUGGUU-
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