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

ptc-miR408-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

AUGCACUGCCUCUUCCCUGGC

miRBase

Precursor miRNA Sequence(5'-3')

AGAGACAGAUGAAGACGGGGAACAGGCAGAGCAUGGAUGGAGCUACUAACAGAAGUACUUGUUUUGGCUCUACCCAUGCACUGCCUCUUCCCUGGCUUGUGGCUC

miRBase

Precursor miRNA Structure(5'-3') 

A   A AGAUG   A       C      A      A        CU     AA 
 GAG C     AAG CGGGGAA AGGCAG GCAUGG UGGAGCUA  AACAG  G
 ||| |     ||| ||||||| |||||| |||||| ||||||||  |||||   
 CUC G     UUC GUCCCUU UCCGUC CGUACC AUCUCGGU  UUGUU  C
-   - --GUG   G       C      A      C        -U     CA

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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