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-miR172g-5p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

GGAGCAUCAUCAAGAUUCACA

miRBase

Precursor miRNA Sequence(5'-3')

CUGUUUGCCUAUGGAGCAUCAUCAAGAUUCACAAGCUUUAUUAGGGCUAGUGUGUGGUGAUGAUGGUGGCUUUUGGUGGUCCCUUUUUUUCAAUCCAAUAGCCCUUUGAAUUGGGAAUCUUGAUGAUGCUGCAGCGGCAAUAA

miRBase

Precursor miRNA Structure(5'-3') 

CUGU     UA  G                A   GC    UU       G  U  GGU  U  U  U    UU 
    UUGCC  UG AGCAUCAUCAAGAUUC CAA  UUUA  AGGGCUA UG GU   GA GA GG GGCU  U
    |||||  || |||||||||||||||| |||  ||||  ||||||| || ||   || || || ||||   
    AACGG  AC UCGUAGUAGUUCUAAG GUU  AAGU  UCCCGAU AC UA   UU UU CC CUGG  U
-AAU     CG  G                G   --    -U       A  C  ACU  U  U  -    UG

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

stu-miR172d-5p      ---GGAGCAUCAUCAAGAUUCACA
aly-miR172f-5p      ---GGAGCAUCAUCAAGAUUCACA
aly-miR172c-5p      ---GGAGCAUCAUCAAGAUUCACA
ptc-miR172g-5p      ---GGAGCAUCAUCAAGAUUCACA
ptc-miR172b-5p      ---GGAGCAUCAUCAAGAUUCACA
csi-miR172d-5p      ---GCGGCAUCAUCAAGAUUCACA
gra-miR172a         ---GCGGCAUUAUCAAGAUUCACA
aly-miR172a-5p      ---GUGGCAUCAUCAAGAUUCACA
gra-miR172b         ---GCAGCAUUAUCAAGAUUCACA
csi-miR172b-5p      ---GCAGCAUCAUCAAGAUUCACA
stu-miR172e-5p      ---GCAACAUCAUCAAGAUUCACA
csi-miR172a-5p      ---GCAGCGUCCUCAAGAUUCACA
gma-miR172b-5p      ---GUAGCAUCAUCAAGAUUCAC-
ppe-miR172a-5p      ---GUAGCAUCAUCAAGAUUCACG
mtr-miR172c-5p      ---GUAGCAUCAUCAAGAUUCACA
stu-miR172a-5p      ---GUAGCAUAAUCAAGAUUCACA
ptc-miR172h-5p      ---GGAGCACCAUCAAGAUUCACA
csi-miR172c-5p      ---GGAGCACCAUCAAGAUUCACA
zma-miR172d-5p      ----CAGCACCAUCAAGAUUCACA
zma-miR172b-5p      ----CAGCACCAUCAAGAUUCACA
bdi-miR172a-5p      ---GCAGCACCACCAAGAUUCACA
zma-miR172c-5p      ----CAGCACCACCAAGAUUCACA
aly-miR172b-5p      ---GCAGCACCAUCAAGAUUCACA
osa-miR172d-5p      ---GCAGCACCAUCAAGAUUCAC-
gma-miR172g         ---GCAGCACCAUCAAGAUUCAC-
ath-miR172b-5p      ---GCAGCACCAUUAAGAUUCAC-
ath-miR172e-5p      ---GCAGCACCAUUAAGAUUCAC-
aly-miR172e-5p      ---GCAGCACCAUUAAGAUUCAC-
stu-miR172b-5p      ---GCAGCACCAUCAAGAUUCACA
gma-miR172h-5p      ---GCAGCAGCAUCAAGAUUCACA
gma-miR172i-5p      ---GCAGCAGCAUCAAGAUUCACA
gma-miR172j         ---GCAGCAGCAUCAAGAUUCACA
mtr-miR172d-5p      AGUGGAGCAUCAUCAAGAUUCACA
stu-miR172c-5p      -----AGCAUCUUCAAGAUUCACA
osa-miR172c         --UGAAUCUUGAUGAUGCUGCAC-
sbi-miR172e         --UGAAUCUUGAUGAUGCUGCAC-
vvi-miR172b         --UGAAUCUUGAUGAUGCUACAC-
vvi-miR172a         --UGAAUCUUGAUGAUGCUACAU-
vvi-miR172d         UGAGAAUCUUGAUGAUGCUGCAU-
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