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-miR477h

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UCUCCCUCAAAGGCUUCCA

miRBase

Precursor miRNA Sequence(5'-3')

UCAGAGGGAGUAUACUCAGGUGUUUGUUUUUCUCCCUCAAAGGCUUCCAACUACAUCAGCAUUCUAUUCCACUUCUGGCUUAAGAUGCAGUGAAUUUGCGUUGUUGUUGGAUGCCUUAGUGGGAGAUGUACAUACCCCUGUCAUUGAUGUGUUGC

miRBase

Precursor miRNA Structure(5'-3') 

UCAGAGGGAGUAUACUC   U  U   UUU      U A     U      U   --------   --     C  UU   C 
                 AGG GU UGU   UCUCCC C AAGGC UCCAAC ACA        UCA  GCAUU UA  CCA U
                 ||| || |||   |||||| | ||||| |||||| |||        |||  ||||| ||  |||  
                 UCC CA ACA   AGAGGG G UUCCG AGGUUG UGU        AGU  CGUAG AU  GGU U
-CGUUGUGUAGUUACUG   C  U   UGU      U A     U      U   UGCGUUUA   GA     A  UC   C

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

ptc-miR477a-5p      -AUCUCCCUCAGAGGCUUCCAA-
ptc-miR477b         -AUCUCCCUCAGAGGCUUCCAA-
vvi-miR477a         -AUCUCCCUCAAAGGCUUCCAA-
mes-miR477f         -AUCUCCCUCAAAGGCUUCCA--
mes-miR477g         -AUCUCCCUCAAAGGCUUCCA--
ptc-miR477d-5p      -AUCUCCCUCAAAGGCUUCCUCU
ppt-miR477h         --UCUCCCUCAAAGGCUUCCA--
ppt-miR477c         -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477a-5p      -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477d         -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477e         -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477b         -CUCUCCCUCAAAGGCUUCCA--
csi-miR477b-5p      -CUCUCCCUCAAGGGCUUCUCU-
mes-miR477d         -CUCUCCCUCAAGGGCUUCUC--
stu-miR477a-5p      CCUCUCCCUCAAGGGCUUCUC--
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