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-miR477e-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UGAGGCCUUUGGGGGAGAGUGG

miRBase

Precursor miRNA Sequence(5'-3')

AUUGUUCACUCUCCCUCAAGGCUUCCAACGCAAUAACCAGCUACGUACAUGUAACUGUGUUACGGCUGCAGGCUUGAGGCCUUUGGGGGAGAGUGGUCAA

miRBase

Precursor miRNA Structure(5'-3') 

A   U              -      C  C  AAUAAC    UA    -   GU 
 UUG UCACUCUCCCUCAA GGCUUC AA GC      CAGC  CGUA CAU  A
 ||| |||||||||||||| |||||| || ||      ||||  |||| |||   
 AAC GGUGAGAGGGGGUU CCGGAG UU CG      GUCG  GCAU GUG  U
-   U              U      -  -  ---GAC    --    U   UC

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

ptc-miR477e-3p      UGAGGCCUUUGGGGGAGAGUGG
csi-miR477d-3p      UGAGGCCGUUGGGG-AGAGUGG
atr-miR477          AGAGGCCUUAGGGG-AGAGUGG
vvi-miR477b-3p      CGAAGUCUUUGGGG-AGAGUGG
ptc-miR477a-3p      GGAUGCCUUUGGGGGAGAUUG-
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