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-miR536f

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UUCGUGCCAAGCUGUGUGCA

miRBase

Precursor miRNA Sequence(5'-3')

UUCGACGUCGUGUUAAGUGUGAUUCCUUAGCAGCCAUAGUUUGGUAUGAAGCUCUCUCUGAACAUCAGAUAUCGGUCGGUAGAGUUGAGGUUUGUUCACAUGACCUUAGCUCUGUUUUCCGAGCGCUUCGUGCCAAGCUGUGUGCAUCUAAGGGAAUCUCACUUCUGAACAGAAAG

miRBase

Precursor miRNA Structure(5'-3') 

UUCGACG  G    ---     U      -    CA  -                  U   UCUGAACAUCAGAUAUCGGUCGGUAGAGUUG 
       UC UGUU   AAGUG GAUUCC UUAG  GC CAUAGUUUGGUAUGAAGC CUC                               A
       || ||||   ||||| |||||| ||||  || |||||||||||||||||| |||                                
       AG ACAA   UUCAC CUAAGG AAUC  CG GUGUCGAACCGUGCUUCG GAG                               U
----GAA  -    GUC     U      G    UA  U                  C   CCUUUUGUCUCGAUUCCAGUACACUUGUUUG

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

ppt-miR536a              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536f              UUCGUGCCAAGCUGUGUGCA--
ppt-miR536b              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536d              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536e              UUCGUGCCAAGCUGUGUGCAAC
mpo-miR-b3.0r1-4273      -CCGUGCCAAGCUGUGUGCAUC
smo-miR536               -UCGUGUCAAGCUGUGUGCAUC
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