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-miR1030f

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UCUGCAUCUGCACCUGCACCA

miRBase

Precursor miRNA Sequence(5'-3')

CCUCUACAUAACUACUCCAAUGCCACGUAUCUGCAUCUGCACCUGCACCAAAGUUUUGUAAUUCUACGGCUCGUGGUAGUCUGUUGUUGUGAAGGUGGGAUGUAGCUGAGUGUAUUACUCGGUGUUCAUUUGAUCAUUAUUACCCGAUGGUGCGGGUUCUUAUGCAGAGCCGUGGCAUUGGAGUAAUCCUCUACUU

miRBase

Precursor miRNA Structure(5'-3') 

CCUCUACAUAAC               UA       CU C          AAGUUUUGUAAUUCUACGGCUCGUGGUAGUCUGUUGUUGUGAAGGUG 
            UACUCCAAUGCCACG  UCUGCAU  G ACCUGCACCA                                               G
            |||||||||||||||  |||||||  | ||||||||||                                               G
            AUGAGGUUACGGUGC  AGACGUA  C UGGGCGUGGU                                               G
-UUCAUCUCCUA               CG       UU U          AGCCCAUUAUUACUAGUUUACUUGUGGCUCAUUAUGUGAGUCGAUGU

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

mpo-miR1030-b3.0r1-10150      UCUGCAUCUGCACCUGCACC-
ppt-miR1030h                  UCUGCAUCUGCACCUGCACCG
ppt-miR1030f                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030g                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030e                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030d                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030c                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030b                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030a                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030j                  CCUGCAUCUGCACCUGCACCA
ppt-miR1030i                  CCUGCAUCUGCACCUGCACCG
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