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-miR1030e

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UCUGCAUCUGCACCUGCACCA

miRBase

Precursor miRNA Sequence(5'-3')

GAAAAUCCUUGAAGCUGCAACGCUACUUUUCUGCAUCUGCACCUGCACCAAGAUGCGAUAACAUGUACAGAUGAACCAAAUACACAGUUGUACUGUCAUGCCCAGUUAGCCACUGGACUUGAUUUGUUGAACAAUUAUUUGUACUCGCUUUAUCGCGUACUGGUGCAGUGCCUAUGCAGACAUGUAGUGUUGUAGCUGGAUGCAGAUC

miRBase

Precursor miRNA Structure(5'-3') 

---GAAA    UUGA              UUU       CU    C       AG         --CAU         AACCAAAUACACA     ---  -U    U C     U 
       AUCC    AGCUGCAACGCUAC   UCUGCAU  GCAC UGCACCA  AUGCGAUAA     GUACAGAUG             GUUGU   AC  GUCA G CCAGU A
       ||||    ||||||||||||||   |||||||  |||| |||||||  |||||||||     |||||||||             |||||   ||  |||| | ||||| G
       UAGG    UCGAUGUUGUGAUG   AGACGUA  CGUG ACGUGGU  UGCGCUAUU     CAUGUUUAU             UAACA   UG  UAGU C GGUCA A
CUAGACG    ----              UAC       UC    -       CA         UCGCU         -------------     AGU  UU    U A     C

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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