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

ppe-miR2111b

Organism

Prunus persica

Species

Mature miRNA Sequence(5'-3')

UAAUCUGCAUCCUGAGGUUUA

miRBase

Precursor miRNA Sequence(5'-3')

UUAGCUCUUCAUACCUUGGUAGAACUGUAGAAGUAUACUGAUCGAUCGUAUUGGGUAAGGAUCGGGUAAUCUGCAUCCUGAGGUUUAGAUCAGCUUUGUUUUGUUGUUUCUAGCCCUCGGGGUGCAGAUUACCUCGUCCUCACUGCCAAUGCAAGACUUGUUAGCUAGUACUAAUAUAUCAAACCAAUGAAGCUAA

miRBase

Precursor miRNA Structure(5'-3') 

U     CU    ACCU    -A  AC    GA     --A    U   -  --       --  A     C                    U     -U    UUU 
 UAGCU  UCAU    UGGU  GA  UGUA  AGUAU   CUGA CGA UC  GUAUUGG  GU AGGAU GGGUAAUCUGCAUCCUGAGG UUAGA  CAGC   G
 |||||  ||||    ||||  ||  ||||  |||||   |||| ||| ||  |||||||  || ||||| |||||||||||||||||||| |||||  ||||    
 AUCGA  AGUA    ACCA  CU  AUAU  UCAUG   GAUU GUU AG  CGUAACC  CA UCCUG UCCAUUAGACGUGGGGCUCC GAUCU  GUUG   U
A     --    ----    AA  --    AA     AUC    -   C  AA       GU  C     C                    C     UU    UUU

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

fve-miR2111a         UAAUCUGCAUCCUGAGGUUU-
fve-miR2111b-5p      UAAUCUGCAUCCUGAGGUUU-
fve-miR2111c         UAAUCUGCAUCCUGAGGUUU-
ppe-miR2111d         UAAUCUGCAUCCUGAGGUUUA
ppe-miR2111c         UAAUCUGCAUCCUGAGGUUUA
ppe-miR2111b         UAAUCUGCAUCCUGAGGUUUA
ppe-miR2111a         UAAUCUGCAUCCUGAGGUUUA
aly-miR2111c-5p      UAAUCUGCAUCCUGAGGUUUA
mes-miR2111b         UAAUCUGCAUCCUGAGGUUUA
mes-miR2111a         UAAUCUGCAUCCUGAGGUUUA
mdm-miR2111b         UAAUCUGCAUCCUGAGGUUUA
mdm-miR2111a         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111f         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111e         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111c         UAAUCUGCAUCCUGAGGUUUA
gma-miR2111b         UAAUCUGCAUCCUGAGGUUUA
mtr-miR2111a-5p      UAAUCUGCAUCCUGAGGUUUA
mtr-miR2111f         UAAUCUGCAUCCUGAGGUUUA
tcc-miR2111          UAAUCUGCAUCCUGAGGUUUA
vvi-miR2111-5p       UAAUCUGCAUCCUGAGGUCUA
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