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

csi-miR399f-5p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

GGGCAAUUCUCCUUUGGCAGA

miRBase

Precursor miRNA Sequence(5'-3')

UUCUGCGGGCCGCGGGUAGAGGAGAAUUCCAGGGCAAUUCUCCUUUGGCAGAAAAUAUUGCGCUUGUACGUACACGCACGGUGCAGUACUUGCACAGGUGCUAUAAUAUAUAAUAUUUGCCGCCAAAGGAGAAUUGCCCUGCCAUUCAACUACUACCAUAUGUAUGCAUAC

miRBase

Precursor miRNA Structure(5'-3') 

UUC    G  CGCG     -  GA    UC                    A A       ----------        --AC    AC     
   UGCG GC    GGUAG AG  GAAU  CAGGGCAAUUCUCCUUUGGC G AAAUAUU          GCGCUUGU    GUAC  GCAC 
   |||| ||    ||||| ||  ||||  |||||||||||||||||||| | |||||||          ||||||||    ||||  ||| G
   ACGU UG    CCAUC UC  CUUA  GUCCCGUUAAGAGGAAACCG C UUUAUAA          CGUGGACA    CAUG  CGUG 
CAU    A  UAUA     A  AA    CC                    C G       UAUAUAAUAU        CGUU    -A

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

dca-miR399-b2.0r1-4355      ---------GGGCAA-UACUCCACUGGCAGU
dca-miR399-b2.0r1-4356      ---------GGGCAA-UACUCCACUGGCAGU
aly-miR399g-5p              ---------GGGCAAAUACUCCAUUGGCAGA
aly-miR399i-5p              ---------GGGCAAAUACUCCAUUGGCAGA
aly-miR399d-5p              ---------GGGCGAAUACUCCUAUGGCAGA
csi-miR399f-5p              ---------GGGCAA-UUCUCCUUUGGCAGA
ppe-miR399b                 UCUGCCAAAGGAGAAUUGCCC----------
                                     **   * * * *