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

mdm-miR530c

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

UGCAUUUGCACCUGCACUUGU

miRBase

Precursor miRNA Sequence(5'-3')

ACAGCGCAGAUGCCAAAAUGUUGCUUUUAUCUGCAUUUGCACCUGCACUUGUGCUCGUUCAUGUUUCUUCCUUCCUUGAAAAACCCUAAAGCCAAAGCUUCAGAGAAUGGAAAAGGUUUUAGAUAUAUGAGAACAAAAAUGACAAGAGGAAAGGAAUAAGGGAARAGAAGGAAAAUGGAAAUCAGAAGGAAGAGCAGGAACAAGCAAGAGGUGCAGGUGCCAGUGCAGGUGAAUGCCAUUUUGGUUCAUUAAAAACA

miRBase

Precursor miRNA Structure(5'-3') 

--ACAGCGCA  U         UU  U            U            -G    C    A    U      --------------     GAAAAA    AAAG  AAAG    AGAGAAUGGAAAAGG     GA 
          GA GCCAAAAUG  GC UUUAUCUGCAUU GCACCUGCACUU  UGCU GUUC UGUU CUUCCU              UCCUU      CCCU    CC    CUUC               UUUUA  U
          || |||||||||  || |||||||||||| ||||||||||||  |||| |||| |||| ||||||              |||||      ||||    ||    ||||               |||||   
          CU UGGUUUUAC  CG AAGUGGACGUGA CGUGGACGUGGA  ACGA CAAG ACGA GAAGGA              AGGAA      GGGA    GG    GGAG               AGAGU  A
ACAAAAAUUA  -         --  U            C            GA    A    G    -      AGACUAAAGGUAAA     -GARAA    AUAA  -AAA    --AACAGUAAAAACA     AU

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

gma-miR530b         --UGCAUUUGCACCUGCACUUUA
gma-miR530c         --UGCAUUUGCACCUGCACUUUA
gma-miR530d         --UGCAUUUGCACCUGCACUUUA
gma-miR530e         --UGCAUUUGCACCUGCACUUUA
gma-miR530a         --UGCAUUUGCACCUGCACUUU-
mtr-miR530          --UGCAUUUGCACCUGCACUUUC
bdi-miR530a         --UGCAUUUGCACCUGCACCUAC
bdi-miR530b         --UGCAUUUGCACCUGCACCUAC
osa-miR530-5p       --UGCAUUUGCACCUGCACCUA-
mac-miR530          --UGCAUUUGCACCUGCACCUAA
tcc-miR530a         --UGCAUUUGCACCUGCACCUC-
fve-miR530          --UGCAUUUGCACCUGCACCUCU
stu-miR530          UCUGCAUUUGCACCUGCACCU--
ppe-miR530          UCUGCAUUUGCACCUGCACCU--
ptc-miR530b         --UGCAUUUGCACCUGCAUCUU-
csi-miR530b-5p      --UGCAUUUGCACCUGCAUCUUG
csi-miR530a-5p      --UGCAUUUGCACCUGCACCUUG
tcc-miR530b         --UGCAUUUGCACCUGCACCUU-
mes-miR530a         --UGCAUUUGCACCUGCACCUU-
mes-miR530b         --UGCAUUUGCACCUGCACCUUA
ptc-miR530a         --UGCAUUUGCACCUGCACCUU-
lus-miR530b         --UGCAUUUGCACCUGCACCUU-
lus-miR530a         --UGCAUUUGCACCUGCACCUU-
mdm-miR530a         --UGCAUUUGCACCUGCACUUGU
mdm-miR530b         --UGCAUUUGCACCUGCACUUGU
mdm-miR530c         --UGCAUUUGCACCUGCACUUGU
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