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

bdi-miR2118a

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

UUUCCGAUGCCUCCCAUUCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GACAAUGUGAGGCAGGUCGGGAAGAGGAAGAGAAGAGGGCCUUAGAGCAGUGGGAGUGGGAACAUGGAGGAAAGCCUGACUUGCUUUGUUUUCACCUCAAGUGUUGGAGGUGAGAACUUGGUUUGGUGCUUUCCGAUGCCUCCCAUUCCUAUUGUUCUCGAGCACUCGUUCCUCUUCCCUUUUGGCUCGCUCAGUU

miRBase

Precursor miRNA Structure(5'-3') 

   AAU     G    UC           GAGAA   G  CUU                  -A   GGA       -    CUU   UU           AAG 
GAC   GUGAG CAGG  GGGAAGAGGAA     GAG GC   AGAGCAGUGGGAGUGGGA  CAU   GGAAAGC CUGA   GCU  GUUUUCACCUC   U
|||   ||||| ||||  |||||||||||     ||| ||   ||||||||||||||||||  |||   ||||||| ||||   |||  |||||||||||    
UUG   CGCUC GUUU  CCCUUCUCCUU     CUC CG   UCUUGUUAUCCUUACCCU  GUA   CCUUUCG GGUU   UGG  CAAGAGUGGAG   U
   ACU     G    -U           ----G   A  AGC                  CC   --G       U    ---   UU           GUU

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

osa-miR2118m      UUCCUGAUGCCUCCCAUUCCUA
bdi-miR2118b      UUCCUGAUGCCUCCCAUUCCUA
osa-miR2118j      UUCCUGAUGCCUCCCAUUCCUA
osa-miR2118f      UUCCUGAUGCCUCCCAUUCCUA
zma-miR2118e      UUCCUGAUGUCUCCCAUUCCUA
osa-miR2118h      UUCCUGAUGCCUCUCAUUCCUA
osa-miR2118k      UUCCUGAUGCCUCUCAUUCCUA
zma-miR2118a      UUCCUGAUGCCUCUCAUUCCUA
osa-miR2118p      UUCCCGAUGCCUCCCAUGCCUA
osa-miR2118d      UUCCUGAUGCCUCCCAUGCCUA
osa-miR2118b      UUCCCGAUGCCUCCCAUUCCUA
osa-miR2118n      UUCCCGAUGCCUCCCAUUCCUA
zma-miR2118b      UUCCCGAUGCCUCCCAUUCCUA
osa-miR2118a      UUCUCGAUGCCUCCCAUUCCUA
bdi-miR2118a      UUUCCGAUGCCUCCCAUUCCUA
osa-miR2118c      UUCCCGAUGCCUCCUAUUCCUA
osa-miR2118q      UUCCCGAUGCCUCCUAUUCCUA
zma-miR2118g      UUCCUGAUGCCUCCUAUUCCUA
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