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

sly-miR169d

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

UAGCCAAGGAUGACUUGCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GAAGAGGGGUUUUAUAUGAAGUUGAGAGUAUUAUUUAGUAGCCAAGGAUGACUUGCCUACUUCAUUUGAUAUAUAGUUUAAAAUAAUAAUAUUGACAAUAUUUGUCAUUUGGUCGUAGGCAAGUUAUCCUGGCUAUCUUGACAUGCUCGUAAUUUUUCAUGUAAGACCUUAUCUUC

miRBase

Precursor miRNA Structure(5'-3') 

     -G              --    A      UAUUUA       A               -U   UU     U   GUUUAA    A 
GAAGA  GGGUUUUAUAUGAA  GUUG GAGUAU      GUAGCCA GGAUGACUUGCCUAC  UCA  UGAUA AUA      AAUA U
|||||  ||||||||||||||  |||| ||||||      ||||||| |||||||||||||||  |||  ||||| |||      ||||  
CUUCU  UCCAGAAUGUACUU  UAAU CUCGUA      UAUCGGU CCUAUUGAACGGAUG  GGU  ACUGU UAU      UUAU U
     AU              UU    G      CAGUUC       -               CU   UU     U   -AACAG    A

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

pha-miR169g         CUUAGCCAAGAAUG-ACUUGCCU----
sit-miR169k         --UAGCCAAGAAUG-ACUUGCCU----
sit-miR169o         --UAGCCAAGAAUG-ACUUGCCU----
tcc-miR169f         --AAGCCAAGAAUG-ACUUGCCUG---
gma-miR169t         --UAGCCAAGGAUGGACUUGCCUA---
vvi-miR169y         --UAGCGAAGGAUG-ACUUGCCUA---
cru-miR169e         --UAGCCAAGGAUG-ACUUGCCUA---
mac-miR169a         --UAGCCAAGGAUG-ACUUGCCUA---
mac-miR169l         --UAGCCAAGGAUG-ACUUGCCUA---
pha-miR169b         --UAGCCAAGGAUG-ACUUGCCUA---
osa-miR169f.1       --UAGCCAAGGAUG-ACUUGCCUA---
osa-miR169g         --UAGCCAAGGAUG-ACUUGCCUA---
sbi-miR169c         --UAGCCAAGGAUG-ACUUGCCUA---
zma-miR169f-5p      --UAGCCAAGGAUG-ACUUGCCUA---
zma-miR169g         --UAGCCAAGGAUG-ACUUGCCUA---
zma-miR169h         --UAGCCAAGGAUG-ACUUGCCUA---
ptc-miR169r         --UAGCCAAGGAUG-ACUUGCCUA---
vvi-miR169x         --UAGCCAAGGAUG-ACUUGCCUA---
sly-miR169d         --UAGCCAAGGAUG-ACUUGCCUA---
sbi-miR169h         --UAGCCAAGGAUG-ACUUGCCUA---
sbi-miR169m         --UAGCCAAGGAUG-ACUUGCCUA---
sbi-miR169n         --UAGCCAAGGAUG-ACUUGCCUA---
tcc-miR169d         --UAGCCAAGGAUG-ACUUGCCUA---
bdi-miR169h-5p      --UAGCCAAGGAUG-ACUUGCCUA---
mes-miR169ab        --UAGCCAAGGAUG-ACUUGCCUA---
bdi-miR169n         --UAGCCAAGGAUG-ACUUGCCUA---
csi-miR169q-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169p-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169l-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169j-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169i-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169h-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169f-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169e-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169d-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169c-5p      --UAGCCAAGGAUG-ACUUGCCU----
csi-miR169b-5p      --UAGCCAAGGAUG-ACUUGCCU----
fve-miR169d         --UAGCCAAGGAUG-ACUUGCCU----
fve-miR169c         --UAGCCAAGGAUG-ACUUGCCU----
fve-miR169b         --UAGCCAAGGAUG-ACUUGCCU----
fve-miR169a         --UAGCCAAGGAUG-ACUUGCCU----
atr-miR169c         --UAGCCAAGGAUG-ACUUGCCU----
atr-miR169a         --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169h         --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169g         --UAGCCAAGGAUG-ACUUGCCU----
mac-miR169n         -UUAGCCAAGGAUG-ACUUGCCU----
pha-miR169a         --UAGCCAAGGAUG-ACUUGCCU----
sbi-miR169d-5p      --UAGCCAAGGAUG-ACUUGCCU----
bra-miR169i         -GUAGCCAAGGAUG-ACUUGCCU----
bra-miR169k         -GUAGCCAAGGAUG-ACUUGCCU----
mac-miR169q         -GUAGCCAAGGAUG-ACUUGCCU----
bra-miR169g         --UAGCCAAGGAUG-ACUUGCCU----
pha-miR169f         --UAGCCAAGGAUG-ACUUGCCU----
mes-miR169ac        --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169a-5p      --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169b-5p      --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169c-5p      --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169d-5p      --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169e-5p      --UAGCCAAGGAUG-ACUUGCCU----
stu-miR169f-5p      --UAGCCAAGGAUG-ACUUGCCU----
mdm-miR169o         --UAGCCAGGGAUG-ACUUGCCU----
tcc-miR169g         --UAGCCAGGGAUG-ACUUGCCUA---
ptc-miR169u-5p      --UAGCCAAGGACG-ACUUGCCUA---
osa-miR169n         --UAGCCAAGAAUG-ACUUGCCUA---
osa-miR169o         --UAGCCAAGAAUG-ACUUGCCUA---
sbi-miR169i         --UAGCCAAGAAUG-ACUUGCCUA---
zma-miR169o-5p      --UAGCCAAGAAUG-ACUUGCCUA---
bdi-miR169d         --UAGCCAAGAAUG-ACUUGCCUA---
pha-miR169h         CUUAGCCAAGAAUG-GCUUGCCU----
csi-miR169c-3p      --CAGGCAG-UCUC--CUUGGCUAAG-
csi-miR169d-3p      --CAGGCAG-UCUC--CUUGGCUAAG-
csi-miR169e-3p      --CAGGCAG-UCUC--CUUGGCUAAG-
csi-miR169l-3p      ---AGGCAG-UCUC--CUUGGCUAAC-
aly-miR169m-3p      ----GGCAG-UCUU--CUUGGCUAUC-
zma-miR169o-3p      ----GGCAGGUCUU--CUUGGCUAGC-
zma-miR169n-3p      ----GGCAGGCCUU--CUUGGCUAAG-
zma-miR169q-3p      ----GGCAGGCCUU--CU-GGCUAAG-
zma-miR169m-3p      ----GGCAUCCAUU--CUUGGCUAAG-
pvi-miRN2531        ---UGGCAAGCAUU--CU-GGUUAAGC
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