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

aly-miR393b-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

AUCAUGCGAUCUCUUUGGAUU

miRBase

Precursor miRNA Sequence(5'-3')

AGCAACUAGAGAAAGCAUCCAAAGGGAUCGCAUUGAUCCUAAUUAAGCUGAUUUAUUCCCCAAUAUUUUAUUUUCCUCAUUCGAAAGUUGGAGAAAAAAAAAAAAAAUUCUAAACAUUUGCUUUCUUUUCCGGAUCAUGCGAUCUCUUUGGAUUCAUUCUUUGGUAGCU

miRBase

Precursor miRNA Structure(5'-3') 

   A         A C                 U     ---UAAUU    ---  A    UUCCCCAAUA    A      UCAUU 
AGC ACUAGAGAA G AUCCAAAGGGAUCGCAU GAUCC        AAGC   UG UUUA          UUUU UUUUCC     C
||| ||||||||| | ||||||||||||||||| |||||        ||||   || ||||          |||| ||||||     G
UCG UGGUUUCUU C UAGGUUUCUCUAGCGUA CUAGG        UUCG   AC AAAU          AAAA AAGAGG     A
   A         A U                 -     CCUUUUCU    UUU  -    CUUAAAAAAA    A      UUGAA

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

pvi-miR393c         -CUCCAAAGGGAUCGCAUUGA---
pvi-miR393d         -CUCCAAAGGGAUCGCAUUGA---
sit-miR393a         -CUCCAAAGGGAUCGCAUUGAU--
mac-miR393a         --UCCAAAGGGAUCGCAUUGAUCU
mac-miR393b         --UCCAAAGGGAUCGCAUUGAUCU
mac-miR393c         --UCCAAAGGGAUCGCAUUGAUCU
mac-miR393d         --UCCAAAGGGAUCGCAUUGAUCU
osa-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUCU
zma-miR393a-5p      --UCCAAAGGGAUCGCAUUGAUCU
zma-miR393c-5p      --UCCAAAGGGAUCGCAUUGAUCU
mdm-miR393a         --UCCAAAGGGAUCGCAUUGAUCU
mdm-miR393b         --UCCAAAGGGAUCGCAUUGAUCU
mdm-miR393c         --UCCAAAGGGAUCGCAUUGAUCU
mes-miR393c         --UCCAAAGGGAUCGCAUUGAUCU
mes-miR393d         --UCCAAAGGGAUCGCAUUGAUCU
fve-miR393b         --UCCAAAGGGAUCGCAUUGAUCU
bra-miR393d         --UCCAAAGGGAUCGCAUUGAUC-
bra-miR393e         --UCCAAAGGGAUCGCAUUGAUC-
bra-miR393a         --UCCAAAGGGAUCGCAUUGAUCC
bol-miR393          ---CCAAAGGGAUCGCAUUGAUCC
bra-miR393b         --UCCAAAGGGAUCGCAUUGAUCC
bra-miR393c         --UCCAAAGGGAUCGCAUUGAUCC
cru-miR393a         --UCCAAAGGGAUCGCAUUGAUCC
cru-miR393b         --UCCAAAGGGAUCGCAUUGAUCC
esa-miR393a         --UCCAAAGGGAUCGCAUUGAUCC
esa-miR393b         --UCCAAAGGGAUCGCAUUGAUCC
ath-miR393a-5p      --UCCAAAGGGAUCGCAUUGAUCC
ath-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUCC
zma-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUCC
aly-miR393a-5p      --UCCAAAGGGAUCGCAUUGAUCC
aly-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUCC
tcc-miR393a         --UCCAAAGGGAUCGCAUUGAUCC
gma-miR393c-5p      --UCCAAAGGGAUCGCAUUGAUCC
gma-miR393d         --UCCAAAGGGAUCGCAUUGAUCC
gma-miR393e         --UCCAAAGGGAUCGCAUUGAUCC
gma-miR393f         --UCCAAAGGGAUCGCAUUGAUCC
gma-miR393g         --UCCAAAGGGAUCGCAUUGAUCC
mes-miR393b         --UCCAAAGGGAUCGCAUUGAUCC
stu-miR393-5p       --UCCAAAGGGAUCGCAUUGAUCC
cpa-miR393          --UCCAAAGGGAUCGCAUUGAUCC
atr-miR393          --UCCAAAGGGAUCGCAUUGAUCC
sbi-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
bdi-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUC-
lus-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
lus-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
lus-miR393c         --UCCAAAGGGAUCGCAUUGAUC-
lus-miR393d         --UCCAAAGGGAUCGCAUUGAUC-
mes-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
ppe-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
fve-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
csi-miR393c-5p      --UCCAAAGGGAUCGCAUUGAUC-
bdi-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
tcc-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
rco-miR393          --UCCAAAGGGAUCGCAUUGAUC-
vvi-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
gma-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
vvi-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
mtr-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUC-
ptc-miR393c         --UCCAAAGGGAUCGCAUUGAUC-
ptc-miR393b-5p      --UCCAAAGGGAUCGCAUUGAUC-
ptc-miR393a-5p      --UCCAAAGGGAUCGCAUUGAUC-
mtr-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
sbi-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
osa-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
sit-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
pha-miR393b         --UCCAAAGGGAUCGCAUUGAUC-
pha-miR393a         --UCCAAAGGGAUCGCAUUGAUC-
mac-miR393f         --UCCAAAGGGAUCGCAUUGAUC-
mac-miR393e         --UCCAAAGGGAUCGCAUUGAUC-
gma-miR393h         -UUCCAAAGGGAUCGCAUUGAUC-
zos-miR393b         -UUCCAAAGGGAUCGCAUUGAU--
gma-miR393i         -UUCCAAAGGGAUCGCAUUGAUC-
zos-miR393a         -UUCCAAAGGGAUCGCAUUGUUC-
gma-miR393j         -UUCCAAAGGGAUCGCAUUGAUC-
gma-miR393k         -UUCCAAAGGGAUCGCAUUGAUC-
csi-miR393b-5p      -UUCCAAAGGGAUCGCAUUGAUC-
pvi-miR393b         --UCCAAAGGGAUCGCAUUGAU--
pvi-miR393a         --UCCAAAGGGAUCGCAUUGAU--
csi-miR393a         -AUCCAAAGGGAUCGCAUUGAUC-
ppe-miR393a         CAUCCAAAGGGAUCGCAUUGA---
ath-miR393b-3p      --AUCA-UGCGAUCUCUUUGGAUU
aly-miR393b-3p      --AUCA-UGCGAUCUCUUUGGAUU
mdm-miR393d         --AUCA-UGCGAUCCCUUCGGACG
mdm-miR393e         --AUCA-UGCGAUCCCUUCGGACG
mdm-miR393f         --AUCA-UGCGAUCCCUUCGGACG
zma-miR393b-3p      --AUCAAUGCGAUCCUUUUGGAGG
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