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

ptc-miR397b

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

CCAUUGAGUGCAGCGUUGAUG

miRBase

Precursor miRNA Sequence(5'-3')

UAAUUAUACACCAUUGAGUGCAGCGUUGAUGAAAUUCUCUUGUUAGCUUACUUAGCUAUUUUCUCACGAUGGCGUGGAAUCAUUUCACCAGCGCUGCAUUCAACCAUGUUUUUC

miRBase

Precursor miRNA Structure(5'-3') 

UAAUUAU   CCA               A      UCUCUUGUUAGCUUACUUAGCU 
       ACA   UUGAGUGCAGCGUUG UGAAAU                      A
       |||   ||||||||||||||| ||||||                       
       UGU   AACUUACGUCGCGAC ACUUUA                      U
--CUUUU   ACC               C      CUAAGGUGCGGUAGCACUCUUU

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

zma-miR397a-5p              UCAUUGAGCGCAGCGUUGAUG---
zma-miR397b-5p              UCAUUGAGCGCAGCGUUGAUG---
ptc-miR397b                 CCAUUGAGUGCAGCGUUGAUG---
hvu-miR397a                 CCGUUGAGUGCAGCGUUGAUG---
sly-miR397-5p               --AUUGAGUGCAGCGUUGAUGA--
stu-miR397-5p               --AUUGAGUGCAGCGUUGAUGAC-
lus-miR397a                 --AUUGAGUGCAGCGUUGAUGAA-
bdi-miR397b-5p              --AUUGAGUGCAGCGUUGAUGAA-
pha-miR397                  ---UUGAGUGCAGCGUUGAUGAGC
pvi-miR397a                 ---UUGAGUGCAGCGUUGAUGAGC
pvi-miR397b                 ---UUGAGUGCAGCGUUGAUGAGC
dca-miR397-b2.0r1-8662      ---UUGAGUGCAGCGUUGAUGAUC
mdm-miR397a                 ---UUGAGUGCAGCGUUGAUGAAA
mdm-miR397b                 ---UUGAGUGCAGCGUUGAUGAAA
mac-miR397                  ---UUGAGUGCAGCGUUGAUGAGA
mes-miR397                  --UUUGAGUGCAGCGUUGAUGA--
osa-miR397b                 UUAUUGAGUGCAGCGUUGAUG---
mes-miR397b                 UCAUUGAGUGCAGCGUUGAUG---
atr-miR397a                 UCCUUGAGUGCAGCGUUGAUG---
fve-miR397                  UCAUUGAGUGCAGCGUUGAUG---
ppe-miR397                  UCAUUGAGUGCAGCGUUGAUG---
mtr-miR397-5p               UCAUUGAGUGCAGCGUUGAUG---
lus-miR397b                 UCAUUGAGUGCAGCGUUGAUG---
gma-miR397b-5p              UCAUUGAGUGCAGCGUUGAUG---
gma-miR397a                 UCAUUGAGUGCAGCGUUGAUG---
tcc-miR397                  UCAUUGAGUGCAGCGUUGAUG---
csi-miR397-5p               UCAUUGAGUGCAGCGUUGAUG---
aly-miR397b-5p              UCAUUGAGUGCAGCGUUGAUG---
aly-miR397a-5p              UCAUUGAGUGCAGCGUUGAUG---
rco-miR397                  UCAUUGAGUGCAGCGUUGAUG---
bdi-miR397a                 UCAUUGAGUGCAGCGUUGAUG---
sbi-miR397-5p               UCAUUGAGUGCAGCGUUGAUG---
vvi-miR397a                 UCAUUGAGUGCAGCGUUGAUG---
ptc-miR397a                 UCAUUGAGUGCAGCGUUGAUG---
osa-miR397a                 UCAUUGAGUGCAGCGUUGAUG---
ath-miR397a                 UCAUUGAGUGCAGCGUUGAUG---
spo-miR397                  UCAUUGAGUGCAGCGUUGAUG---
ath-miR397b                 UCAUUGAGUGCAUCGUUGAUG---
cru-miR397a                 UCAUUGAGUGCAGCGUUGAUGU--
bra-miR397                  UCAUUGAGUGCAGCGUUGAUGU--
cru-miR397b                 UCAUUGAGUGCAGCGUUGAUAU--
atr-miR397b                 UCAUUGAGUGCAGCGUUGGUG---
ptc-miR397c                 UCAAUGAGUGGAGCUUUGAUG---
stu-miR397-3p               --CAUCAACGCUACACUCAAUCA-
hvu-miR397b-3p              ---AUCAACGCUGCACUCAACGGC
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