Table 2 |
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|
Putative target genes of non-conserved miRNAs and miRNA candidates identified in Populus. |
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|
miRNA Family |
Populus Predicted Target |
Homolog in Arabidopsis |
Target Predicted Function |
|
|
|||
|
miRNA with target predicted in Populus with homolog in Arabidopsis |
|||
|
|
|||
|
ptr-miR7000* |
CX173939 |
At4g12800.1 |
Photosystem I reaction center subunit |
|
ptr-miR7001 |
DT522234 |
At1g12230.1 |
Transaldolase ToTAL2 |
|
ptr-miR7002 |
TA2404_3696 |
At3g54190 |
Hypothetical protein |
|
ptr-miR7006 |
TA2404_3696 |
At3g54190 |
Hypothetical protein |
|
ptr-miR7007 |
Grail3.0035010701 |
At4g17980 |
No apical meristem (NAM) |
|
EstExt_fgenesh4_pg.C_LG_II1399 |
At1g33060 |
Transcription factor (ANAC014) |
|
|
ptr-miR7009-1 |
Eugene3.00060403 |
At2g41450 |
PAXIP1L protein |
|
Fgenesh4_pg.C_LG_XII000915 |
At1g66350 |
Scarecrow transcription factor |
|
|
ptr-miR7009-2 |
Eugene3.00060403 |
At2g41450 |
PAXIP1L protein |
|
Fgenesh4_pg.C_LG_XII000915 |
At1g66350 |
Scarecrow transcription factor |
|
|
ptr-miR7009-3 |
Eugene3.00060403 |
At2g41450 |
PAXIP1L protein |
|
Fgenesh4_pg.C_LG_XII000915 |
At1g66350 |
Scarecrow transcription factor |
|
|
ptr-miR7009-4 |
Eugene3.00060403 |
At2g41450 |
PAXIP1L protein |
|
Fgenesh4_pg.C_LG_XII000915 |
At1g66350 |
Scarecrow transcription factor |
|
|
ptr-miR7010 |
Gw1.X.2191.1 |
At3g12530 |
DNA replication protein-related |
|
Gw1.41.327.1 |
At4g09350 |
DNAJ heat shock |
|
|
ptr-miR7013 |
EstExt_Genewise1_v1.C_LG_V0549 |
At1g34190 |
No apical meristem (NAM) |
|
Fgenesh4_pm.C_scaffold_29000148 |
At2g38250 |
DNA-binding protein-related |
|
|
Eugene3.00110906 |
At1g53140 |
Dynamin family protein |
|
|
EstExt_fgenesh4_pg.C_LG_II1399 |
At1g33060 |
Transcription factor (ANAC014) |
|
|
EstExt_fgenesh4_pg.C_LG_XIV0205 |
At4g17980 |
Transcription factor (ANAC071) |
|
|
ptr-miR7015 |
Fgenesh4_pg.C_LG_XVIII000967 |
At2g24300 |
Calmodulin-binding protein |
|
Gw1.245.24.1 |
At5g36930 |
Toll-Interleukin-Resistance (TIR) |
|
|
EstExt_Genewise1_v1.C_LG_XVIII0864 |
At5g11790 |
Ndr family protein |
|
|
Eugene3.00190231 |
At4g27220 |
ATP binding |
|
|
Gw1.245.9.1 |
At5g36930 |
TIR-NBS-LRR |
|
|
Gw1.3272.9.1 |
At5g36930 |
TIR-NBS-LRR |
|
|
Gw1.I.4710.1 |
At5g36930 |
TIR-NBS-LRR |
|
|
Gw1.XI.1412.1 |
At5g36930 |
TIR-NBS-LRR |
|
|
Gw1.XI.1580.1 |
At5g36930 |
TIR-NBS-LRR |
|
|
ptr-miR7018 |
Grail3.0033032901 |
At2g45620 |
Nucleotidyltransferase |
|
Fgenesh4_pg.C_LG_VIII001448 |
At5g43630 |
Nucleic acid binding |
|
|
ptr-miR7021 |
Gw1.117.167.1 |
At5g36930 |
TIR-NBS-LRR class |
|
ptr-miR7022 |
TA14145_3694 |
At5g41680.2 |
Putative senescence-associated |
|
ptr-miR7023 |
CN519776 |
At5g15270.1 |
KH domain-containing protein |
|
Eugene3.00041046 |
At5g15270 |
KH domain-containing protein |
|
|
TA578_3690 |
At4g09350 |
Hypothetical protein |
|
|
Fgenesh4_pg.C_scaffold_70000157 |
At3g06350 |
Dehydroquinate dehydratase |
|
|
Gw1.41.327.1 |
At4g09350 |
DNAJ heat shock |
|
|
Gw1.I.8684.1 |
At4g23740 |
Kinase protein |
|
|
Gw1.X.2191.1 |
At3g12530 |
DNA replication protein Psf2 |
|
|
ptr-miR7024 |
EstExt_fgenesh4_pg.C_LG_IX0044 |
At1g76310 |
B-like cyclin |
|
EstExt_fgenesh4_pg.C_LG_XVI0015 |
At5g47630 |
Acyl carrier family protein (ACP) |
|
|
Grail3.0083002901 |
At5g49980 |
F-box |
|
|
ptr-miR7025 |
DN496261 |
At3g19830 |
C2 domain-containing protein |
|
ptr-miR7032 |
TA4511_293756 |
At3g05560.1 |
60S ribosomal protein |
|
ptr-miR7033-1 |
Fgenesh4_pg.C_LG_III000186 |
At5g57010 |
Calmodulin-binding family protein |
|
ptr-miR7033-2 |
Fgenesh4_pg.C_LG_III000186 |
At5g57010 |
Calmodulin-binding family protein |
|
ptr-miR7033-3 |
Fgenesh4_pg.C_LG_III000186 |
At5g57010 |
Calmodulin-binding family protein |
|
ptr-miR7033-4 |
Fgenesh4_pg.C_LG_III000186 |
At5g57010 |
Calmodulin-binding family protein |
|
ptr-miR7034 |
Fgenesh4_pg.C_LG_XII000915 |
At4g08250 |
Scarecrow transcription factor |
|
ptr-miR7035 |
Eugene3.00020435 |
At4g30720 |
Expressed protein |
|
ptr-miR7036 |
Eugene3.00020435 |
At3g63390 |
Expressed protein |
|
ptr-miR7040-1* |
TA11116_113636 |
At4g27220.1 |
NBS-LRR type disease resistance |
|
ptr-miR7040-2* |
TA11116_113636 |
At4g27220.1 |
NBS-LRR type disease resistance |
|
ptr-miR7041 |
CK096204 |
At5g53130.1 |
Cyclic nucleotide-gated channel C |
|
TA14492_3694 |
At5g28450.1 |
Chlorophyll a-b binding 7 |
|
|
TA16704_3694 |
At1g80550 |
Hypothetical protein |
|
|
TA20868_47664 |
At5g53130.1 |
Cyclic nucleotide-gated channel C |
|
|
ptr-miR7042 |
CK092266 |
At5g27380.1 |
Glutathione synthetase |
|
ptr-miR7044 |
TA1634_80863 |
At3g59480.1 |
Putative fructokinase 2 |
|
ptr-miR7046-1 |
EstExt_Genewise1_v1.C_1840054 |
At1g17860 |
Trypsin and protease inhibitor |
|
ptr-miR7046-2 |
EstExt_Genewise1_v1.C_1840054 |
At1g17860 |
Trypsin and protease inhibitor |
|
|
|||
|
miRNA with annotated target predicted in Populus with no homolog in Arabidopsis |
|||
|
|
|||
|
ptr-miR7005** |
AJ777690 |
no |
Polyphenol oxidase |
|
Eugene3.00100932 |
no |
Polyphenol oxidase |
|
|
ptr-miR7012 |
CK110871 |
no |
Hypothetical protein |
|
ptr-miR7014** |
AJ777690 |
no |
Polyphenol oxidase |
|
ptr-miR7016 |
AJ773830 |
no |
Hypothetical protein |
|
TA3964_3691 |
no |
Ac1147-like protein |
|
|
TA7847_3695 |
no |
CDH1-D |
|
|
ptr-miR7017 |
Gnl|PPLGI|CK106645 |
no |
Hypothetical protein |
|
ptr-miR7019 |
Gnl|PPLGI|TC19799 |
no |
Histidine kinase like ATPase |
|
ptr-miR7020 |
AJ773830 |
no |
Hypothetical protein |
|
TA3964_3691 |
no |
Ac1147-like protein |
|
|
TA7847_3695 |
no |
CDH1-D [Gallus gallus (Chicken)] |
|
|
ptr-miR7030 |
AJ777857 |
no |
Polyphenol oxidase |
|
DN483929 |
no |
Polyphenol oxidase |
|
|
TA14535_3695 |
no |
Polyphenol oxidase |
|
|
ptr-miR7037 |
TA12949_3694 |
no |
Hypothetical protein ART3 |
|
|
|||
|
miRNA with target predicted non-annotated in Populus with no homolog in Arabidopsis |
|||
|
|
|||
|
ptr-miR7003 |
Gnl|PPLGI|TC35094 |
no |
- |
|
ptr-miR7004 |
BU871048 |
no |
- |
|
ptr-miR7014 |
Eugene3.89590001 |
no |
- |
|
ptr-miR7026 |
DN487711 |
no |
- |
|
ptr-miR7029-1 |
CV259704 |
no |
- |
|
CV259944 |
no |
- |
|
|
DT491789 |
no |
- |
|
|
ptr-miR7029-2 |
CV259704 |
no |
- |
|
CV259944 |
no |
- |
|
|
DT491789 |
no |
- |
|
|
ptr-miR7029-3 |
CV259704 |
no |
- |
|
CV259944 |
no |
- |
|
|
DT491789 |
no |
- |
|
|
ptr-miR7039 |
CV230379 |
no |
- |
|
ptr-miR7047 |
BU873871 |
no |
- |
|
|
|||
|
"-" indicates that no target was found in Populus. "no" indicates that no Arabidopsis homolog of the Populus target was found. Other target were found for some miRNAs, but they have no significant similarity either to Arabidopsis (*) or other plant (**) protein sequences. |
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|
Barakat et al. BMC Genomics 2007 8:481 doi:10.1186/1471-2164-8-481 |
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