Table 2.
Targets of new candidate microRNAs in Brassica juncea
| miRNA | referred toArabidopsis | Category | Cleavage Site | MF-Rep Norm reads | CMS-Rep Norm reads | Annotation |
|---|---|---|---|---|---|---|
| PC-3p-30 |
AT4G28000.1 |
4 |
77 |
1 |
|
P-loop containing nucleoside triphosphate hydrolases superfamily protein |
| AT4G38850.1 |
4 |
272 |
|
0.111111 |
SAUR-like auxin-responsive protein family |
|
| PC-3p-41 |
AT1G07920.1 |
3 |
1202 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
| AT1G07930.1 |
3 |
1214 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| AT1G07930.2 |
3 |
983 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| AT1G07940.1 |
3 |
1206 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| AT1G07940.2 |
3 |
1333 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| AT1G35550.1 |
4 |
303 |
|
0.111111 |
elongation factor Tu C-terminal domain-containing protein |
|
| AT5G60390.1 |
3 |
1158 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| AT5G60390.2 |
3 |
1158 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| AT5G60390.3 |
3 |
1148 |
1 |
3.361111 |
GTP binding Elongation factor Tu family protein |
|
| PC-3p-65 |
AT1G18400.1 |
2 |
460 |
2 |
|
BR enhanced expression 1 |
| AT1G18710.1 |
4 |
792 |
0.333333 |
|
myb domain protein 47 |
|
| AT1G62750.1 |
3 |
82 |
|
0.4 |
Translation elongation factor EFG/EF2 protein |
|
| AT1G76720.1 |
4 |
1493 |
0.2 |
|
eukaryotic translation initiation factor 2 (eIF-2) family protein |
|
| AT1G76810.1 |
4 |
1225 |
0.2 |
|
eukaryotic translation initiation factor 2 (eIF-2) family protein |
|
| AT1G76820.1 |
4 |
878 |
0.2 |
|
eukaryotic translation initiation factor 2 (eIF-2) family protein |
|
| AT2G26630.1 |
4 |
761 |
0.25 |
0.2 |
transposable element gene |
|
| AT2G27710.1 |
3 |
505 |
0.535714 |
0.142857 |
60S acidic ribosomal protein family |
|
| AT2G27710.2 |
3 |
502 |
0.535714 |
0.142857 |
60S acidic ribosomal protein family |
|
| AT2G27710.3 |
3 |
433 |
0.535714 |
0.142857 |
60S acidic ribosomal protein family |
|
| AT2G27710.4 |
3 |
454 |
0.535714 |
0.142857 |
60S acidic ribosomal protein family |
|
| AT2G30860.1 |
3 |
128 |
|
1 |
glutathione S-transferase PHI 9 |
|
| AT2G30860.2 |
3 |
128 |
|
1 |
glutathione S-transferase PHI 9 |
|
| AT2G33810.1 |
4 |
409 |
1 |
|
squamosa promoter binding protein-like 3 |
|
| AT3G06870.1 |
2 |
585 |
0.4 |
|
proline-rich family protein |
|
| AT4G09255.1 |
4 |
62 |
0.5 |
|
transposable element gene |
|
| AT4G11420.1 |
4 |
538 |
|
1 |
eukaryotic translation initiation factor 3A |
|
| AT5G21274.1 |
4 |
63 |
|
1 |
calmodulin 6 |
|
| AT5G57290.2 |
2 |
348 |
3 |
0.333333 |
60S acidic ribosomal protein family |
|
| AT5G57655.1 |
4 |
1553 |
|
0.5 |
xylose isomerase family protein |
|
| AT5G57655.2 |
4 |
1592 |
|
0.5 |
xylose isomerase family protein |
|
| PC-5p-12 |
AT3G25100.1 |
3 |
823 |
0.5 |
|
cell division cycle 45 |
| AT5G28800.1 |
4 |
13 |
0.166667 |
|
unknown protein |
|
| AT5G40340.1 |
2 |
380 |
0.85 |
|
Tudor/PWWP/MBT superfamily protein 6 |
|
| AT5G52830.1 |
4 |
1040 |
|
1 |
WRKY DNA-binding protein 27 |
|
| AT5G62750.1 |
2 |
212 |
2 |
|
unknown protein |
|
| PC-5p-20 |
AT2G28056.1 |
2 |
677 |
2 |
|
MIR172/MIR172A; miRNA |
| PC-5p-32 |
AT1G70700.1 |
4 |
958 |
|
0.5 |
TIFY domain/Divergent CCT motif family protein |
| AT1G70700.2 |
4 |
886 |
|
0.5 |
TIFY domain/Divergent CCT motif family protein |
|
| AT2G24270.1 |
2 |
1736 |
0.75 |
|
aldehyde dehydrogenase 11A3 |
|
| AT2G24270.2 |
2 |
1633 |
0.75 |
|
aldehyde dehydrogenase 11A3 |
|
| AT2G24270.3 |
2 |
1622 |
0.75 |
|
aldehyde dehydrogenase 11A3 |
|
| AT2G24270.4 |
2 |
1633 |
0.75 |
|
aldehyde dehydrogenase 11A3 |
|
| AT2G39720.1 |
4 |
1004 |
|
1 |
RING-H2 finger C2A |
|
| PC-5p-51 |
AT2G20585.1 |
4 |
375 |
0.333333 |
|
nuclear fusion defective 6 |
| AT2G20585.2 |
4 |
375 |
0.333333 |
|
nuclear fusion defective 6 |
|
| AT2G20585.3 |
4 |
375 |
0.333333 |
|
nuclear fusion defective 6 |
|
| PC-5p-52 |
AT2G27760.1 |
4 |
42 |
|
0.5 |
tRNAisopentenyltransferase 2 |
| AT2G45960.1 |
4 |
148 |
0.166667 |
|
plasma membrane intrinsic protein 1B |
|
| AT2G45960.2 |
4 |
148 |
0.166667 |
|
plasma membrane intrinsic protein 1B |
|
| AT2G45960.3 |
4 |
148 |
0.166667 |
|
plasma membrane intrinsic protein 1B |
|
| AT2G47700.1 |
4 |
32 |
|
0.5 |
RING/U-box superfamily protein |
|
| AT3G03340.1 |
4 |
67 |
0.1 |
0.1 |
LUC7 related protein |
|
| AT3G09980.1 |
4 |
71 |
0.333333 |
|
Family of unknown function (DUF662) |
|
| AT3G57870.1 |
4 |
81 |
1 |
|
sumo conjugation enzyme 1 |
|
| AT5G18310.1 |
0 |
31 |
1.5 |
|
unknown protein |
|
| AT5G18310.2 |
0 |
24 |
1.5 |
|
unknown protein |
|
| PC-5p-53 |
AT3G46040.1 |
3 |
131 |
1 |
|
ribosomal protein S15A D |
| AT4G02660.1 |
2 |
8902 |
1 |
|
Beige/BEACH domain ;WD domain, G-beta repeat protein |
|
| AT4G34230.1 |
2 |
178 |
|
1 |
cinnamyl alcohol dehydrogenase 5 |
|
| AT4G34230.2 |
2 |
175 |
|
1 |
cinnamyl alcohol dehydrogenase 5 |
|
| AT5G53530.1 |
4 |
993 |
1 |
|
vacuolar protein sorting 26A |
|
| AT5G59850.1 |
2 |
122 |
2.333333 |
0.333333 |
Ribosomal protein S8 family protein |
|
| PC-5p-56 |
AT4G12800.1 |
2 |
385 |
4 |
4 |
photosystem I subunit l |
| AT5G19290.1 |
4 |
387 |
|
1 |
alpha/beta-Hydrolases superfamily protein |
|
| PC-5p-64 |
AT1G20260.1 |
4 |
648 |
|
0.5 |
ATPase, V1 complex, subunit B protein |
| AT1G50500.1 |
4 |
533 |
0.333333 |
|
Membrane trafficking VPS53 family protein |
|
| AT1G50500.2 |
4 |
548 |
0.333333 |
|
Membrane trafficking VPS53 family protein |
|
| AT1G67410.1 |
0 |
1638 |
6 |
|
Exostosin family protein |
|
| AT1G71680.1 |
4 |
1781 |
1 |
|
Transmembrane amino acid transporter family protein |
|
| AT1G76030.1 |
4 |
654 |
|
0.5 |
ATPase, V1 complex, subunit B protein |
|
| AT2G38040.1 |
4 |
1257 |
0.5 |
2.5 |
carboxyltransferase alpha subunit |
|
| AT2G38040.2 |
4 |
1232 |
0.5 |
2.5 |
carboxyltransferase alpha subunit |
|
| AT4G25050.1 |
4 |
355 |
|
0.5 |
acyl carrier protein 4 |
|
| AT4G25050.2 |
4 |
416 |
|
0.5 |
acyl carrier protein 4 |
|
| AT4G35300.1 |
4 |
2370 |
|
0.2 |
tonoplast monosaccharide transporter2 |
|
| AT4G35300.2 |
4 |
2371 |
|
0.2 |
tonoplast monosaccharide transporter2 |
|
| AT4G35300.3 |
4 |
2331 |
|
0.2 |
tonoplast monosaccharide transporter2 |
|
| AT4G35300.4 |
4 |
2370 |
|
0.2 |
tonoplast monosaccharide transporter2 |
|
| AT4G35300.5 |
4 |
2251 |
|
0.2 |
tonoplast monosaccharide transporter2 |
|
| AT4G36640.1 |
1 |
281 |
1.5 |
|
Sec14p-like phosphatidylinositol transfer family protein |
|
| AT4G36640.2 |
1 |
185 |
1.5 |
|
Sec14p-like phosphatidylinositol transfer family protein |
|
| AT5G19770.1 |
4 |
558 |
0.5 |
|
tubulin alpha-3 |
|
| AT5G19780.1 |
4 |
591 |
0.5 |
|
tubulin alpha-5 |
|
| AT5G54960.1 |
4 |
1869 |
0.5 |
0.5 |
pyruvate decarboxylase-2 |
|
| PC-5p-74 | AT3G09800.1 |
2 |
689 |
3 |
2 |
SNARE-like superfamily protein |
| AT3G17900.1 |
4 |
905 |
|
1 |
unknown protein |
|
| AT3G53710.1 |
4 |
1391 |
0.5 |
|
ARF-GAP domain 6 |
|
| AT3G53710.2 |
4 |
1333 |
0.5 |
|
ARF-GAP domain 6 |
|
| AT3G56850.1 |
4 |
1331 |
|
1 |
ABA-responsive element binding protein 3 |
|
| AT4G09510.1 |
0 |
1861 |
6.5 |
3 |
cytosolic invertase 2 |
|
| AT4G09510.2 |
0 |
1916 |
6.5 |
3 |
cytosolic invertase 2 |
|
| AT5G27860.1 |
4 |
463 |
0.5 |
|
unknown protein |
|
| AT5G27860.2 |
4 |
463 |
0.5 |
|
unknown protein |
|
| AT5G39740.1 |
2 |
838 |
0.75 |
0.5 |
ribosomal protein L5 B |
|
| AT5G39740.2 |
2 |
880 |
0.75 |
0.5 |
ribosomal protein L5 B |
|
| AT5G47040.1 |
1 |
2243 |
|
4 |
lon protease 2 |
|
| ATMG01360.1 |
2 |
1453 |
13 |
2 |
cytochrome oxidase |
|
| AT4G31480.1 |
4 |
2477 |
0.333333 |
|
Coatomer, beta subunit |
|
| AT4G31480.2 |
4 |
2557 |
0.333333 |
|
Coatomer, beta subunit |
|
| AT4G31490.1 | 4 | 2399 | 0.333333 | Coatomer, beta subunit |