Table 2

Predicted phased and trans-acting loci.

Location

Sequences

Phased sequences

Number of Targets (perfect match)

Phasing trigger

Genomic context


LG_III:13629357..136296081

7

6

0

CDS

LG_III:13638142..136383931

7

6

0

CDS

LG_III:13654756..13655007

7

5

1(0)

CDS/intergenic

LG_VI:551356..551607

25

9

4(0)

si39621

Intergenic

LG_VI:14747098..14747349

13

6

5(2) MYB

ptc- miR828

CDS

LG_X:19646453..196471872

62

14

8(1)

ptc- miR482.2

UTR

LG_XII:9812366..9812617

20

7

2(0)

CDS/intergenic

LG_XV:5567507..5567758

13

6

3(0)

CDS/intergenic

LG_XIX:138605..138856

12

7

28(1) NBS- LRR

Intergenic

scaffold_70:624107..6243583

13

6

10(1) PPR

ptc- miR475c

CDS

scaffold_70:867516..867767

4

4

10(3) PPR

ptc- miR475c

CDS

scaffold_180:454350..454601

7

5

16(7) NBS- LRR

Intergenic


Predicted phased and trans-acting loci with p <0.00001. Where a locus targets many genes from a particular class, this is shown after the number of targets. The number of predicted targets at each locus is shown with the number of perfect-match siRNA-targets indicated in parenthesis. Target predictions were made using the psRNATarget web tool. 1These two loci are duplicates. 2Manually corrected coordinates, as described in Materials and Methods. 3There is a second locus just adjacent to this (scaffold_70:624403..624654) with p 0.000026, suggesting that the two may represent a single locus.

Klevebring et al. BMC Genomics 2009 10:620   doi:10.1186/1471-2164-10-620

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