Table 1.

Description of transcript ends originating from the psbB operon

End number	Genome position	Notes
TSS, +TAP 5′ ends
1	72 200	PpsbB -171, described in (57). Seen in barley
2	72 409	Internal to psbB. Distal promoter for psbT?
3	74 393	PpsbH -92, described in (60)
4	76 153	Internal to petB exon 2. Distal promoter for petD?
5	76 375–76 376	Upstream petD
6	76 391	Internal to petD intron
7	76 780	Internal to petD intron
8	75 482	Antisense to petB intron. Distal promoter for psbN ?
Processed 5′ ends, −TAP 5′ends
1	72 320	psbB -51 mature end, described in (57)
2	73 211	Internal to psbB. Highest peak from a region with multiple 5′ends. Degradation intermediate?
3	73 658	Internal to psbB. Highest peak from a region with multiple 5′ends. Degradation intermediate?
4	74 418	psbT-psbH intergenic region, psbH -67 mature end, described as a precise endoribonuclease cleavage in (60). See also 3′ end #7
5	74 441	psbT-psbH intergenic region, psbH -44 mature end. Main psbH 5′ end, processing depends on HCF107, described in (58,59)
6	74 794	psbH-petB intergenic region, petB -47 mature end. Processing depends on HCF152, described in (61,62). See 3′ end #9
7	74 847	first nucleotide of petB intron. Sign of a hydrolytic splicing?
8	76 627	internal to petD intron. Degradation intermediates?
9	76 679	internal to petD intron. Degradation intermediates?
10	76 760	internal to petD intron. Degradation intermediates?
11	76 830	internal to petD intron. Degradation intermediates?
12	76 863	internal to petD intron. Highest peak from a region with multiple 5′ ends. Degradation intermediates?
3′ ends
1	72 601	Internal to psbB. Degradation intermediate?
2	72 786	Internal to psbB. Degradation intermediate?
3	73 371	Internal to psbB. Degradation intermediate? Downstream of numerous 5′ends, see 5′end #2, maybe the signature of an endo-ribonuclease cleavage?
4	73 838	Internal to psbB. Degradation intermediate? Downstream of numerous 5′ends, see 5′end #3, maybe the signature of an endo-ribonuclease cleavage?
5	74 082	First nucleotide of psbT, might be the 3′ end of a cDNA identified in (30)
6	74 242	3′ end of psbT, psbT +60, defined by a stem loop that also defines the 3′ end of the antisense psbN transcript, see 3′ end #17. Described in (30)
7	74 405	psbT-psbH intergenic region, 3′ end of psbT, psbT +223, described as a precise endo-ribonuclease cleavage in (60). See also 5′ end #4
8	74 687	Internal to psbH, 20 nt upstream of the stop codon. Degradation intermediate?
9	74 814	psbH-petB intergenic region, psbH +109 mature end. Processing depends on HCF152, described in (61,62). See 5′ end #6
10	76 358	petB-petD intergenic region, petB +67 mature end. Processing depends on CRP1, described in (63)
11	76 543	internal to petD intron. Degradation intermediates?
12	77 014	internal to petD intron. Degradation intermediates? 5 nt downstream of a smRNA footprint.
13	77 047	internal to petD intron. Degradation intermediates?
14	77 765	3′ end of petD, petD +94, defined by a stem loop that also defines the 3′end of the antisense rpoA transcript, see 3′ end #16. Processing requires mTERF6, described in (64)
15	77 892	3′ end of petD, petD +221.
16	77 716	3′ end of rpoA, rpoA +185, defined by a stem loop that also defines the 3′end of the antisense petD transcript, see 3′ end #14. Processing requires mTERF6, described by (64)
17	74 211	3′ end of psbN, psbN +39, defined by a stem loop that also defines the 3′ end of the antisense psbT transcript, see 3′ end #6. Described in (30)