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. 2009 Sep;21(9):2762–2779. doi: 10.1105/tpc.109.068536

Table 1.

Transcription Initiation Sites and Processing Sites Detected by 5′-RACE

Col-0
 rpoTmp
Gene 5′ End Sequence +TAP −TAP +TAP −TAP
cox1 Pcox1-88 CTCTCAAGAACTCGTAGACTATGGA 2/8 0/7 n.a. n.a.
cox1 cox1-241a,b GAATCCAATGGTAGGCCTGGGCTCT n.a. n.a. n.a. n.a.
cox1 Pcox1-355a AATTTATTCAATTATATaATAATAA n.a. n.a. 6/8# n.a.
nad1 Pnad1e4-275 TACAAAAACATTCTAGGaAAGGGCT 6/10 1/8 2/2 n.a.
nad1 Pnad1e4-775 CGACTGCTATCTAAGAGAAgATAAG 4, 3, 2/13 7, 0, 7/15 8/8 n.a.
nad1 Pnad1e4-838 GGCAATTTATCGTATAGaAGAATAG 3, 6/12 0, 0/13 14, 0/14 n.a.
nad1 nad1e4-892 GACCAAGCAAATCTCCTCTTCTAGT – 2/2 – –
matR PmatR∼3*,e CAATATGAAGAAAGAAaGAAGGGTT
matR PmatR∼58*,e GCCTTTGATTATAAAAAaGGGGAGC
nad1 Pnad1e5-427 ACTAATTATATATATATaATAAGGT 5/7 0/10 2/8 n.a.
nad1 Pnad1e5-927 CAAATATTGTAAATCAAgAAGGTGG 5/18 0/10 2/13 n.a.
ccmC PccmC-45 CTTTGATTGCGTATTATaGATCCAT 4/16 0/15 1/14 n.a.
ccmC PccmC-487ce TATCGATCGGCGTAAGaAAAgATTC 1, 2, 1/15 0, 2, 1/12 1, 1/8 n.a.
ccmC PccmC-1159 GATTCGTCATGGTAGAGaAGAAAAA 6/6 – 8/8 –
ccmC ccmC-1634 CCTCGAATTCTGTAAGCTAGCTTGG 1/1 n.a. 9/9 n.a.
ccmC PccmC-1677 CTACCAAACGTGCTAATAAAAGAGC 8/9 0/7 – –
ccmC PccmC-1817 AAGTAATTCATTATAAgATAAGTaA 1, 3, 9/13 0, 0, 4/8 2, 2/9 n.a.
ccmC PccmC-1834e ACACTACTATATAAGATAAGTAATT 2, 0/2 1,4/6 n.a. n.a.
rps4 rps4+2b GAGTCCCAGGGACGCAAtGTGGCTG 13/13 n.d 8/8# n.a.
rps4 Prps4-477 AGAAAGCTCAAGTATGTaAACAACC 6/7 n.a. 8/8 n.a.
rps4 Prps4-1509 AGATAGGTCAGGTATATaTAGCGAT 4/6 0/8 3/3# –
nad2 Pnad2e1-114be CACTATCATTAtATTATATaTTCAT 6,10, 4/32 5, 3, 2/18 3, 1/7 n.a.
nad2 Pnad2e1-299 CAAGATATTGCGTATaAATATATAT 2/28 n.a. 1/8 n.a.
nad2 Pnad2e1-413 GAACAAAAGATGTAATGaAAAgATA 2, 3/10 n.a. 4, 3/8 n.a.
nad6 Pnad6-88 GAAGAAAATGAAATAGGAaCAACCG 2,10/16 0,1/7 7/15 n.a.
nad6 Pnad6-143 ATTGAGATTCCGTAAGTaACTCAGT 3/8 n.a. 9/16 n.a.
nad6 nad6-179b GGGTACAAGATCGAAAAgAATGCAT 14/17 12/14 3/7 n.a.
nad6 Pnad6-333 GATGATTATGTTGAAAAaGATCGAA – – 8/8 0/7
nad6 Pnad6-401 CGGGTACAGTAGTAGGTaAACTTGA 18/19 2/8 8/8 –
ccmFc ccmFc-124b AAGTCCCTCCTTCCGCTCCTGGTGT n.a. n.a. n.a. n.a.
ccmFc PccmFc-379e TTGGATTATCGTAGAATAAGAGGAG 6/7 6/7 n.a. n.a.
ccmFc PccmFc-743 TTTATTATTCTATTATAaTAGTCTA – – 8/8 –
nad9 nad9-211/210c GGCGATCCACGAATTTGATCATTCG 1, 2/8 n.a. n.a. n.a.
nad9 Pnad9-1241e TACGAAATATAGTAAATATCGTAAA 3/3 n.a. n.a. n.a.
nad9 Pnad9-1371 TTCTCGTAATGTATTTAACCATAAA 2/8 n.a. – –
nad9 nad9-1400 CAAACTAAATGCTATAAGCATAGAA 1/2 n.a. n.a. n.a.
nad9
 Pnad9∼1730e
 GATTGATAAAGGTAATAGATATGAT
 n.a.
 n.a.
 n.a.
 n.a.

TSSs and processing sites determined for the wild type (Col-0) are underlined in sequences; lowercase positions denote sites mapped for rpoTmp. CATA, CGTA, TCTA, ATTA, AGTA, and GGTA motifs frequently found associated with mitochondrial promoter sequences (Fey and Marechal-Drouard, 1999; Kühn et al., 2005) are in bold. The number of clones sequenced for each site is given together with the frequency of the respective transcript 5′ end as determined from TAP-treated (+TAP) or untreated (−TAP) seedling RNA. Where more than one nucleotide is marked in one sequence, 5′ end frequencies are given in 5′-to-3′ order. Mutant transcript 5′ ends were mostly analyzed from rpoTmp-2 5′-RACE products. In a few cases where products amplified for rpoTmp-2 were extremely faint but rpoTmp-1 products formed a clear band, the latter were cloned and sequenced (numbers marked #). As reported by Forner et al. (2007), matR 5′ ends were poorly defined (sites marked *; see Supplemental Figure 7 online for identified 5′ ends). The first codons of the annotated MATR and RPS4 coding sequences are italicized. –, Signal absent in 5′-RACE; n.a., not analyzed.

a

Determined previously (Kühn et al., 2005).

b

Determined previously (Forner et al., 2007).

c

Determined previously (Forner et al., 2008) with minor differences.

e

Putative promoters for which experimental data are insufficient to support their function as TSS.