Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae

Table 1.

Biological investigations of candidates

Pattern results
fsORF	Chr.	Location	gDNA^a	mRNA^b	cDNA^c	FS	Class
1^*,^d	I	192541-196178	+1 nt	-	-	-	both
2	II	289386-290383	yes	yes	yes	6.0 ± 1	left
3^e	II	454780-457622	yes	yes	yes	1.1 ± 1	left
5	II	701799-700347	yes	no	-	-	left
6^*	III	200170-197617	yes	yes	yes	0.1 ± 0	both
10^*	IV	167806-164992	yes	yes	yes	3.0 ± 0	both
14	IV	809035-808330	yes	yes	yes	1.8 ± 0	none
15^e	IV	890828-890321	yes	no	-	-	none
17^*	V	298948-301706	yes	no	-	-	left
19^e	VI	15473-14309	yes	yes	yes	9.0 ± 1	both
20^*	VII	1068995-1067213	yes	no	-	-	left
22^*	VII	270340-267730	yes	yes	yes	0.5 ± 0	both
23	VII	425616-425971	yes	yes	yes	n.a.	none
24	VII	677871-678301	yes	yes	yes	13.0 ± 1	none
32^d	XI	172169-171299	yes	yes	yes	0.1 ± 0	left
34^*	XI	549085-551003	+1 nt	-	-	-	left
37^*	XII	200413-200654	yes	no	-	-	none
38	XII	203255-204786	yes	yes	yes	n.a	both
40^*	XII	857539-861524	yes	no	-	-	both
42	XIII	349605-348426	yes	yes	yes	n.a	left
43^*,^e	XIII	436627-438788	yes	yes	yes	5.0 ± 1	both
44^*	XIII	509318-507416	yes	yes	yes	5.0 ± 1	left
45	XIII	623212-622159	no	-	-	-	left
46	XIII	650035-651026	yes	yes	yes	10.0 ± 1	left
48	XIV	40618-42065	yes	no	-	-	left
51	XV	1026837-1028101	yes	yes	yes	7.0 ± 1	left
52	XV	742910-744210	yes	yes	yes	5.0 ± 1	left
53	XV	758330-759354	yes	no	-	-	left
56	XVI	117365-117062	yes	yes	yes	0.1 ± 0	none
57	XVI	138830-139449	yes	yes	yes	3.0 ± 1	left

HMM results
fsORF	Chr.	Location	gDNA	mRNA^b	cDNA	FS	Class	Rank
19^e	VI	15473-14309	yes	yes	yes	9.0 ± 1	both	1
29^*,^d	X	405173-406968	+1 nt	-	-	-	both	2
28^*	X	219713-217406	yes	yes	yes	2.1 ± 0	both	3
12^*	IV	384077-381986	yes	yes	yes	11.0 ± 1	both	4
43^*,^e	XIII	436627-438788	yes	yes	yes	5.0 ± 1	both	5
18^*	VI	123462-129904	yes	no	-	-	both	6
41^*	XIII	263477-266754	yes	yes	yes	n.a	both	7
33	XI	374144-374853	yes	yes	yes	12.0 ± 1	left	1
25	VIII	262554-262197	yes	yes	yes	0.1 ± 0	left	2
4^d	II	554266-553504	+1 nt	-	-	-	left	3
36^d	XI	639597-638535	+1 nt	-	-	-	left	4
3^e	II	454780-457622	yes	yes	yes	1.1 ± 1	left	5
11	IV	205690-205988	yes	yes	yes	0.1 ± 0	none	1
50	XIV	537790-538010	yes	yes	yes	0.8 ± 0	none	2
27	VIII	499891-499585	yes	no	-	-	none	3
47	XIV	394359-394026	yes	yes	yes	n.a	none	4
54	XV	782222-782003	yes	no	-	-	none	5
14^e	IV	809035-808330	yes	yes	yes	1.8 ± 0	none	6
15^e	IV	890828-890321	yes	no	-	-	none	7
31	X	74021-74610	yes	intron	-	-	right	1
55	XV	80639-81189	yes	intron	-	-	right	2
35	XI	611160-611899	yes	yes	yes	7.0 ± 1	right	3
13	IV	630075-630598	yes	intron	-	-	right	4
7^*,^f	III	220178-218372	yes	no	-	-	right
8^f	III	222829-223097	yes	yes	yes	0.1 ± 0	none
9^f	III	91686-91455	yes	no	-	-	none
16^f	V	183582-183327	yes	no	-	-	none
21^f	VII	146543-146769	yes	no	-	-	none
26^f	VIII	35126-34916	yes	no	-	-	none
30^f	X	732756-732555	yes	no	-	-	none
39^f	XII	767116-766933	yes	no	-	-	none
49^f	XIV	429214-428983	yes	no	-	-	none
58^f	XVI	935319-935028	yes	no	-	-	none

For each tested candidate, we have reported its location, examined the genomic DNA sequence, tested for the presence of an mRNA, and in some cases, analyzed a cDNA sequence, and experimentally evaluated - 1 frameshifting (FS). For Hidden Markov Models (HMM) candidates, the calculated rank is also reported for each class.
Selected candidates are in bold and are described in Table 2.
↵* RT-PCR was carried with two sets of primers
↵a “yes” reports the presence of the expected gDNA sequence, “no” reports the lack of amplification of the corresponding genomic region, and “+1” reports the presence of an additional nucleotide, leading to an in-frame structure spanning both ORF0 and ORF-1
↵b “yes” or “no” states the presence or absence of an mRNA spanning the two ORFs, respectively; “intron” reports the presence of a previously unidentified intron
↵c “yes” states the presence of the expected cDNA sequence
↵d Reannotated by the Saccharomyces Genome Database (SGD)
↵e Candidates retrieved by both the HMM and protein pattern searches
↵f Control

This Article

Genome Res. 2005. 15: 1411-1420

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