Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data

BMC Genomics

Table 2 Expression data for intron retention candidates

Gene/Tag	Intron	Intron length	F-1	F-6	DF1	DF-6	DF10	N2-1	DAU
B0041.3
TACGATTTCA	2	48	1	2	1	2	0	1	2
C08B6.13
AGGATACAAT	1	81	4	6	1	1	1	1	0
C14C6.5
CGGTTATTGC	3	69	27	7	31	1	73	10	3
C24G6.3
TGAAATAATA	12	51	0	0	1	5	0	0	2
D1054.10
ATCGGTGTGT	2	91	0	0	4	0	3	0	0
F07C6.2
TAATGAATTT	2	56	1	1	1	2	0	1	2
R09E10.3
TCAATAAATA	8	82	9	0	0	0	0	0	0
T23G7.5
TTTTATATAA	4	47	2	3	3	0	1	8	1
W01A8.3
AAAACAATAA	5	70	8	1	0	0	0	0	0
Y116A8C.30
TATTGGAATC	3	97	0	0	1	0	0	0	3

SAGE data for ten tags selected for validation of intron retention by RT-PCR. The Intron column indicates which intron was predicted to be retained and the Intron Length column shows the length of that intron in nucleotides. The other columns show the normalized tag counts in the SAGE libraries made from the RNA preparations used in validation experiments: F-1, 6: fer-15 at days 1 and 6 of adulthood; DF-1, 6, 10: daf-2; fer-15 at days 1, 6 and 10 of adulthood; N2-1: N2 at day 1 of adulthood; DAU: young dauer larvae. Tags in all libraries were normalized to 100,000 total tags.

ISSN: 1471-2164