Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns

Table 1 Unusual TG splice acceptors identified in the human transcriptome

	Intron		3' Splice site pair		ESTs for unusual 3' splice sites
Gene	No.	Length	Distance	Motif	Fraction	No.
GNAS	3	7843	3	CTG,CAG\|	0.15-0.62*^†	282
PCGF2	1	224	3	AAG\|ATG,	0.50	4
CNBP	3	168	3	TTGTTG,AAG\|	0.25	257
	3	168	6	TTG,TTGAAG\|	0.01	10
FBXO17 ^‡	3	1999	3	CAG\|ATG,	0.14	4
C21orf63	3	9975	3	CAG\|ATG,	0.09	2
BRUNOL4	6	1147	3	CAG\|CTG,	0.07	2
PCID2	2	2162	3	CAG\|ATG,	0.04	7
TNNT2	1	4354	3	TTG,GAG\|	0.04	2
*CACNA1A*	9	2532	3	TTGTTG,GAG\|	?^†	-
	9	2532	6	TTG,TTGGAG\|	0.17^†	-
GPBP1	9	1377	4	CAG\|GATG,	0.03	2
KIAA0494	1	1459	5	TTG,AGCAG\|	0.09	2
OSBPL8	2	36530	6	CTG,TTGTAG\|	0.11	2
SAP30	1	1892	6	CTG,TTTCAG\|	0.04	2
*DRD2*	6	1485	6	CTG,GTGCAG\|	0.02^†	5^†
SUV420H2	5	134	7	CTG,GCTCCAG\|	0.20	3
SSRP1	1	489	7	TTG,AATTCAG\|	0.20	16
FREQ	2	16849	7	CTG,CCTCCAG\|	0.04	2
IL21	3	2753	8	TTG,ATTTCTAG\|	0.13	2
*RYK*	7	3107	9	TTG,GCTCCTTAG\|	0.77	27
*DLG4*	5	131	9	CTG,GAGTTGCAG\|	0.62	8
SMARCA4	29	6174	9	TTG,ACCCTGAAG\|	0.41	34
FBXL10	15	177	9	TTG,GCCTACAAG\|	0.21	3
HNRPR	7	2839	9	TTG,GTTTAACAG\|	0.13	15
RRAD	1	214	9	CTG,ATCCCCTAG\|	0.06	2
TGM1	6	454	10	CTG,TCCTGGGCAG\|	0.13	2
ALAS1	11	1599	11	CTG,TTTCTCCTCAG\|	0.04	5
*ARS2*	18	182	12	TTG,TACTCCCCCCAG\|	0.74	75
*PCBP2*	7	1337	12	CTG,ACTCTCTCCCAG\|	0.43	169
PTPN11	10	4269	12	TTG,GCTCTACTCCAG\|	0.33	3
MSH5	6	164	12	CTG,ATCCCCTCCCAG\|	0.25	5
SYTL2	9	1259	13	TTG,CCCTCCTGAGTAG\|	0.09	3
TOMM40	1	95	16	CTG,ACCTCTCCCCTAGCAG\|	0.07	2
MARK3	3	20478	17	TTG,TTTGTTTTTTTTTTTAG\|	0.07	3
*BAT3*	6	832	18	CTG,ACTCTCCCCTACCTTCAG\|	0.01	1
*SH3D19*	6	838	21	TTG,GTTTTGTTTTGGTCTCGTCAG\|	0.07	1
*LOC346653*	1	3097	27	CTG,ACCCATGTACCTGAGGCTGATTTCCAG\|	0.60	3
ACAD9	10	253	28	TTG,TTTCTTGTGTTTTTTCTGAACACTCCAG\|	0.09	4

Entries in bold have RefSeq transcripts supporting the unusual TG acceptor site. Each TG splice variant is supported by at least two ESTs and at least 3% of all covering ESTs, except for some RefSeq-supported cases, CACNA1A [24,35], DRD2 [19] and BAT3. In the 'Motif' column, a vertical line (|) indicates a canonical splice site, and a comma (,) marks the TG splice site. Splice ratios are given as absolute EST counts (No.) as well as the fraction of TG splice variants. A question mark indicates that an explicit fraction is not given in the referenced article, although the authors performed quantitative experiments. *EST ratio depends on the exon junction; the upstream exon 3 may be skipped. ^†Splice variants were previously quantified by others: GNAS [16,26], CACNA1A (splice ratio cited from [24,35]), DRD2 (splice ratio cited from [19]). ^‡Alternative splicing at FBXO17 intron 3 was not experimentally reproducible in this study.

ISSN: 1474-760X