Identification of the Alternative Splicing of the UL49 Locus of Human Cytomegalovirus

Table 4

Sequences of novel HCMV UL49 alternatively spliced RNA fragments (group B).

Name of novel transcript	HCMV sequence (nt)^a	Nested PCR product length (bp)	Intron length (bp)	Splice donor (exon/intron)^b	Splice acceptor (intron/extron)^b	GenBank accession number
UL49B1	71608–71179; 70097–69667	861	1081	GTCTACAGCA/TGGACTGTCT	CGCACGGGCA/CGGCCTGCTG	GW314889
UL49B2	71608–71548; 70691–69667	1086	856	CACCAGGCTC/TGCGCCGTCT	GAGGAGGCTC/GACGGCGGCA	GW314890
UL49Y	71608–71276; 71180–69667	1847	95^C	CGAATGGCTG/GTGTGTCGGC	ACGTCTACAG/CATGGACTGT	GU376796
UL49B4	71608–71282; 70097–69667	758	1184	CCTGCGCGAA/TGGCTGGTGT	CGCACGGGCA/CGGCCTGCTG	GW314891
UL49B5	71608–71527; 70021–69667	437	1505	TTCGCGCCCC/TCTGCGTTCA	GCGCCCCGCTG/TGTCGGGGCT	GW314892
UL49B6	71608–71284; 69951–69667	610	1332	TTCCTGCGCG/AATGGCTGGT	CAGGCGCGCG/GCGGTTTAGC	GW314893
UL49B7	71608–71576; 70166–69667	533	1409	CGCTCCGCAC/ACCGCGACTG	CGGCACGCAC/CTGCGACTCC	GW314894
UL49B8	71608–71501; 69968–69667	410	1532	CCATTTCCAT/GTGCAGCTGG	GCGGCCACAT/TGTGCAGCAG	GW314895
UL49B9	71608–71543; 70007–69667	407	1535	GGCTCTGCGC/CGTCTCTTCG	GGGGCTGCGC/GCTGGTTAAA	GW314896
UL49B10	71608–71533; 69925–69667	335	1607	CGTCTCTTCG/CGCCCCTCTG	TTCCTCTTCG/TCCTCCCCCC	GW314897
UL49B11	71608–71341; 70131–69667	733	1209	TTCGTGACGG/ATAAGCGCTT	GGCGTGACGG/TCCCGCGTCT	GW314898
UL49B12	71608–71276; 71180–70822; 69882–69667	908	95^C; 939	CGAATGGCTG/GTGTGTCGGC; CACGCCGGGA/AGGTACCCTG	ACGTCTACAG/CATGGACTGT; CGCGCCGGGA/CCCACGGTGG	GW314899
UL49B13	71608–69667	1942	—	—	—	GW314900

Numbering refers to HCMV genomic sequences (GenBank Accession no. AY315197.2).
^bUnderlines indicate direct repeat sequences. ^CIntrons conform to the GT-AG rule.
—: There is no intron in the transcript of UL49B13.