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

Table 2

Sequences of novel HCMV UL49 alternatively spliced RNA fragments by 3′RACE.

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
UL49RA1	70403–70116; 68959–68629	619	1156	GTCTCCTGCG/CCTCACTTCG	GTCCTGTGCG/TTGTAAATGA	GW314860
UL49RA2	70403–70271; 68672–68629	177	1598	TGGACAGCGC/TGCGTACGCG	AGCCCAGCGC/GTAGTCTAGG	GW314861
UL49RA3	70403–70138; 69948–68626	1456	189	GTACGCGGCG/TGACGGTCCC	GCGCGCGGCG/GTTTAGCAGC	GW314862
UL49RA4	70403–70121; 68966–68626	624	1151	GCGTCTCCTG/CGCCTCACTT	TGTGGTCCTG/TGCGTTGTAA	GW314863
UL49RB1	70403–70146; 70001–69610	650	144	CTGTGGTGGT/ACGCGGCGTG	GCGCGCTGGT/TAAACAGACC	GW314864
UL49RB2	70403–70163; 70092–69610	724	70	GCGGCACGCACCTGC/GACTC	GGGCACGGCC/TGCTGTGCGC	GW314865
UL49RB3	70403–70207; 69777–69610	365	429	TACGATCACC/GGCTGGCTTT	GTTGGCCACC/ATGCTGAGCA	GW314866
UL49RB4	70403–70090; 69906–69610	611	183	CGGGCACGGCCTGC/TGTGC	CCACGGCCTGCC/CCATGTCT	GW314867
UL49RB5	70403–70133; 69857–69610	519	275	CGGCGGGACG/GTCCCGCGTC	AAGCGGGACG/AAAAACACCG	GW314868
UL49RB6	70403–70138; 69948–69610	605	189	GTACGCGGCG/TGACGGTCCC	GCGCGCGGCG/GTTTAGCAGC	GW314869

These RNA fragments were acquired by nested PCR with Primer 1 and 3′RACE Outer primer for outer PCR and Primer 2 and 3′RACE Inner prime for inner PCR. ^aNumbering refers to HCMV genomic sequences (GenBank Accession no. AY315197.2). ^bUnderlines indicate direct repeat sequences.