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.