BioMed Research International

Research Article

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

Table 3

Novel sequences of HCMV UL49 alternatively spliced RNA fragments (group A).


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

UL49A1	71608–71124; 69003–68783	706	2120	GTTTCGAACG/CTACGACACC	TGTTCGAACG/TGGAGGGCGG	GW314870
UL49A2	71608–71530; 70080–68783	1377	1449	CTCTTCGCGC/CCCTCTGCGT	CTGTGCGCGC/GCTGTCAGAC	GW314871
UL49A3	71608–71321; 69108–68783	614	2212	TCTGAATCGC/GAGCTGGGCG	GGAGCGGCGC/CAGACGCAGC	GW314872
UL49A4	71608–71490; 70001–68783	1338	1488	TGCAGCTGGT/GATCGGCCGC	GCGCGCTGGT/TAAACAGACC	GW314873
UL49A5	71608–71288; 68963–68783	502	2324	ACGCTTCCTG/CGCGAATGGC	TGTGGTCCTG/TGCGTTGTAA	GW314874
UL49A6	71608–71457; 69101–68783	381	2355	CGGAGGAAGC/GGCGGTAGAA	CGCCAGACGC/AGCGACGTTG	GW314875
UL49X	71608–71530; 69188–68783	485	2341	CTCTTCGCGC/CCCTCTGCGT	GAACTCGCGC/GATGGGTGGC	GW314876
UL49A8	71608–71416; 69108–68783	519	2307	TTTGCGGCGC/AGACGTCGGC	GGAGCGGCGC/CAGACGCAGC	GW314877
UL49A9	71608–71565; 69157–68783	419	2407	CCGCGACTGA/GGAGTTCCAC	CAGAAACTGA/ATATTGACTG	GW314878
UL49A10	71608–71562; 69450–68783	715	2111	CGACTGAGGA/GTTCCACCAG	GCACTGAGGA/CGTTCTGCGT	GW314879
UL49A11	71608–71321; 68989–68783	495	2331	TCTGAATCGC/GAGCTGGGCG	GGGCGGTCGC/AGCACGCGTA	GW314880
UL49A12	71608–71515; 69142–68783	454	2372	TGCGTTCACG/AGGACCATTT	GACTGGCACG/CGGTTGAAAG	GW314881
UL49A13	71608–71519; 68957–68783	265	2561	CCTCTGCGTT/CACGAGGACC	CCTGTGCGTT/GTAAATGACT	GW314882
UL49A14	71608–71478; 69231–68783	580	2246	TCGGCCGCGG/TGCGCTGCAG	GCGGCCGCGG/CCGCTCGATG	GW314883
UL49A15	71608–71561; 70695–68783	1961	865	GACTGAGGAG/TTCCACCAGG	CGCGGAGGAG/GCTCGACGGC	GW314884
UL49A16	71608–71276; 71180–71114; 69028–68783	646	95^C 2085	CGAATGGCTG/GTGTGTCGGC CTACGACACC/GACTACCTGC	ACGTCTACAG/CATGGACTGT GTCCAACACC/AGCCGACTGT	GW314885
UL49A17	71608–71276; 71180–71079; 69107–68783	760	95^C 1971	CGAATGGCTG/GTGTGTCGGC TCTACCCGCC/CGAGCGGCTG	ACGTCTACAG/CATGGACTGT GAGCGGCGCC/AGACGCAGCG	GW314886
UL49A18	71608–71276; 71180–70683; 68860–68783	909	95^C 1822	CGAATGGCTG/GTGTGTCGGC CGACGGCGGC/AGCTGCGGCG	ACGTCTACAG/CATGGACTGT CTCCAGCGGC/GTTTCGGTCC	GW314887
UL49A19	71608–71276; 71180–71055; 69115–68783	792	95^C 1939	CGAATGGCTG/GTGTGTCGGC CGTTGTTGGA/CGGTGTCACC	ACGTCTACAG/CATGGACTGT CGGTGTTGGA/GCGGCGCCAG	GW314888

These RNA fragments were amplified by nested PCR with Primer 3 and Primer 4 for outer PCR and Primer 5 and Primer 6 for inner PCR. ^aNumbering refers to HCMV genomic sequences (GenBank Accession no. AY315197.2). ^bUnderlines indicate direct repeat sequences. ^CIntrons conform to the GU-AG rule.