Table 1. PCR and pyrosequencing primers and assays for each gene.
| GeneA | Assay | CpG sitesB | Primers | SequenceC |
| 6: 882 | 892 | Forward | 5′-TTAGGGGGAGGGAGGGTTT-3′ | |
| ALVE-region1 | 905 | 911 | Reverse | 5′-GGGACACCGCTGATCGTTTA CCATCTTCACATCTCGCTACACAA-3′ |
| 914 | 919 | Sequencing | 5′-GAGGGTTTTTTTTTTAGGT-3′ | |
| Assay | 5′-TYGGAGTGTA TYGAGAAATT AGTAAYGGAG YGGYGAATYG-3′ | |||
| 5: 7171 | 7178 | Forward | 5′-GTATATGGGTGGTGGTATGAAATTTG-3′ | |
| ALVE-region2 | 7186 | 7194 | Reverse | 5′-GGGACACCGCTGATCGTTTA TTCCCCCTCCCTATACAAAAAC-3′ |
| 7196 | Sequencing | 5′-GAGGGGATTATAGTATGTAT-3′ | ||
| Assay | 5′-AGGYGAAAGG YGGGGTTTYG GTTGTAYGYG GTTAGGAGTT-3′ | |||
| 3′ LTR | 5′LTR | Forward | 5′-TGGYGATTAGATAAGGAAGGAATG-3′ | |
| ALVE -region3/4 | 4: 7359 | 4: 108 | Reverse | 5′-GGGACACCGCTGATCGTTTA TATCCATCTACCCAAATACACACCA-3′ |
| 7375 | 124 | Sequencing | 5′-YGATTAGATAAGGAAGGAAT-3′ | |
| 7381 | 130 | Assay | 5′-GAYGTAAGGA TATATGGGYG TAGAYGAAGT TATGTAYGATTATATAAGTT-3′ | |
| 7393 | 142 | |||
| 4: 3793 | Forward | 5′-AGGCGTTTATTGTTTGGTTAGAAG-3′ | ||
| ALVE -region5 | 3795 | Reverse | 5′-GGGACACCGCTGATCGTTTA CAAAAAAATATCAACCTCCTTACC-3′ | |
| 3800 | Sequencing | 5′-TTATTTTTTTGATTATTAAG-3′ | ||
| 3808 | Assay | 5′-TTAYGYGTTT YGGTAGTGYG AATTTTTGGT AAGGAGGTTG ATAT-3′ | ||
| Forward | 5′-ATGTGTAGGTTATGGGAAGGGTAT-3′ | |||
| TVB | 3: 1282407 | Reverse | 5′-GGGACACCGCTGATCGTTTA AAAACTAAACTACTCCCACCATTT-3′ | |
| 1282435 | Sequencing | 5′-GGTTATGGGAAGGGTA-3′ | ||
| 1282444 | Assay | 5′-TAAYGTGGTT ATGGTGTTTT TGTTTGGTTG TYGTTGTTTA YGTA-3′ | ||
| Universal | 5′-/Biotin labeled/GGGACACCGCTGATCGTTTA-3′ | |||
A:
ALVE-region1, 2, 3/4: based on the conserved DNA sequence between ALVE1 (AY013303) and ALVE3 (AY013304). The relative product of ALVE region1 is p19 matrix protein of gag gene. ALVE region2 is the consensus sequence of oncogene Direction Repeat Sequence (DRS). ALVE region3/4 is the conserved DNA sequence-U3 region, which located in 5′LTR and 3′LTR of ALVEs. ALVE region5: based on the unique DNA sequence (reverse transcriptase alpha subunit) in ALVE1 (AY013303,[48]. TVB: based on the UCSC DNA sequence (May 2006, Chr22) that BLAT from TVB cDNA sequence (AF161712), it is on the promoter region of TVB.
B:
The CpG site numbers and positions.
C:
Y and R stand for C/T and G/A, respectively. Bold Y is the CpG sites assayed in each region.