Table 1. TDM loci confirmed by MSP or bisulfite sequencing.
| RLGS
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Loci | Chr | Location, MB | CpG island | NotI site location | Gene | Function | Liv | Kid | Brain | Col | Mus | Tes |
| PvuII | ||||||||||||
| 2 | 11 | 114.98 | No | Exon | mRNA AK037416 | Mct transporter | 0 | 0 | 0 | 0 | 0 | 2 |
| 4 | 7 | 10.22 | Yes | 3′ exon | RefS D430030K24Rik | Ring Zn finger | 0 | 0 | 0 | 0 | 0 | 1 |
| 6 | 17 | 47.12 | Yes | 5′ promoter | RefS C330046L10Rik | Ubiquitin hydrolase | 0 | 0 | 0 | 0 | 0 | 1.5 |
| 8 | 4 | 58.76 | Yes | 5′ promoter | Est BE134335 | DNA J domain | 0 | 0 | 0 | 0 | 0 | 2 |
| 29 | 14 | 47.79 | Yes | 5′ promoter | RefS 4930548G07Rik | Chromatin binding | 0 | 0 | 0 | 0 | 0 | 1 |
| 42 | 1 | 16.79 | Yes | 5′ promoter | mRNA 6130401J04Rik | Ubiquitin-conj. E2 | 0 | 0.1 | 0.1 | 0.5 | 0 | 2 |
| 66 | 11 | 43.4 | Yes | 3′ exon | RefSeq Adra1b | G protein receptor | 0.1 | 2 | ND | 2 | 1 | 2 |
| PstI | ||||||||||||
| 3 | 13 | 111.46 | Yes | 5′ promoter | RefS Ddx4 | RNA helicase | 0 | 0 | 0 | 0 | 0 | 2 |
| 6 | 17 | 34.63 | Yes | 3′ exon | RefS HSP1-Like | Heat shock | 0 | 0 | 0 | 0 | 0 | 2 |
| 32 | 12 | 67.21 | Yes | 3′ exon | RefS Dact1 | Dsh signaling | 0 | 0.5 | 0 | 0 | 0 | 2 |
| 33 | 4 | ND | No | Exons | mRNA BC059845 | Unknown | 0 | 0.5 | 0 | 0 | 0 | 2 |
| 61 | 6 | 89.64 | Yes | 5′ promoter | mRNA GATA-2 | Transcription | 0 | 2 | 2 | 2 | 2 | 2 |
| 21 | 19 | 6.3 | No | Intron | Predicted gene | Unknown | 2 | 0.2 | 0 | 0 | 0 | 0 |
| 46 | 17 | 17.6 | No | Intron | Predicted gene | Unknown | 0 | 2 | 0 | 0 | 2 | 2 |
Shown is the chromosomal location (University of California, Santa Cruz, Bioinformatics Database, October 2003 assembly available at http://genome.ucsc.edu), whether the TDM was located within a designated CpG island, and the location of the TDM NotI site relative to a nearby gene. Gene and function information were also taken from links to the University of Califnornia, Santa Cruz, Genome Bioinformatics database. The RLGS spot intensity for each tissue is given, with 2 corresponding to a diploid single copy sequence, 1 indicating haploid spot intensity, and 0 indicating that the spot is absent. Values in bold indicate that the sequence is unmethylated (0.5–2 intensity). Values of <2 suggest that methylation is heterogeneous with the tissue. A complete listing of all TDM loci identified by VI-RLGS can be found in Table 4. MB, megabase pair; conj., conjugating enzyme; Mct, monocarboxylate transporter; Chr, chromosome; Liv, liver; Kid, kidney; Col, colon; Mus, muscle; Tes, testis.