Table 3.
Cloned AscI Spots (See Supplemental Data Online for a Complete List of Cloned RGLS Fragmentsf)
| RLGS spot | Chr. positiona | Chr. band | CpG islandb | Methylationc | Gene or EST homologyd | Contexte | |
|---|---|---|---|---|---|---|---|
| Primary | Cell lines | ||||||
| A2D16g | chrNA_rdm:9890705-9892163 | ? | Y | L | L HN LU MB | DRD4/PTDSS2 | 5′end/Body |
| A5E46 | chrX:17627774-17629763 | Xp22.13 | Y | L | L HN LU | – | – |
| A4G14 | chr1:256787415-256787746 | 1q41 | Y | L | L LU | – | – |
| A2D08 | chr1:68251887-68253584 | 1p32.1 | Y | L | LU | JUN | Body |
| A3F22 | chr1:108979505-108982150 | 1p22.1 | Y | L | L | – | – |
| A3F38 | chr1:201154777-201155644 | 1q24.2 | N | L HN MB | L LU | PMX1 | 5′ end |
| A6E17 | chr1:133792275-133794522 | 1p13.2 | Y | L | L LU | – | – |
| A3F30 | chr1:8129740-8132794 | 1p36.23 | N | L | LU | EST | – |
| A5E43 | chr1:127726863-127728875 | 1p13.3 | Y | L HN MB | L HN LU MB | ALX3 | 5′ end |
| A4E32 | chr1:22646645-22648732 | 1p36.32 | Y | L | L LU | – | – |
| A3H43 | chr1:2844351-2849754 | 1p36.32 | Y | L | L HN LU | – | – |
| A2F45 | chr2:117320895-117322735 | 2q13 | N | L HN MB | L HN LU MB | EST | – |
| A3E38 | chr2:179015764-179017423 | 2q31.1 | N | L | L | – | – |
| A4D36 | chr2:138670622-138671469 | 2q21.2 | N | L | L LU | – | – |
| A4G44 | chr3:220718143-220722411 | 3q29 | Y | L | HN LU | EST | – |
| A5F32 | chr3:153653591-153655489 | 3q22.1 | N | L MB | L LU MB | – | – |
| A5G07 | chr3:8664656-8665380 | 3p26.1 | Y | L HN | L HN LU | GRM7 | 5′ end |
| A5E28 | chr3:3902165-3903025 | 3p26.1 | Y | L | L HN LU | – | – |
| A4B07 | chr3:146695171-146695918 | 3q21.3 | Y | L | HN LU | EST | – |
| A2E14 | chr4:5349208-5351766 | 4p16.1 | Y | L MB | L LU | HSA250839 | 5′ end |
| A2D23 | chr4:171849449-171850978 | 4q32.1 | Y | L HN | L HN LU | GLRB | 5′ end |
| A3E31 | chr4:181006489-181008945 | 4q32.3 | Y | L | L LU | TLL1 | 5′ end |
| A6E16 | chr5:49418697-49420952 | 5p11 | Y | L | L LU | EST | – |
| A4F02 | chr5:187652008-187654787 | 5q35.1 | Y | L | EST | – | |
| A6D30 | chr5:195984026-195984768 | 5q35.2 | Y | MB | MB | B4GALT7 | 5′ end |
| A3G33 | chr5:83731413-83731663 | 5q13.3 | Y | L | L HN LU | MGC15435 | 3′ end |
| A4C25 | chr6:103613999-103614941 | 6q15 | Y | L | LU | BACH2 | 5′ end |
| A3E39 | chr6:86748700-86751107 | 6q14.1 | Y | L HN | L HN LU | EST | – |
BLAT search results based on http://genome.ucsc.edu/cgi-bin/hgBlat, Aug. 2001 Freeze.
Y indicates that the AscI site is within a CpG island, N indicates that it is not.
Indicates methylation found in a primary tumor or cell line as indicated: (L) Lung carcinoma; (MB) medulloblastoma; (HN) head and neck squamous cell carcinoma; (LU) leukemia.
Known genes found in the Refseq database or spliced ESTs.
5′ end indicates that the CpG island includes the region immediately upstream of exon 1 and/or exon 1. The 3′ end indicates that the CpG island is found in 3′ most exon. Body indicates that the CpG island is found within the genomic structure of the gene excluding the 5′-most and 3′-most known exons.
Genes share same CpG island in their 5′ end and are transcribed in opposite directions.
Bold indicates the RLGS fragments that were cloned directly using the mixing gels.