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. 2000 Mar 7;97(6):2814–2819. doi: 10.1073/pnas.050397097

Figure 2.

Figure 2

(A) Panhandle variant PCR products from der(11) chromosome in marrow DNA at 12 mos from neuroblastoma diagnosis. (Right) Negative control reactions, designated (−) ligase and dH2O. (B) Summary of panhandle variant PCR products containing der(11) breakpoint junction. The 31-base sequence of primer 3 used in final round of PCR and its complement are at 5′ and 3′ ends, respectively. The 4643–4645 bases of bcr sequence, including primer 3, are 5′ of MLL breakpoint at position 4662, 4663, or 4664 in intron 8 (corkscrew arrow). Depending on MLL breakpoint location, 1034–1036 bases of 3′ sequence are GAS7 partner DNA (GenBank accession no. AC005747). MLL breakpoint is 3′ of an AluY. GAS7 breakpoint is 5′ of an AluY. Identical 5′-AT-3′ sequences in MLL and GAS7 (outlined) preclude more precise assignment of breakpoint positions. Short homologies between MLL and GAS7 are underlined. (C) Genomic organization of 167-kb human GAS7 gene derived from alignment of genomic (GenBank accession no. AC005747) and cDNA sequences (GenBank accession nos. AB007854 and AJ224876). Boxes show the 14 exons. GAS7 der(11) breakpoint (corkscrew arrow) corresponds to nucleotide 165462, 165461, or 165460 upstream of exon 1 in GenBank accession no. AC005747; but sequence in GenBank entry is reverse complement relative to transcriptional orientation of the ORF (GenBank accession nos. AB007854 and AJ224876) and breakpoint corresponds to position 1240, 1241, or 1242 if GenBank accession no. AC005747 were in sense orientation. BamHI site indicates 3′ end of GAS7 sequence in panhandle variant PCR products shown in B.