Table 2.
Overview on the characteristics of the deletions
| Gene | Family number | Deletion size (bp) |
Position breakpoints |
Breakpoint sequences | DNA sequence motifs |
|---|---|---|---|---|---|
| EXT1 | 89 | 259.450 | Proximal: 118.829.422-118.829.425 Distal: 119.088.871-119.088.874 |
ATTTTCCTTGAAAGGAGGCCTCTAGTTTTC|accaagttatcaaaaatattcaaga-- --catcttccacccatttggatggattttttc|CTGTTCTCAGAAGCTGGGTTTGACC |
TATTCA: Deletion hotspot consensus sequence (complement) |
| EXT1 | 200 | 5885 | Proximal: 118.891.184-118.891.186 Distal: 118.897.068-118.897.070 |
ACAGGCGGGAGCCACTGTACCTGGCCAA|cattgttgttcgttttaaaggagtt-- --ggtgtaggtaatcacaacctaatttcaa|TTTTCTAGCAGATGCTCACCATCCC |
GCTCA: Immuno heavy chain class swith repeat (complement) |
| EXT1 | 250 | 148.254 | Proximal: 118.914.819 - 118.914.854 Distal: 119.063.074-119.063.109 |
TTTTTTTAGTAGAACTGGGGTTTCGCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTC| aagtgatctgcctgccttggcctcc-- --tatttttagtagagatggtgtttcaccatgttggccaggctggtcttgaactcctgacctc|GTGATCCACCTGCCTCAGCCTCCCA |
TGGGG: Immuno heavy chain class swith repeat GGGGT: Immuno heavy chain class swith repeat GATCCA: Deletion hotspot consensus sequence (complement) GCCTCA: Deletion hotspot consensus sequence (complement) |
| EXT1 | 300 | 6176 | Proximal: 118.896.107-118.896.110 Distal: 118.902.282-118.902.285 |
CTCACATACTTTTTTTCTCAGCTATATCA|ctgctacacgaagaagagattctgg-- --caggtgtgaattcagagaggatgtcatca |TCCTTACTATAACTTCTGGAAGAAG |
- |
| EXT1 | 338 | 5688 | Proximal: 118.877.923 - 118.877.925 Distal: 118.883.610-118.883.612 |
ATTCTACCAAACAGTATTTCTAGTAATT|catacatctttaacaaaaaaatcta-- --attacagtaggctatgttagcctttatt| TTGGTGGTTCTCAAATACCTGGTGA |
- |
| EXT1 | 361 | 205.798 | Proximal: 118.805.191 - 118.805.193 Distal: 119.010.988-119.010.990 |
AAATCTATTGAGCCTGCTTATGATTCTTT|ggttttggaggaggagggcactaat-- --ttgttttgttttgttttgttttttgcttt| TCTGAGATGGAGTTTTGCTCTCGTT |
TGAGC: Immuno heavy chain class swith repeat AGGAGGGC: Translin binding site (complement) |
| EXT2 | 122, 334 | 8690 | Proximal: 44.143.251-44.143.282 Distal: 44.151.940 - 44.151.971 |
GATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGG| cgtgagccaccgcgcccggcccaca-- --catctcctgatcttgtgatccgcctgcctcggcctcccaaagtgctgggattacagg|TGTGAGCCACCGCGCCCGGCCTTTT |
TGAGC: Immuno heavy chain class swith repeat TGAGC: Immuno heavy chain class swith repeat |
| EXT2 | 150 | 2749 | Proximal: 44.084.367-44.084.368 Distal: 44.087.115 - 44.087.116 |
ATGCAAATTCAGGGATGGAAAGAACTG|ttggtgttcgtctttgtaaatgaat-- --gaagcaggtctgtatgggacaagcttg|AAGTACACGTGCGTTCATTTTTCCC |
- |
| EXT2 | 279 | 41.025 | Proximal: 44.130.050 Distal: 44.171.074 |
TTTGGCCATTCTAATAGATATGTAT|ttgtatcttattgctgttttaattt-- --gctattcatatctatacataagggg|GACTGATAAAACAGGCCTGAGTCAT |
TATTCA: Deletion hotspot consensus sequence (complement) TGAGTC: Deletion hotspot consensus sequence |
The positions of the proximal and distal breakpoints or breakpoint regions were given according to the UCSC Human Genome Browser assembly from March 2006 (NCBI36/hg18) on the respective chromosomes (the reverse strand of chromosome 8 for EXT1 and the forward strand of chromosome 11 for EXT2). Breakpoint sequences were given, including 25 bp down-and upstream from the breakpoints or breakpoint regions if homologous sequences (marked in grey) were present at the breakpoints. Down-and upstream borders of the deleted sequences are indicated in small characters. Alternating purine-pyrimidine sequences are underlined. Finally, DNA sequence motifs associated with deletions are marked in bold, while the motif sequence and the deletion-associated motif type can be found in the last column.