Supplemental Information for
Evolution’s Cauldron: Duplication, Deletion, and Rearrangement in the Mouse and Human Genomes.
Breaks |
Position |
aligned |
span |
breakPerMb |
Genes in region |
759 |
chr19:52283288-55023011 |
355617 |
2739723 |
277.04 |
Sialic acid binding (ig like cluster) and Zinc finger cluster |
307 |
chr19:11912709-12980044 |
123180 |
1067335 |
287.63 |
KRAB C2H2 Zinc finger cluster |
282 |
chr19:57924332-58994674 |
163649 |
1070342 |
263.47 |
KRAB C2H2 Zinc finger cluster |
228 |
chr2:129802976-130894216 |
284128 |
1091240 |
208.94 |
Ptpn18, cryptic (gene poor) |
215 |
chr22:19036955-20094010 |
132206 |
1057055 |
203.4 |
Contains Ig lambda light chain locus and Rhabdoid tumor deletion region |
212 |
chr19:9294092-10142345 |
100712 |
848253 |
249.93 |
KRAB C2H2 Zinc finger cluster |
209 |
chr8:6948129-8102614 |
205566 |
1154485 |
181.03 |
Ig region (defensin cluster) |
199 |
chr6:28560342-29380273 |
99588 |
819931 |
242.7 |
Olfactory receptor cluster |
164 |
chr12:11050382-11876400 |
124173 |
826018 |
198.54 |
6 Taste receptors and 5 salivary gland genes |
160 |
chr3:19755611-22829219 |
94791 |
3073608 |
52.06 |
HMGB1, mostly gene desert |
158 |
chr1:153813433-154249175 |
48153 |
435742 |
362.6 |
CD1, immune response cluster |
140 |
chr11:90897985-91367162 |
75731 |
469177 |
298.39 |
RNF18, gene poor region |
124 |
chr17:21859306-22267186 |
116716 |
407880 |
304.01 |
TL132 protein, gene poor region |
120 |
chr19:15050464-15453575 |
38600 |
403111 |
297.68 |
KRAB C2H2 Zinc finger, olfactory cluster |
115 |
chr18:13919892-15073531 |
145639 |
1153639 |
99.68 |
2 melocortin GPCRs |
Table S1 – Long runs of short chains in the top level of the net. "Breaks" gives the number of short chains in the region, "Position" the location in the human genome (November 2002 freeze), "aligned" the number of aligned bases in the region, "span" the total length of the region (in human genome coordinates). "BreaksPerMb" the average number of breaks between chains in each megabase in the region, and "Genes in region" lists the properties of or accessions of human RefSeq genes from the region. This table lists only the top few "hotspots" with the most consecutive short chains, excluding pericentormeric and telomeric regions , matches to human chromosome Y (since little sequence is available from mouse chromosome Y), and one region with extensive simple repeats of longer period than we masked. Hotspots of this type cover 5-10% of the human genome. Some are associated with clusters of mobile genes in the olfactory or zinc finger families (see text). Others are associated with immune genes. One of the largest of these regions (5th entry in the table) is on chromosome 22 near the Ig Lambda light chain locus. This locus rearranges somatically during B-cell maturation . Possibly a low level of the RAG proteins responsible for this somatic rearrangement are expressed in germ cells and occasionally cause recombination in germ cell lines in this region in mammals as well as other vertebrates . There are a number of RAG ESTs isolated from cells not in the B-cell lineage, including GenBank accession N92955.