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SUPPLEMENTARY FIGURE LEGENDS:
Figure S1: Relationship of the finished sequence map to genetic and radiation hybrid
maps of chromosome 18. Red diamonds represent the physical positions of genetic
markers on the sex-averaged DeCode genetic map17. Blue diamonds represent the
physical positions of markers on the Whitehead radiation hybrid map18.
Figure S2: Example of gene model extension. Annotations of phosphatidylinositol
glycan, class N (PIGN) are shown along the chromosome 18 axis. 5’ is to the left.
Horizontal lines represent gene models, red for RefSeq, blue for Broad Institute. Green
lines represent ESTs. Thin horizontal lines represent introns. Thicker bars or boxes
represent exons. Blowups show detail of evidence for extension at 3’ and 5’ ends. As
supported by extensive EST evidence shown, the Broad gene model extends 70 bp further
5’ and adds 325 bp to the 3’ UTR. We also annotated a canonical polyA-addition signal
(AATAAA) at the extreme 3’ terminus of the last exon (not shown).
Figure S3: Relationship between gene density and median intron length, demonstrating a
genome-wide inverse correlation between intron size and gene density. Gene density of a
chromosome is defined as average number of genes per Mb. Extreme chromosomes are
indicated. Chromosome 18 has the longest median intron length of all chromosomes.
Note: In order to compare all human autosomes in an unbiased manner, we generated a
standardized annotation of all autosomes with our automated pipeline. These annotations
can differ significantly from manual annotations due to lack of manual review as well as
differences in methodology. Published manual annotations are not yet available for all
autosomes.
Figure S4. Distributions of Z-scores for conserved elements analysis. (a) Decomposition
of full distribution (blue) of conservation scores into a neutral component (red) and
selected component (green). (b and c) Distribution for composite mouse-dog aligning
windows: all windows (black), windows contained in ancient repeats (blue), windows in
exons (red), (b) coding exons only.