Genes are ordered from centromere to telomere. Gene name is the official Human Gene Nomenclature designation, where available; aliases are included in some cases; spliced ESTs are usually designated by a nucleotide accession number. Start/stop position are the nucleotide locations within the chromosome 21 long arm sequence. Contig refers to the 340 kb segments into which the long arm was divided (contigs number 2-106); for annotation in the Genotator software, each contig was divided into two 170 kb segments (-1 and -2). Start and stop position within the relevant contigs are given for each gene. Span is the genomic size of the gene; strand refers to transcription direction, F is centromere to telomere, R is telomere to centromere. Type indicates gene structures supported by spliced ESTs (EST) and/or consistent coding exon predictions (EP). Class: C, highly conserved in mouse (most exons completely conserved w? >80% identity); MC, minimally conserved in mouse (few exons conserved and w/ <75% identity); NC, no detectable sequence similarity (>65% identity over >50 nt) of any exon anywhere in the mouse genomic sequence. # Ex, # of exons in gene model; #Con, # conserved in mouse; # Rep, # of exons all or mostly repetitive sequence. Prod, length of longest open reading frame. Com, estimate if gene structure is complete (COM), of 5’, or 3’ incomplete (inc). CpG island data lists the distance 5’ or 3’ to the nearest CpG island and gives island characteristics.

Table 2. List of mouse genes annotated in the orthologous regions of mouse chromosomes 16, 17 and 10.

(See Table 1 for description of fields)

Table 3. Functional annotation of human chromosome 21/mouse orthologous genes.

Genes are listed in order from centromere to telomere and by the human name. Contig, location with the annotated human genomic sequence. Accession #, human cDNA accession number. Domain, functional associations and similarities: information is derived from literature reports and/or analysis of domain/motif similarities based on SMART and PFAM.

Table 4. Keratin associated protein (KRTAP) on the human chromosome 21

Table 5. Genes on the short arm of the chromosome 21 (21p)