Distinguishing protein-coding and noncoding genes in the human genome - PubMed (original) (raw)

An example gene report card for a small gene, HAMP, on chromosome 19. Report cards for all 22,218 putative genes in Ensembl v35 are available at

www.broad.mit.edu/mammals/alpheus

. The report cards provide a visual framework for studying cross-species conservation and for spotting possible problems in the human gene annotation. Information at the top shows chromosomal location; alternative identifiers; and summary information, such as length, number of exons, and repeat content. Various panels below provide graphical views of the alignment of the human gene to the mouse and dog genomes. “Synteny” shows the large-scale alignment of genomic sequence, indicating both aligned and unaligned segments. The human sequence is annotated with the exons in white and repetitive sequence in dark gray. “Alignment detail” shows the complete DNA sequence alignment and protein alignment. In the DNA alignment, the human sequence is given at the top, bases in the other species are marked as matching (light gray) or nonmatching (dark gray), exon boundaries are marked by vertical lines, indels are marked by small triangles above the sequence (vertex down for insertions, vertex up for deletions, number indicating length in bases), the annotated start codon is in green, and the annotated stop codon is in purple. In the protein alignment, the human amino acid sequence is given at the top, and the sequences in the other species are marked as matching (light gray), similar (pink), or nonmatching (red). “Frame alignment” shows the distribution of nucleotide mismatches found in each codon position, with excess mutations expected in the third position. Matching are shown in light gray, and mismatches are shown in dark gray. “Indels, starts and stops” provides an overview of key events. Indels are indicated by triangles (vertex down for insertions, vertex up for deletions) and marked as frameshifting (red) or frame-preserving (gray). Start codons are marked in green and stop codons in purple. “Splice sites” shows sequence conservation around splice sites, with two-base donor and acceptor sites highlighted in gray and mismatching bases indicated in red. “Summary data” lists various conservation statistics relative to mouse and dog, including RFC score, nucleotide identity, number of conserved splice sites, frameshifting and nonframeshifting indel density/kb, and gene neighborhood. The gene neighborhood shows a dot for the three upstream and downstream genes, which is colored gray if synteny is preserved and red otherwise.