Notes to self re: the chicken genome

• no [SINEs] have been active in the chicken genome for the last ~50Myr.
  
• there is a detectable signal in orthologous splice site comparisons beyond the consensus derived from comparing non-orthologous splice sites (PDF). [E]ither some subtle classes of splice site sequences are conserved beyond the generic consensus that can only be observed at the bird–mammal evolutionary distance, or that there is a significant but weak conservation in mammalian introns that is not detectable in mammalian–bird alignments
• introns of ion channel genes are particularly enriched for conserved sequences, in agreement with reports that such introns contain RNA-editing targets
• Sequences expressed in the chicken brain ... are more conserved than testis-expressed sequences
• 43% of the chicken genes are present in 1:1:1 orthology relationships for [human:fugu:chicken]
  
• 72% (7,606) of chicken–human 1:1 orthologues also possess a single orthologue in [fugu]
• Genes absent from chicken. Genes encoding vomeronasal receptors, casein milk proteins, salivary-associated proteins (statherin and histatins) and enamel proteins seem to be absent from the chicken: from within both the EST sets and the genome. This is unlikely to result from imperfections in the chicken genome assembly because it preserves orthologues of closely linked (syntenic) mammalian genes.
• gene density shows a strong negative association with chromosome length
• ... a strong correlation between the length of a gene and the size of the chromosome in which it is found, an effect that is determined largely by variation in intron size
• Intron length in the chicken correlates negatively with recombination ..., G+C content ..., and gene density ..., as has been reported previously for other genomes
• The synteny maps confirm ... that the human genome is closer to the chicken than to
  rodents in terms of chromosomal organization of genes
• only 2.5% of the human sequence aligned with chicken [44% protein-coding, 25% intronic ; 31% intergenic]