Humans and birds diverged over 300 Mya; protein sequence evolution over that time is easier to estimate than DNA evolution; at the typical vertebrate neutral DNA substitution rate, any nucleotide that is not under strong selection is likely to have undergone multiple substitutions in that amount of time, making it very difficult to identify homologous, neutrally-evolving nucleotides. Thus, the only segments that can be confidently aligned are, as Andreas Pfenning said, quite limited.

The vertebrate 28-way multiple sequence alignment contains the chicken genome.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099589/

There is an alignment between the chicken and human genome: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/vsGalGal3/

My impression is that regulatory elements (transcription factor binding sites) are quite similar, but the DNA sequence overall has a large amount of difference, making an alignment difficult beyond genes.

Humans and birds diverged over 300 Mya; protein sequence evolution over that time is easier to estimate than DNA evolution; at the typical vertebrate neutral DNA substitution rate, any nucleotide that is not under strong selection is likely to have undergone multiple substitutions in that amount of time, making it very difficult to identify homologous, neutrally-evolving nucleotides. Thus, the only segments that can be confidently aligned are, as Andreas Pfenning said, quite limited.

Thank you! Most helpful. This seems to make it quite unlikely that RNA from avain cells should give any signals with mammalian (human) probes

I remember a paper in the 90s that suggested that sequence which is not under purifiying selection (e.g. most of the introns) will have diverged sufficiently during the 300 My that separate humans and chickens to be no more similar than unrelated sequences (this pair of species is therefore good for screening for conserved non-coding regions). The cross-hybridisation between coding sequences of mRNAs, which is presumably what you're looking for, will depend on how conserved the gene is. I know of at least one (highly conserved) gene that gives a decent Northern signal on chicken RNA when human cDNA is used as the probe. As mentioned above, you should be able to calculate % identity at the nucleotide level and find some literature figure for the threshold similarity needed for cross-hybridisation (or choose your probe accordingly to include the most highly conserved region...).

The chicken and human transferrin gene have been compared.The human gene is 33 .5 kb long wheraas the chicken gene is 10;5 kb long.Both are organized in 17 exons and I6introns.he sizes of the exons are comparable and in many cases identical.The sizesof the introns are widely different and explain the overall difference in size of the two genes.Both genes derive from a common ancestor.E.Schaeffer et al.,Gene,1987,109-116

Georges Cohen ,Institut Pasteur,Paris

The first step in getting the right answer is asking the right question. Whether sequences are homologous (have diverged from a common ancestral sequence, and therefore at one time played _identical_ roles in the life of the ancestor, a very powerful piece of information) is an entirely different question than whether two sequences are similar enough to cross-hybridize. Homologous sequences can fail to cross-hybridize, and sequences which cross-hybridize may not be homologous.

If you know the "probe" sequences, it is probably faster and more informative to search the other genome computationally, rather than by hybridization. If your sequences come from some other bird (e.g. a passeriform), be aware that the chicken is not very closely related to most birds. You may want to search for your sequences in the new zebrafinch genome.

The Chicken genome paper from Nature 2004 does a pretty good job at comparing human and chicken (as well as many references to earlier work). In terms of chromosomal arrangements the conservation is way better than between human and mouse. For specific genes there are specific answers. but the nature paper and the huge amount of supplementary material is a good start.

BINGO! Thanks Dirk-Jan, the nature paper was EXACTLY what I was looking for. Wonder how I failed to pick it up in the literature search (slightly embarrassed). kind regards, Harald