Oh, I think I'm beginning to see what you may have meant - although I am unconvinced in so far as lack of an example is concerned!
Something like this might have an application:
acgtgtatgctgctgatcgtgtgttgtg<gene>agtacacggagcatgcgt<RNA>agtcgtcacccagtc<CDS>acgtgtgtca</CDS></RNA>
The question remains whether sequence features are always hierarchic, and I have a strong intuitive feeling that they are not!
How are you going to illustrate complex protein kinks in a markup language? Genetic engineering, in so far as whole organisms are concerned, must take account first of DNA sequence features, second of RNA folding, third of the four levels of protein structure, plus chemical gradients and structures that establish tissues and wire up neurons in the right places, etc. etc.
It sounds more like a streaming format would be required rather than a human-readable markup language (that is the entire point of a markup language!)
So to repeat my previous words, with emphasis:
Sayonara, can you please stop bullshitting about representing DNA or protein sequences in a markup format? So I'm not sure whether I can be judged to have been owing you an explanation, but here we are.
Greetings,
Phoenix