What is inside that 1% difference in DNA between humans and chimpanzees?

The difference between humans and chimpanzees is estimated to be 10 times greater than the difference between two humans.

The main genetic difference between humans and other primates is the number of chromosomes. Humans have 23, and other primates have 24, because at some point in our ancestral history, two chromosomes joined by telomeres, giving rise to what is now our chromosome # 2.

There are other differences, as some segments of genes that we share are inverted in what of our genome would be chromosomes 1, 4, 5, 9, 12, 15, 16, 17 and 18.

From there, we know that the genes we share are very similar, with the same functions, but with differences that change the codon bias (the tendency to have a certain number of anticodons), the amount of expression (transcription factors, strength of promoters, terminators, distal promoters), which are very subtle changes that lead to very drastic things, such as the transcription factor P2 (FOXP2), which acts on many genes, but the particular difference of expression that it has in humans, helped to develop skills such as the ability to speak.

In a previous study, the researcher compared the insulin gene in humans with that of other animals in BLAST, a tool used to compare sequences of genomes and genes. The tool was also used to compare the complete FOXP2 gene (with promoter and all) with the genome of Pan troglodytes (common chimpanzee) to see if we can see the differences indicated in the literature.

According to the results, the sequence is aligned with a segment of chimpanzee chromosome 7, the red section corresponds to the reading frame, where there is the sequence of amino acids to follow. If you look, it is where there is more similarity with the human gene. However, the first section that has less red corresponds to the regulatory part of the gene, which determines, how much, when and how that transcription factor will be expressed. That's where it differs most and that part does not express any protein in itself.

This is where the differences between "similar" species lie. Not so much in the reading frames, that although there are important differences, they are not as important as the differences in the regulatory genes and their post-transcriptional modifications.