I'm writing an article on palindromes (the words) and I wanted to mention the existence of palindromic gene sequences. Roughly how many palindromes exist in the human genome? I understand the number will vary from person to person. All I want to know is the order of magnitude. Is it 10^2, 10^3, 10^6?

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    $\begingroup$ Note that a DNA palindromic sequence does not really match the usual meaning of palindrome. .For instance, GAATTC is a palindromic sequence, but does not match its reverse, CTTAAG. Instead it matches the reverse of its complement, which is a useful biological property. ('C' is the complement of 'G', 'T' of 'A', etc.) $\endgroup$ – mgkrebbs Mar 24 at 20:49
  • $\begingroup$ @mgkrebbs. Thanks for the detail. I understand it is not exactly the same, but the principle is analogous, which is fine for my purpose. $\endgroup$ – Ray N. Franklin Mar 25 at 2:14

The human genome contains approximately 1.25*10^7 palindromes longer than 6 bp (that is 8 bp or longer). Some interesting facts are also known about their distribution.

We found that 24 palindrome-abundant intervals are mostly located on G-bands, which condense early, replicate late, and are relatively A+T rich. In general, palindromes are overrepresented in introns but underrepresented in exons. Upstream region has enriched palindrome distribution, where palindromes can serve as transcription factor binding sites. We created a Human DNA Palindrome Database (HPALDB) which is accessible at http://vhp.ntu.edu.sg/hpaldb . It contains 12,556,994 entries covering all palindromes in the human genome longer than 6 bp.

And no, the number of shorter ones (shorter than 8 bp) isn't mentioned in the paper because they are considered unimportant, biologically.


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