Tuesday 27 December 2016

bioinformatics - What could I call such nucleic-acid-Sequence? A sort of palindromic sequence? is there any term called mirror repeat?


5'... ATGCC|CCGTA ...3'


3'... TACGG|GGCAT ...5'


or say


5'... AAGT|TGAA ...3'



3'... TTCA|ACTT ...5'


or in generalised way; on each strand;


ABCDEF|FEDCBA


Is there any terminology for such-sort of repeat? A sort of palindromic sequence? A sort of inverted repeat? or mirror-repeat? Does they really exist in nature? (I could not yet found any helpful answer in web, including wikipedia.)


UPDATE


I asked this question because the term "palindromic sequence" is not like the situation in OP but "palindromic sequence" is like this:


5'... ATGCTTTC|GAAAGCAT ...3'


3'... TACGAAAG|CTTTCGTA ...5'


or in general;


5'... A B C D E F | M N P Q R S ...3'



3'... S R Q P N M | F E D C B A ...5'


Where on single-strand there is no symmetry when read (3'---> 5') and (5' ---> 3').


BUT I'm not telling like that. i'm telling about a situation where a reflection-symmetry present in each single strand when read (3'---> 5') or (5' ---> 3').


like


5'... A B C D E F | F E D C B A ...3'


3'... S R Q P N M | M N P Q R S ...5'


From no angle it is a palindromic-sequence because the symmetry is not between 2 opposite strand.


This question came to my mind when for first- time I'd taught about palindromic sequence. I was unable to "literally" match it with verbal palindromes like "AND MADAM DNA" . Rather it was looking to me like


I EAT CAKE


EKAC TAE I



So I thought, if really there exist any sequence literally like "AND MADAM DNA"... whatever if there is any terminology for it or not.





One other Q/A site mentions about a term "mirror repeat", with exact same situation as OP, but gave no reference and further biological importance.



enter image description here http://www.answers.com/Q/Mirror_repeats_in_DNA



Latest revision of Wikipedia also mentions a term mirror repeat and everted repeat, but no further explanation and hyperlink is given.


Another result from google search.




https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg URL: https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg





Answer



It's simply called a palindromic sequence. As you can see here, these sequences are called inverted repeats when random nucleotides are found between the initial sequence and its reverse complement (e.g. TTACGnnnnnnCGTAA), while when there are no nucleotides between them they're called palindromes.


UPDATE
Sorry for my previous answer, I must've missed the point.
I think the situation you showed should be called mirror-everted repeats: to my knowledge, it's a very rare occurring, and I only found some reference in this and this articles, even though no graphic explanation is provided.
P.S. Should you not be able to access the full text of the second article, just let me know.


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