telomeric ends fasta

Question

[2nelly]

Hi all,

I am wondering if there is any source to obtain the sequences of telomeric ends of human chromosomes. These regions are masked in both NCBI and UCSC.

Thank you in advance.

[GenoMax]

If you are referring to the N's at ends then those are likely not masked. Since these regions are hard to sequence with existing technologies those N's are placeholders to indicate heterochromatin that is not sequenced.

Answer 1

[agata88]

Maybe here:

http://telomerase.asu.edu/sequences_telomere.html

Also EMBL-EBI seems to have telomeric chromosome sequences:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000781

Best,

Agata

[2nelly]

Dear Agata,

thank you for your answer, but unfortunately there is no source to download any sequence in this db

[agata88]

Hmm... are you sure that each chromosome has different telomeric end? Because I found that In humans the telomere sequence is TTAGGG which can be repeated around 3000 times. I don't think you are going to find telomeric sequence database since those sequences are related to age (their ends are cutted), so It's very various. I think that is the reason they are masked in NCBI and UCSC database. But I am not very familiar with tellomers, I might be mistaken.

Best,

Agata

[2nelly]

Dear Agata, yes, telomeric ends are repeats of TTAGGG and yes the size it s age related. However, I suppose that some additional bases interpolate between these repeats. This is what I want to see.