I am trying to submit sequences of COX-1 gene(mitochondrial gene) to gene bank. My sequences is almost 100% identical to a published one. It return a message saying that they contain stop codons and that this hinders their publishing. Now, I checked similar seq. from gene bank and they also contains a stop codons ? if this is hindering, how did those one were published ?
Could any one help to explain why is this and how can I deal with this problem ?
Thanks
Earlier there was no stringent checking of sequences submitted. They were accepted as submitted. But now they use software to check sequences submitted. This happened even for genome submissions. For example when we submitted genome sequence of one of the indica rice cultivar (RP Bio-226) NCBI identified presence of Large number of Pseudomonas aeruginosa sequences and asked us to remove those contigs containing P. aeruginosa sequences. But when we checked the reference indica rice genome published earlier, it also contained large number of P. aeruginosa sequences. This identification of contamination with P. aeruginosa sequences led us to hypothesize that it must be due to co-sequencing of endophytic P. aeruginosa present in rice plants and we proved it later. In your case the presence of stop codon may be due to sequencing error or it can be a mutation. You can re-sequence to confirm this.
In addition to Dr Kandasamy's reply, I want to add that the observed stop codon might be due to incorrect selection of the reading frame. You are required to provide the correct reading frame in the gene annotation. The another possibility is your sequence might have stop codon in the right frame, which the GenBank staff wants you to confirm.You need to recheck your sequence electropherograms and confirm. Please go through the GenBank email carefully and do the needful.
best wishes,
SD
Kandasamy Ulaganathan :
Thanks for your comment. However, I just would like to clarify that I am not sequencing a host gene, where there might be some mixing up with other genes. Indeed, I sent a PCR product for particular gene with a known size and was previously confirmed in conventional PCR. So, I think having mixed up contents is not expected.
Dear Samir
I did not mean that you got a mixup. I gave it as an example to show that NCBI was accepting sequences as submitted but now they are verifying the sequences.
Sincerely
K.ULAGANATHAN
Most of the time is due to sequencing error, and gets solved after resequencing. Or sometimes due to sequencing error one nucleotide is less and hence the frame shifts creating erroneous protein sequence.
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