Question: How to submit the stop codon free complete mitochondrial genome sequence in Genbank/BankIt?
1
gravatar for nazninislamnif
29 days ago by
nazninislamnif20 wrote:

I have done the complete mitochondrial genome sequence of a mammal. Mitochondrial genome contains 37 genes (13 protein coding genes; 22 tRNA genes and two ribosomal RNA genes). So I want to submit the sequence in Genbank. But the protein-coding genes I have annotated are showing stop codons error, so the Sequin software is giving me a hard time. Kindly tell me the steps how can I make my sequence stop codon free?enter image description here

assembly next-gen gene genome • 174 views
ADD COMMENTlink written 29 days ago by nazninislamnif20

which mammal is this you've sequenced? are you borrowing the start-stop coordinates from human mtdna?

ADD REPLYlink modified 29 days ago • written 29 days ago by Jeremy Leipzig19k

No. I m sequencing cow genome.

ADD REPLYlink written 29 days ago by nazninislamnif20

ok did you use these coordinates? https://www.ncbi.nlm.nih.gov/nuccore/LC576822.1

ADD REPLYlink written 29 days ago by Jeremy Leipzig19k

Yes. We followed the NCBI co-ordinates. At first submission theye didn’t show any erro. Then they mail us to correct the pcg's directions. This tine whenever tried to upload any feature they are showing the stop codon error everytime.

ADD REPLYlink written 27 days ago by nazninislamnif20
2

oh this is udderly problematic. if every gene is generating this maybe you are facing a 1-off frameshift error?

ADD REPLYlink written 27 days ago by Jeremy Leipzig19k

this would make sense if you sequenced a Bos Indicus instead of a Bos Taurus? https://www.ncbi.nlm.nih.gov/nucleotide/NC_005971.1

ADD REPLYlink written 27 days ago by Jeremy Leipzig19k

We have sequenced Bos frontalis mitogenome.

ADD REPLYlink written 26 days ago by nazninislamnif20

Yes. Every gene is showing error. I and my team wanted to upload a mitogenome through BankIt. First, we uploaded it without any problem. But then NCBI mailed us informing "Some or all of the sequences contain incorrect annotation and/or contain little similarity to other sequences in the database based on BLAST searches. Please also review your nucleotide sequences for issues such as low-quality data or frameshifts.". They asked us to correct them and resubmit the data. But when we tried to resubmit the data the following error is continually showing on the screen _ "You have not entered the anticodon interval (that is, start and stop) or the anticodon product. Please enter at least one, and preferably both." What should we do now to complete the submission successfully?

ADD REPLYlink written 26 days ago by nazninislamnif20

what is 1-off frameshift error?

ADD REPLYlink written 26 days ago by nazninislamnif20

the reading frame is mooved over is off by 1 or maybe 2 nucleotides, so you are seeing a stop codon instead of the correct amino acid. Make sure you are using the correct coordinates for Bos frontalis by aligning your sequence with one of the ones here https://www.ncbi.nlm.nih.gov/nuccore/?term=Bos+frontalis+mitochondrion

ADD REPLYlink written 26 days ago by Jeremy Leipzig19k
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