Question: gDNA annotation, exon and intron boundary identification
gravatar for chethusomashekar
3.2 years ago by
United States
chethusomashekar0 wrote:

Dear Biostars members,


Hi, I am Chethana from India, working on multigene phylogenetic analysis of Colletotrichum species prevalent in India on varied host. I am using  Actin, B-tubulin, ITS, GPDH, CHS, CylH3, ApMAt genes for analysis. I am annotating my sequences for the above genes using NCBI Blast tool. Most of my sequences have 96-100% similarity to the Colletotrichum reference sequences which were downloaded from CBS database. Using this method I was able to annotate all the genes but while submitting to GENBANK only ITS and CHS sequences were ok but for other gene sequences stop codons were reported by Genbank(NCBI). Below is the mail which I have recieved from NCBI portal regarding submission of other genes. If I submit after removing the stop codons after alignment in BioEdit or MEGA they reply stop codons are missing in your sequence and they suggest to add stop codons and to resubmit. I would greatly appreciate your help in  annotating my sequences.


Regarding the internal stop codons that BankIt is reporting, these need

to be fixed before accession numbers will be assigned (you need to fix them before completing this BankIt submission). Most of these are due to incorrect boundaries between the exons and introns with resulting frameshifts and incorrect protein translations. 


Complete feature annotation has not been included for some or all of the sequence(s) you have submitted.
  A. Please resubmit your sequence(s) with relevant features such as:

        - coding regions (CDS features), partial or complete, including
          nucleotide spans and reading frame. Using this information,
          our software will add the amino acid translations for you.
        - structural RNAs such as rRNAs, tRNAs, misc_RNAs, with
          nucleotide spans
        - features which may describe your sequence, such as
          repeat_regions, UTRs, promoters with nucleotide spans


Thanks and Regards



sequencing sequence gene • 1.2k views
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