Tag: Coding sequences (CDS)

New wizard for submitting mRNA sequences to GenBank

New wizard for submitting mRNA sequences to GenBank

Do you submit eukaryotic nuclear mRNA sequences to GenBank? A new mRNA submission wizard is available! Built on the modern Submission Portal framework, this new wizard will bring you an enhanced experience, including:  

    • Guided submission experience specific for mRNA sequences 
    • Automated trimming of vector and removal of short sequences  
    • Easier input for source metadata 
    • New feature annotation web forms for coding region (CDS) and untranslated region (5’ UTR, 3’ UTR)  
    • Extensive feature previews (Figure 1) 
    • Faster sequence processing and accession assignment  
    • Access to a fix error workflow prior to accession assignment 

Watch a short video (4 min) to see how to annotate CDS features in this new wizard!  Continue reading “New wizard for submitting mRNA sequences to GenBank”

Troubleshooting GenBank Submissions: Annotating the Coding Region (CDS)

This article is intended for GenBank data submitters with a basic knowledge of BLAST who submit sequence data from protein-coding genes.

One of the most common problems when submitting DNA or RNA sequence data from protein-coding genes to GenBank is failing to add information about the coding region (often abbreviated as CDS) or incorrectly defining the CDS. Incomplete or incorrect CDS information will prevent you from having accession numbers assigned to your submission data set, but there is a procedure that will help you troubleshoot any problems with the CDS feature annotation: doing a BLAST analysis with your sequences before you submit your data.

NOTE: We have changed BLAST search results displays since publishing this blog. For updated guidance on using Nucleotide BLAST (blastn) to help you troubleshoot coding region annotation, see the articles in the  NCBI Support Center.

Here’s how to use nucleotide BLAST (blastn) and the formatting options menu to analyze, interpret and troubleshoot your submissions:

1. To start the BLAST analysis, go to the BLAST homepage and select “nucleotide blast”.

nucleotide blast link. click to start BLAST analysis
Figure 1. Select “nucleotide blast”.

Continue reading “Troubleshooting GenBank Submissions: Annotating the Coding Region (CDS)”

Designing exon-specific primers for the human genome

A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.

Here are the steps to follow to design primers to amplify exon 15 from human BRCA1:

Continue reading “Designing exon-specific primers for the human genome”