You can use a Nucleotide BLAST (blastn) search with the CDS feature display to analyze sequences from protein-coding genes. It will help you determine their properties. At the same time, you can check for any sequencing errors. 

To set up a blastn search:

• Click the Nucleotide BLAST box on the BLAST home page 
• Enter your sequence in the Enter Query Sequence box:
  • Paste a single sequence as raw sequence (nucleotides only) or in the FASTA format.
  • For two or more sequences, you must use the FASTA format.
• Select the Database you want to search. The default selection is Nucleotide collection (nr/nt).
• Keep the default Program Selection: Highly similar sequences (megablast).  
• Modify your selection if you don't get any results. You can try alternative programs such as blastx, or genomic blast.
• Use the BLAST button to run the search.

To set up the CDS feature display on the new BLAST results pages (released in August 2019), follow these steps:  

• Click the Alignments tab.
• Use the default, Pairwise, Alignment view. (Or change it based on your preferences.)
• Click the CDS feature box next to the alignment view selection.

Pairwise alignments from the described search/display consist of several elements. We describe these in the article on interpreting pairwise alignments with CDS feature display.