We are currently preparing to submit our gene sequences to GenBank, and we are encountering several issues during the submission process. The sequence in question is a partial gene, and therefore it lacks both start and stop codons. As a result, we have not included the transl_table qualifier. We are unsure if this is acceptable in the GenBank submission system.

We prepared the submission using Geneious and followed the instructions outlined in the GenBank submission tutorial. However, upon testing the submission, we received the following error messages:

  • Local identifier longer than 50 characters BIOSEQ: lcl|Alignment_has_been_manually_modified.Original_options:: raw, rna len= 615
  • Gene cross-reference is not on expected strand FEATURE: exon: [lcl|Alignment_has_been_manually_modified.Original_options::c>615- [lcl|EB8B2E928D4007E9_1]
  • 7 internal stops. Genetic code [11]
  • Bad characters in author field DESCRIPTOR: Pub: ?Unpublished BIOSEQ-SET: nuc-prot
  • We are particularly concerned about the internal stop codons and the missing transl_table, since this is a partial coding sequence (CDS). We would appreciate feedback on:

    • Whether these errors are critical and will prevent successful submission.
    • If there are recommended solutions for formatting partial genes correctly for GenBank.
    • How to properly handle metadata like the author field and local identifiers.

    Any guidance or suggestions would be greatly appreciated!

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