Why does a GenBank record show no internal stops?

NCBI's submission check writes the /translation itself and refuses a CDS with an internal stop unless it is marked pseudo, so a deposited record rarely carries one. A map from a lab notebook or a plasmid repository has not been through that check.

What does the read-through number mean?

How many codons translation adds past the annotated end before the sequence supplies a stop. The expected value beside it is what a random sequence of the same base composition would give, so a tail far longer than that is worth a look.

Is anything uploaded?

No. Every check runs in the browser on the maps in your project.

Analyze

Reagent audit: does each annotated CDS code for what the map says, and are its cryptic promoters, splice sites and repeats worse than chance

Check that each annotated coding sequence of a vector map codes for what the map says it does. Every CDS is read from the map's own bases under its own genetic code: a frame that does not close, a stop inside the frame, a first codon that cannot start translation, a last codon that is not a stop, and a /translation the bases do not give. Where an annotation ends without a stop, translation is read on to where it really stops, and the panel says which annotated CDS it runs into and how long a tail a random backbone would give.

Open Reagent audit: does each annotated CDS code for what the map says, and are its cryptic promoters, splice sites and repeats worse than chance Open the Reagent audit sample

Five vector maps deposited in GenBank in 2024, each CDS checked against its own bases and genetic code, the annotations that end without a stop read on to where translation really stops, and each map’s strongest cryptic promoter, splice site and repeat tested against shuffles of itself

What it does

01Every annotated CDS checked for a frame that does not close, a stop inside the reading frame, a first codon the genetic code cannot start with and a last codon that is not a stop
02The record's own /translation compared with what its bases give under its own genetic code
03Partial ends and /pseudo CDS recognised and left unjudged
04Annotations that end without a stop read on in frame, round the origin of a circular map, to where translation really stops
05Which annotated CDS a read-through runs into, and the read-through a random backbone of the same composition would give

What it runs on

Location extraction and translation checked against Biopython on all 1,871 CDS of 695 vector records deposited in GenBank in 2024. The panel runs on @ports/workflow.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Why does a GenBank record show no internal stops?: NCBI's submission check writes the /translation itself and refuses a CDS with an internal stop unless it is marked pseudo, so a deposited record rarely carries one. A map from a lab notebook or a plasmid repository has not been through that check.
What does the read-through number mean?: How many codons translation adds past the annotated end before the sequence supplies a stop. The expected value beside it is what a random sequence of the same base composition would give, so a tail far longer than that is worth a look.
Is anything uploaded?: No. Every check runs in the browser on the maps in your project.

Also searched as

plasmid annotation check · CDS annotation audit · internal stop codon in plasmid map · frameshift in annotated CDS · translation does not match sequence · missing stop codon read-through · vector map quality check · GenBank CDS validation