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A very short, 15 amino acid (45 nucleotides) long gene: FreddyB (44340-44384 bp)?
| Link to this post | posted 20 Jan, 2024 08:29 | |
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I don’t like the fact that I see no coding potential at FreddyB (subcluster F1) position 44340-44384 bp (MNTYRIPNPVEATQZ) and the fact that it would be the shortest gene I had ever seen. However, this potential gene would be part of an operon with 4 bp (ATGA) overlaps with both the upstream and downstream genes. Given Guiding Principle #12a, the ribosome prefers a 1bp or 4 bp overlap, irrespective of RBS score. I wonder how a ribosome would skip over these two 4 bp ATGA overlaps to exclude this potential short gene that would make part of an operon. BLASTp shows more than 20 hits, with q2:S108, 100% identity, e-value = 0.43. Thoughts? See attached: |
328Kb| Link to this post | posted 20 Jan, 2024 23:28 | |
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Fred, i haven't looked at this specifically, but the cluster F1s are notorious for having MANY tiny genes that have the 1-4bp overlap with the preceding and next genes. So there are calls 'without' coding potential. As you have mentioned, it just makes sense to call them. Please remember that coding potential is not the end-all. The math (and remember that coding potential is an interpolated markov model - a mathematical calculation - that may or may not hold true when applied to small genes. debbie |
| Link to this post | posted 21 Jan, 2024 07:58 | |
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Thank you, Debbie! Case closed! Fred |