What Could Irregular Deletions Do?

What Could Irregular Deletions Do? · What About Pseudo-Genes Starting to Code?

I am here supposing, for argument's sake, that deletions in a gene may come in other quantities than threes, sixes, nines, etc of base pairs and these with the same limits as the triplets of bases there to start with.

I'll start off with a Coding table and a gene of 4 triplets, and then take what such deletions (if they exist) could do.

Help:Protein coding sequences/Codon table
https://parts.igem.org/Help:Protein_coding_sequences/Codon_table

mttc is the start of keratin 16:

https://www.ncbi.nlm.nih.gov/protein/AAD15829.1

m = Methionine, also start
t = Threonine
c = Cysteine

I'm not sure exactly how the gene for keratin 16 (of Homo sapiens) is coded, but I'll give a possible sequence:

AUG ACA ACA UGU

Obviously, deleting three according to where the threes are will only take away one of the coding parts mttc => mtc, mtt, or even ttc, potentially meaning it is not start of a protein strand.

But suppose we get to the interstices, like the threes from 3 to 5 ...

/AUG/ ACA ACA UGU
A/UG A/CA ACA UGU
AU/G AC/A ACA UGU
AUG /ACA/ ACA UGU
AUG A/CA A/CA UGU
AUG AC/A AC/A UGU
AUG ACA /ACA/ UGU
AUG ACA A/CA U/GU
AUG ACA AC/A UG/U
AUG ACA ACA /UGU/

Those between the two identical ones will by the way give simplification to one.

A/UG A/CA ACA UGU
AU/G AC/A ACA UGU
AUG A/CA A/CA UGU
AUG AC/A AC/A UGU
AUG ACA A/CA U/GU
AUG ACA AC/A UG/U

The remaining four would rearrange as:

ACA ACA UGU = ttc (just deleting the m)
AUA ACA UGU = Isoleucine, t, c
AUG ACA AGU = m, t, Serine
AUG ACA ACU = m, t, t (both ACA and ACU = t = Threonine)

That's what one deletion-mutation would do to keratin 16. And note, the first four are so of over 421 base pairs.

But what if the deletion were on top of that irregular in number, like 4 base pairs deleted? The last three begin with mt, as the original proteine. All but the last two end in GU... and the last two in AU... and AC...

/AUG A/CA ACA UGU = CAA CAU GU... Glutamine, Histidine
A/UG AC/A ACA UGU = AAA CAU GU... Lysine, Histidine
AU/G ACA/ ACA UGU = AUA CAU GU... Isoleucine, Histidine
AUG /ACA A/CA UGU = AUG CAU GU... m, Histidine
AUG A/CA AC/A UGU = AUG AAU GU... m, Asparagine
AUG AC/A ACA/ UGU = AUG ACU GU... m, Threonine = mt
AUG ACA /ACA U/GU = AUG ACA GU... mt
AUG ACA A/CA UG/U = AUG ACA AU... mt
AUG ACA AC/A UGU/ = AUG ACA AC... mt

What are the remainder of the first batch after mttc? It's srqfts.

UCU GCU CAA UUU ACU UCU
or
serine alanine glutamine phenylalamine threonine serine

Rearrange for starting two letters earlier:

GUU / AUU / ACU CUG CUC AAU UUA CUU CU...

Now it's instead:

valine / isoleucine / threonine leucine leucine asparagine leucine leucine (+ further displacements)

So, let's spell out the fourth version of the deletions, we replace

methionine threonine threonine cysteine serine arginine glutamine phenylalanine threonine serine (orthodox beginning of keratine 16)
with
methionine histidine valine leucine leucine asparagine leucine leucine

Somehow, I don't just think this would be dysfunctional as keratine, but it would be dysfunctional anywhere else in the body. But let those who know about such stuff comment on it.

Hans Georg Lundahl
Paris
St. Deusdedit of Brixen
10.XII.2021

PS, I am relieved this wording was "dysfunctional as keratine" and not "dysfunctional as muscles" - I had mixed up the Greek words for "horn" (keras, etymology for keratine which is found in horns, hooves, nails and, as I recall, hairs as well) and "flesh" (krear, etymology for the widely different proteine called kreatine, which is found in muscles). So, the question is, if there was a deletion in the gene for nail or hair matter (or one of parallel ones), would the resulting widely different proteine be useful anywhere at all? I am off to quora to have a look, requested answers yesterday./HGL