ACTL10: is the Swiss-Prot sequence the protein, and what do its two IBA rows rest on?
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The human genome encodes 167 uninterrupted in-frame codons immediately upstream of Q5JWF8's annotated initiator, within the single-exon MANE transcript's own 5-prime leader, and their translation is actin, including the phosphate-binding loop 1 motif absent from the annotated protein. The reading frame is proven rather than assumed, by first asserting that the annotated CDS translates to the Swiss-Prot sequence.
"After the last stop there are **167 uninterrupted codons** running straight into the annotated initiator"
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Twenty of the thirty-eight filament-interface positions previously scored as gaps for ACTL10 are not substitutions but positions the annotated sequence never reaches. Repaired, ACTL10 scores 11 of 38 chemically compatible, identical to ACTL8 and to Sapajus ACTL10, rather than the 5 of 18 that made it look like the most degraded actin relative in the family.
"counts contact positions the query sequence does not reach at all - an absence in the annotation"
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The five nucleotide-site positions the annotated sequence fails to reach are exactly actin's phosphate-binding loop 1, and the extended reading frame retains all five as four identical residues plus one conservative substitution. The nucleotide pocket is therefore preserved, not decayed, which removes any residue-decay argument for removing ACTL10's function annotation.
"motif that grips the nucleotide beta-phosphate, and the most diagnostic single feature of the actin fold"
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Within PTHR11937, GO:0005200 is asserted by IBD at the single node PTN000940351 and then negated by IRD at eight descendant nodes covering every divergent-actin clade PAINT has curated, while ten human genes still receive it from PTN000940351: four conventional muscle actins plus ACTL9, ACTL10, ACTR10 and ACTRT1-3.
"and then **negated on descent at 8 nodes**:"
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ACTL10 orthologue lengths do not follow the phylogeny; in four of four sister-taxon pairs tested, two members of one mammalian family carry different annotated lengths, which is what first indicated a gene-model rather than a biological explanation.
"If the variation were biological it would track the species tree. It does not"