Describing alleles

Allele description rules

These are rules for allele descriptions, not names!

Allele type	Example
amino acid insertion	A858AMKGYP (insertion of MKGYP after A858, note A before and after number)
amino acid substitution(s)	K132A or F256A,F310A
amino acid insertion and substitution	A858AMKGYP,F124D
amino acid insertion and deletion	A858AMKGYP,100-200,P500*
partial deletion and amino acid change	100-200,F124D,P500*
partial deletion, amino acid	Specify deleted residues - eg. 100-200 OR 10-20,40-50. Use P500* for nonsense mutation
nucleotide insertion	C132CAATTT (insertion of AATTT after C132, note C before and after number)
nucleotide substitution(s)	A25G, OR A(-25)G (for residues upstream of ATG -protein coding- or transcription start -RNA genes-)
partial deletion, nucleotide	Specify deleted residues - eg. 100-200 OR (-20)-(-30) (for residues upstream of ATG -protein coding- or transcription start -RNA genes-)
partial deletion and nucleotide change	100-200,A124T,C128G (for residues upstream of ATG -protein coding- or transcription start -RNA genes- use negative numbers in parenthesis)
nucleotide insertion and substitution	T858TAAGA,T(-124)A (for residues upstream of ATG -protein coding- or transcription start -RNA genes- use negative numbers in parenthesis)

Allele naming rules

These are rules for allele names, not descriptions!

These naming rules are fully detailed in Lera-Ramírez et al. 2023.

Variant type		Example
Wild type		ase1+
Knockout / deletion		ase1Δ
Partial deletion	Indicate what’s left	ase1(1-35) ase1(1-35, 40-700)
	Indicate what’s missing	ase1Δ(114-120) ase1Δ(114-120,150-200)
Residue insertion		ase1-P114PVPAL
Substitution or deletion-insertion	Single residues	ase1-P114A,Q117A ase1-P114*
	Consecutive residues	ase1-PLI114AAA ase1-PLI114LAVKK
Combinations of the above		ase1Δ(10-20)-P114A,Q117A
Forward genetics, variant unknown		ase1-35 (must be unique)
CTD	All repeats mutated	rpb1-CTD-Y1F
	Some repeats mutated	rpb1-CTD-Y1F(r1-r12)
	Some repeats deleted	rpb1-CTD-Δ(r11-r29)
	Motifs mutated every 2 repeats, from repeat 1 to 29.	rpb1-CTD-Y1F(r1-r29-2)
	Combinations of the above	rpb1-CTD-S5A(r1-r12)Δ(r13-r29)
	CTD and non-CTD mutations	rpb1-N494D-CTD-Δ(r11-r29)