Describing Residues Modified or Mutated

Describing amino acid residues for protein modifications etc

• Single Amino acid AA single letter code, residue number residue=K54 (residue=54 was used in legacy annotations but is now deprecated
• Multiple single amino acid residues either residue=K54|residue=K22 or residue=K22,K54 as appropriate
• Range of amino acids residue=A114-A660 (114-660 was used in legacy annotation but is now deprecated)
• Region not fully defined used residue=region_A114-A660
• Special case i) in RNA pol II CTD domain residues tend to be referred to in context of the CTD domain and are annotated as CTD,S2|CTD,S5 (TODO FIX THESE)
• Special case ii) Cleavage sites. Are defined as a range of 2 amino acids flanking the cleaved peptide bond, may not be the best way to do this... eg residue=R179-N180

Describing amino acid or nucleotide residues in allele descriptions

Amino acids

Choose the allele type from the Canto pulldown

• Mutation of single amino acid residue: K132A
• Mutation of multiple amino acid residues
  • not consecutive: comma separate, e.g. K132A,K144A
  • consecutive: wild-type sequence in single letter code, number of first position in range, mutated sequence, e.g. KEN26AAA
• Partial deletion: indicate the positions of the deleted residues, e.g. 100-200
• Note that for almost all proteins, amino acid numbering is based on the unmodified protein. The annoying exception is histones, which are numbered assuming removal of the initiator methionine.
• Nonsense mutation (i.e. mutation of an amino acid to a stop codon) * specific stop codons: W234->opal, W234->amber, W234->ochre
  • without specifying which stop codon: W234->stop
• Note that for almost all proteins, amino acid numbering is based on the unmodified protein. The annoying exception is histones, which are numbered assuming removal of the initiator methionine.
• Legacy data (Artemis): all allele data in Artemis which is not in the form allele=name(description) is ALL in the form allele=name ONLY e.g. allele=htbK119R

Nucleotides

• Select the appropriate "... nucleotide ..." allele type in Canto
• Follow patterns as for amino acids, e.g.
  • single changes: A25G
  • multiple consecutive changes: AG25TT
  • multiple non-consecutive changes: A25T,G35T
  • partial deletions: 100-200
• Number starting from the first nucleotide of the coding sequence, i.e. position 1 is the A of the initiator ATG. Use negative numbers for positions upstream of the ATG.