wiki:DescribingResidues

Describing Residues Modified or Mutated

Describing amino acid residues for protein modifications etc

  • Single amino acid residue: AA single letter code, residue number, e.g. residue=K54 (legacy annotations that were missing the amino acid code have been corrected)
  • Multiple non-consecutive amino acid residues: either residue=K54|residue=K22 or residue=K22,K54 as appropriate (pipe for OR, comma for AND, as usual)
  • Range of amino acid residues: residue=A114-A660 (legacy annotations that were missing the amino acid code have been corrected)
  • Region not fully defined used residue=region_A114-A660
  • Special cases
    • Phosphorylated residues in RNA polymerase II carboxy-terminal domain (CTD) repeats are specified relative to a canonical CTD repeat, rather than by position in the entire protein (it usually isn't feasible to tell how many repeats are actually phosphorylated on potential sites). They are annotated as residue=CTD_S2, residue=CTD_S5, etc.
    • Cleavage sites are defined as a range of 2 amino acids flanking the cleaved peptide bond, e.g. residue=R179-N180. (This may change someday, if we ever think of a better way to do it.)

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.
Last modified 5 years ago Last modified on Aug 27, 2015, 2:11:36 PM