wiki:DescribingResidues

Version 45 (modified by vw253, 6 years ago) (diff)

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Describing Residues Modified or Mutated

Describing Amino Acid Residues for 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 Residues and Bases to for allele descriptions

Amino Acids

  • Mutation of amino acids to specific stop codons (i.e important if generating read-through) allele=name(W234->opal)
  • Mutation of single amino acid residue: allele=name(K132A)
  • Mutation of multiple single AA residues (not consecutive): allele=name(K132A,K144A)
  • Mutation of multiple consecutive AA residues: range in single letter code, number of first AA in range, range of residues mutated to e.g. allele=Rhp54Km(KEN26AAA);
  • Legacy data (In 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
  • Partial AA deletion: allele=name(del_100-200) for proteins
  • 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.
  • Allele=heterozygous for heterozygous diploid? (check at next inhouse meeting)

Bases

  • No examples yet curated; if any needed, follow patterns as for amino acids, but include 'nt' to indicate nucleotides, e.g.
    • single changes: ntA25G
    • partial deletions: delnt_100-200
  • Note that if neither 'aa' nor 'nt' is included, 'aa' (amino acids) will be assumed

Data for curation tool allele table

description e.g. text to appear in box other help text other action
deletion text box not required n/a autopopulate allele name with xxxdelta
unknown text box not required n/a allele name becomes required (unless really dim they will have filled this in, but enforce presence at table completion
WT overexpression text box not required n/a autopopulate allele name with ???
knockdown text box not required n/a autopopulate allele name with ???
mutation of single amino acid residue e.g. K132A --
mutation of multiple non-consecutive amino acid residues e.g. K132A,K144A--
mutation of multiple consecutive amino acid residues e.g. KEN26AAA original residues, number of first AA in range, new residues
partial deletion, amino acid e.g.100-200 -infer the del_ behind the scenes, maybe this isn't even required when we have constrained fields, depends how stored?
partial deletion, nucleotidee.g.100-200- infer the delnt_ behind the scenes, maybe this isn't even required when we have constrained fields, depends how stored?
mutation of a single nucleotide e.g. A25G --
other free text field "please provide free text description" -description will appear in the table for curators to sort
  • text for all allele description column

"Select only one option/ or select the most appropriate option?" (may not be required)