| 16 | | === Amino Acids === |
| 17 | | * Mutation of amino acids to specific stop codons (i.e important if generating read-through) |
| 18 | | allele=name(W234->opal) |
| 19 | | * Mutation of single amino acid residue: allele=name(K132A) |
| 20 | | * Mutation of multiple single AA residues (not consecutive): allele=name(K132A,K144A) |
| 21 | | * 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); |
| 22 | | * 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 |
| 23 | | * Partial AA deletion: allele=name(del_100-200) for proteins |
| | 16 | === Amino acids === |
| | 17 | Choose the allele type from the Canto pulldown |
| | 18 | * Mutation of single amino acid residue: K132A |
| | 19 | * Mutation of multiple amino acid residues |
| | 20 | * not consecutive: comma separate, e.g. K132A,K144A |
| | 21 | * consecutive: wild-type sequence in single letter code, number of first position in range, mutated sequence, e.g. KEN26AAA |
| | 22 | * Partial deletion: indicate the positions of the deleted residues, e.g. 100-200 |
| 25 | | * Allele=heterozygous for heterozygous diploid? (check at next inhouse meeting) |
| | 24 | * Nonsense mutation (i.e. mutation of an amino acid to a stop codon) * specific stop codons: W234->opal, W234->amber, W234->ochre |
| | 25 | * without specifying which stop codon: W234->stop |
| | 26 | * 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. |
| | 27 | * 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 |
| 27 | | |
| 28 | | === Bases === |
| 29 | | * No examples yet curated; if any needed, follow patterns as for amino acids, but include 'nt' to indicate nucleotides, e.g. |
| 30 | | * single changes: ntA25G |
| 31 | | * partial deletions: delnt_100-200 |
| 32 | | * Note that if neither 'aa' nor 'nt' is included, 'aa' (amino acids) will be assumed |
| | 29 | === Nucleotides === |
| | 30 | * Select the appropriate "... nucleotide ..." allele type in Canto |
| | 31 | * Follow patterns as for amino acids, e.g. |
| | 32 | * single changes: A25G |
| | 33 | * multiple consecutive changes: AG25TT |
| | 34 | * multiple non-consecutive changes: A25T,G35T |
| | 35 | * partial deletions: 100-200 |
| | 36 | * 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. |
