HIV molecular immunology database


Symbols Used in Variants

Symbol Meaning Example
x Lower case letters indicate a mutation. Variant SLYNTVAvL indicates a mutation from T to V in the epitope SLYNTVATL.
(x) Round brackets in the epitope variant designate an insertion. Variant PLTF(a)GWCYKL has an A inserted between 4F and 5G (Nef 139F and 140G) in the epitope PLTFGWCYKL. Insertion position within the epitope is reported as (4.1)A, and insertion position in the protein is reported as Nef (139.1)A.
'-' Dash in the epitope variant denotes a deletion. Variant RAEQ-SQdV of epitope RAEQASQEV has lost amino acid A at position 5.
{xxx} Curly brackets in the variant are used to designate a flanking region when there is a mutation upstream or downstream of the epitope. Variant {p}ISPRTLNAW of epitope {A}lSPRTLNAW means that there is an A-to-P mutation upstream of the epitope N-terminus.
'+n' Mutation in the downstream epitope flanking region. Variant SPAIFQSSM{TKILd} of the epitope SPAIFQSSM{TKILE} has an E-to-D mutation 5 amino acids downstream of the epitope C-terminus.
'-n' Mutation in the upstream epitope flanking region. Variant {rWEKI}RLRPGGKKK of the epitope {KWEKI}RLRPGGKKK has a K-to-R mutation 5 amino acids upstream of the epitope N-terminus.
'*' A non-mutated amino acid in the epitope flanking region either upstream or downstream of the epitope. Each '*' is one amino acid, and its sequence location is specific. This notation is used when the amino acids between the epitope and the mutation site are not reported in the original publication. Variant KIRLRPGGK{*t} of epitope KIRLRPGGK has an R-to-T processing mutation 2 amino acids downstream. The intervening amino acid was not reported.
'...' An unspecified number of amino acids were present between the mutation position in the flanking region and the epitope. This notation is used when the exact mutation position upstream or downstream is >5 amino acids away, or was not reported in the original publication. In the former case, the mutation position is reported. Variant {q...}TSnLQEQIGW of epitope {H...}TSTLQEQIGW has an unspecified number of non-mutated amino acids between the N-terminus of the epitope and the upstream H-to-Q mutation.
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