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Add prM protein, remove PRO (pr) protein
The precursor protein is cleaved into ~10 proteins including the precusor membrane protein (prM). prM is subsequently cleaved by the host protease furin resulting in protein M (aka MP). The previous annotation included CDSs PRO and MP, but not the (parent) prM protein. prM is cleaved directly from the polyprotein and is functional, forming heterodimers with protein E (similar behaviour across all flaviviruses I believe). NCBI's genome viewer shows both prM as well as both the sub-proteins after cleavage, pr and M. pr would correspond to the previous PRO annotation. I've not seen protein pr referenced anywhere else so I've not included that here. Note that this change wasn't desirable before Auspice could display overlapping CDSs <nextstrain/auspice#1684>. References: <https://www.microbiologyresearch.org/content/journal/jgv/10.1099/vir.0.18723-0> <https://www.ncbi.nlm.nih.gov/gene/7751225>
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Lines changed: 4 additions & 3 deletions

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config/zika_outgroup.gb

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -100,9 +100,10 @@ FEATURES Location/Qualifiers
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CDS 91..456
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/product="capsid protein"
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/gene="CA"
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CDS 457..735
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/product="propeptide"
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/gene="PRO"
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CDS 457..960
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/note="Modified by Nextstrain; Differs from ref"
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/product="precursor membrane protein"
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/gene="prM"
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CDS 736..960
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/product="membrane protein"
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/gene="MP"

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