From 169856e14a20140d4fcf6a05382314b66d25bb21 Mon Sep 17 00:00:00 2001 From: realmarcin <4625870+realmarcin@users.noreply.github.com> Date: Tue, 4 Aug 2020 18:39:18 -0700 Subject: [PATCH 1/3] adding 9c synonyms to ORF14 --- curated/ORFs/uniprot_sars-cov-2.gpi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index af9b52da..9c6747fb 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -74,5 +74,5 @@ UniProtKB P0DTD1-PRO_0000449631 nsp14 Proofreading exoribonuclease ExoN|P0DTD1(5 UniProtKB P0DTD1-PRO_0000449632 nsp15 Uridylate-specific endoribonuclease P0DTD1(6453-6798)|nsp15 (SARS2)|NendoU (SARS2)|ORF1ab/Clv:nsp15 (SARS2)|PRO_0000449632|UniProtKB:P0DTD1, 6453-6798|endoRNAse (SARS2)|Non-structural protein 15|nsp-15|nsp15|ns15|ns-15|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 15|uridylate-specific endoribonuclease protein taxon:2697049 UniProtKB:P0DTD1 PR:000050287 UniProtKB P0DTD1-PRO_0000449633 nsp16 2'-O-methyltransferase P0DTD1(6799-7096)|2'-O-methyltransferase|nsp16 (SARS2)|2'-O-ribose methyltransferase (SARS2)|UniProtKB:P0DTD1, 6799-7096|PRO_0000449633|ORF1ab/Clv:nsp16 (SARS2)|Non-structural protein 16|nsp-16|nsp16|ns16|ns-16|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 16 protein taxon:2697049 UniProtKB:P0DTD1 PR:000050288 UniProtKB P0DTD2 ORF9b accessory protein 9b ORF9b|ORF-9b|PRO_0000449657|accessory protein 9b (SARS2)|ORF-9b (SARS2)|ORF9b (SARS2)|P0DTD2|Protein 9b|Accessory protein 9b|ORF-9b|9b protein|9b accessory gene|9b accessory protein|9b protein taxon:2697049 PR:P0DTD2 -UniProtKB P0DTD3 ORF14 Uncharacterized protein 14 ORF14 (SARS2)|P0DTD3|PRO_0000449658|Uncharacterized protein 14|ORF14|ORF-14 protein taxon:2697049 PR:P0DTD3 +UniProtKB P0DTD3 ORF14 Uncharacterized protein 14 ORF14 (SARS2)|P0DTD3|PRO_0000449658|Uncharacterized protein 14|ORF14|ORF-14|9c|ORF9c|ORF-9c protein taxon:2697049 PR:P0DTD3 UniProtKB P0DTD8 ORF7b Accessory protein 7b ORF7b|ns7b|ns7b (SARS2)|accessory protein 7b (SARS2)|ORF7b (SARS2)|ORF 7b|PRO_0000449799|P0DTD8|protein 7b|ns7b|ns-7b|Accessory protein 7b|7b protein taxon:2697049 PR:P0DTD8 From 15d85f8421bbcc94d53151f584bed29facecb824 Mon Sep 17 00:00:00 2001 From: realmarcin <4625870+realmarcin@users.noreply.github.com> Date: Tue, 4 Aug 2020 18:44:34 -0700 Subject: [PATCH 2/3] purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates purging UniProt sourced gene names with letter and coordinates --- curated/ORFs/uniprot_sars-cov-2.gpi | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index 9c6747fb..16561dfe 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -47,9 +47,9 @@ UniProtKB P0DTC1 pp1a Replicase polyprotein 1a ORF1a|1a|pp1a|ORF1a/ClvPrd (SARS2)|ORF1a proteolytic cleavage product protein taxon:2697049 PR:P0DTC1-1 UniProtKB P0DTC1-PRO_0000449645 nsp11 Non-structural protein 11 P0DTC1(4393-4405)|rep/Clv:nsp11 (SARS2)|UniProtKB:P0DTC1, 4393-4405|nsp11 (SARS2)|PRO_0000449645|Non-structural protein 11|nsp-11|nsp11|ns11|ns-11|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 11 protein taxon:2697049 UniProtKB:P0DTC1 PR:000050280 UniProtKB P0DTC2 S protein Spike glycoprotein S|S protein|S glycoprotein (SARS2)|surface glycoprotein (SARS2)|E2 (SARS2)|S (SARS2)|peplomer protein (SARS2)|Spike glycoprotein|Spike|spike gene|Spike (S) glycoprotein|Spike (S)|S glycoprotein|spike surface glycoprotein (S)|E2|E2 protein|E2 protein taxon:2697049 PR:P0DTC2 -UniProtKB P0DTC2-PRO_0000449647 S(13-685) Spike protein S1 P0DTC2(13-685)|S|UniProtKB:P0DTC2, 13-685|PRO_0000449647|S1 (SARS2)|Spike (S1) glycoprotein|Spike protein S1|S1 protein|spike (S1) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050267 -UniProtKB P0DTC2-PRO_0000449648 S(686-1273) Spike protein S2 P0DTC2(686-1273)|S|PRO_0000449648|UniProtKB:P0DTC2, 686-1273|S2 (SARS2)|Spike (S2) glycoprotein|Spike protein S2|S2 protein|spike (S2) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050268 -UniProtKB P0DTC2-PRO_0000449649 S(816-1273) Spike protein S2' P0DTC2(816-1273)|S|UniProtKB:P0DTC2, 816-1273|S2' (SARS2)|PRO_0000449649|Spike (S2') glycoprotein|Spike protein S2'|S2' protein|spike (S2') protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050269 +UniProtKB P0DTC2-PRO_0000449647 Spike protein S1 Spike protein S1 P0DTC2(13-685)|S|UniProtKB:P0DTC2, 13-685|PRO_0000449647|S1 (SARS2)|Spike (S1) glycoprotein|Spike protein S1|S1 protein|spike (S1) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050267 +UniProtKB P0DTC2-PRO_0000449648 Spike protein S2 Spike protein S2 P0DTC2(686-1273)|S|PRO_0000449648|UniProtKB:P0DTC2, 686-1273|S2 (SARS2)|Spike (S2) glycoprotein|Spike protein S2|S2 protein|spike (S2) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050268 +UniProtKB P0DTC2-PRO_0000449649 Spike protein S2' Spike protein S2' P0DTC2(816-1273)|S|UniProtKB:P0DTC2, 816-1273|S2' (SARS2)|PRO_0000449649|Spike (S2') glycoprotein|Spike protein S2'|S2' protein|spike (S2') protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050269 UniProtKB P0DTC3 ORF3a ORF3a protein ORF3a|3a|protein U274 (SARS2)|PRO_0000449650|ORF3a (SARS2)|protein X1 (SARS2)|accessory protein 3a (SARS2)|P0DTC3|Protein 3a|Accessory protein 3a|Protein U274|Protein X1|3a|3a protein|3a accessory gene|3a accessory protein protein taxon:2697049 PR:P0DTC3 UniProtKB P0DTC4 E protein Envelope small membrane protein sM protein (SARS2)|envelope protein (SARS2)|E protein (SARS2)|E (SARS2)|PRO_0000449651|P0DTC4|Envelope small membrane protein|small envelope protein (E)|small envelope protein|E protein|E protein taxon:2697049 PR:P0DTC4 UniProtKB P0DTC5 M protein Membrane protein E1 glycoprotein|Matrix glycoprotein|Matrix protein (M)|Membrane glycoprotein|Matrix protein|Matrix (M) protein protein taxon:2697049 PR:P0DTC5 From 470cc65af8e2ecd62350b1311e398707b581dbbd Mon Sep 17 00:00:00 2001 From: realmarcin <4625870+realmarcin@users.noreply.github.com> Date: Tue, 4 Aug 2020 18:48:09 -0700 Subject: [PATCH 3/3] removing 'S' synonyms for S1/S2/S2' --- curated/ORFs/uniprot_sars-cov-2.gpi | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index 16561dfe..e8e88679 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -47,9 +47,9 @@ UniProtKB P0DTC1 pp1a Replicase polyprotein 1a ORF1a|1a|pp1a|ORF1a/ClvPrd (SARS2)|ORF1a proteolytic cleavage product protein taxon:2697049 PR:P0DTC1-1 UniProtKB P0DTC1-PRO_0000449645 nsp11 Non-structural protein 11 P0DTC1(4393-4405)|rep/Clv:nsp11 (SARS2)|UniProtKB:P0DTC1, 4393-4405|nsp11 (SARS2)|PRO_0000449645|Non-structural protein 11|nsp-11|nsp11|ns11|ns-11|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 11 protein taxon:2697049 UniProtKB:P0DTC1 PR:000050280 UniProtKB P0DTC2 S protein Spike glycoprotein S|S protein|S glycoprotein (SARS2)|surface glycoprotein (SARS2)|E2 (SARS2)|S (SARS2)|peplomer protein (SARS2)|Spike glycoprotein|Spike|spike gene|Spike (S) glycoprotein|Spike (S)|S glycoprotein|spike surface glycoprotein (S)|E2|E2 protein|E2 protein taxon:2697049 PR:P0DTC2 -UniProtKB P0DTC2-PRO_0000449647 Spike protein S1 Spike protein S1 P0DTC2(13-685)|S|UniProtKB:P0DTC2, 13-685|PRO_0000449647|S1 (SARS2)|Spike (S1) glycoprotein|Spike protein S1|S1 protein|spike (S1) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050267 -UniProtKB P0DTC2-PRO_0000449648 Spike protein S2 Spike protein S2 P0DTC2(686-1273)|S|PRO_0000449648|UniProtKB:P0DTC2, 686-1273|S2 (SARS2)|Spike (S2) glycoprotein|Spike protein S2|S2 protein|spike (S2) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050268 -UniProtKB P0DTC2-PRO_0000449649 Spike protein S2' Spike protein S2' P0DTC2(816-1273)|S|UniProtKB:P0DTC2, 816-1273|S2' (SARS2)|PRO_0000449649|Spike (S2') glycoprotein|Spike protein S2'|S2' protein|spike (S2') protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050269 +UniProtKB P0DTC2-PRO_0000449647 Spike protein S1 Spike protein S1 P0DTC2(13-685)|UniProtKB:P0DTC2, 13-685|PRO_0000449647|S1 (SARS2)|Spike (S1) glycoprotein|Spike protein S1|S1 protein|spike (S1) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050267 +UniProtKB P0DTC2-PRO_0000449648 Spike protein S2 Spike protein S2 P0DTC2(686-1273)|PRO_0000449648|UniProtKB:P0DTC2, 686-1273|S2 (SARS2)|Spike (S2) glycoprotein|Spike protein S2|S2 protein|spike (S2) protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050268 +UniProtKB P0DTC2-PRO_0000449649 Spike protein S2' Spike protein S2' P0DTC2(816-1273)|UniProtKB:P0DTC2, 816-1273|S2' (SARS2)|PRO_0000449649|Spike (S2') glycoprotein|Spike protein S2'|S2' protein|spike (S2') protein protein taxon:2697049 UniProtKB:P0DTC2 PR:000050269 UniProtKB P0DTC3 ORF3a ORF3a protein ORF3a|3a|protein U274 (SARS2)|PRO_0000449650|ORF3a (SARS2)|protein X1 (SARS2)|accessory protein 3a (SARS2)|P0DTC3|Protein 3a|Accessory protein 3a|Protein U274|Protein X1|3a|3a protein|3a accessory gene|3a accessory protein protein taxon:2697049 PR:P0DTC3 UniProtKB P0DTC4 E protein Envelope small membrane protein sM protein (SARS2)|envelope protein (SARS2)|E protein (SARS2)|E (SARS2)|PRO_0000449651|P0DTC4|Envelope small membrane protein|small envelope protein (E)|small envelope protein|E protein|E protein taxon:2697049 PR:P0DTC4 UniProtKB P0DTC5 M protein Membrane protein E1 glycoprotein|Matrix glycoprotein|Matrix protein (M)|Membrane glycoprotein|Matrix protein|Matrix (M) protein protein taxon:2697049 PR:P0DTC5