# Information on all confirmed and candidate ORFs and mature proteins of SARS-CoV-2.
# 
# Notes:
# - Coordinates in "Intervals" column do not include stop codon.
# - UniProtId, UniProtName, and UniProtFunctionDescription come from UniProt.
# - SubsPerSite42 and SubsPerNeutralSite42 use whole-genome 42-strain tree that excludes
#     the two most distant strains (which are not aligned in ORF8)
# - ExpectedAAchangeSNVsPerCodon and ExpectedAAchangeSNVsPerCodonPval have the expected
#      number of amino-acid changing SNV per codon using linear regression with
#      the fraction of amino acids that are conserved as the independent variable, and the
#      corresponding p-value.
# - CodAlignView and UCSCView links show ORF or mature protein and 5 codons of the
#     neighbor on each side in CodAlignView (color-coded alignment) and
#      UCSC Genome Browser.
#
ShortName	Name	LongName	UniProtId	UniProtName	SometimesCalled	Type	Start	End	Intervals	NumCodons	PhyloCSFperCodon	PhyloP	PhastCons	SubsPerSite	SubsPerNeutralSite	SubsPerSite42	SubsPerNeutralSite42	ConservedAAs	ConservedAAsPerCodon	AAchangeSNVs	AAchangeSNVsPerCodon	ExpectedAAchangeSNVsPerCodon	ExpectedAAchangeSNVsPerCodonPval	AAchangeSNVsInCons	AAchangeSNVsInConsPerConsCodon	AAchangeSNVsInNoncons	AAchangeSNVsInNonconsPerNonconsCodon	SynConstrainedCodons	SynConstrainedCodonsPerCodon	SynSNVs	SynSNVsPerCodon	SynSNVsInCons	SynSNVsInConsPerConsCodon	SynSNVsInNoncons	SynSNVsInNonconsPerNonconsCodon	CodAlignView	UCSCview	MatureProteinPosition	SubgenomicRNAEvidence	ProteomicsEvidence	FinkelRiboseqEvidence	UniProtFunctionDescription
1a	ORF1a	ORF1a polyprotein	P0DTC1	R1A_SARS2		ORF	266	13480	266-13480	4405	11.93	1.67211614496	0.887903975233	1.5	3.6	1.2	2.9	2711	0.615437003405	456	0.103518728717	0.133846579512	5.55050034448e-10	227	0.0837329398746	229	0.135182998819	569	0.129171396141	265	0.0601589103292	25	0.0439367311072	240	0.0625651720542	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;265;13215;0&v=1-13218&p=15&e=15&w=0&m=4476&mp=ORFs+and+Mature+Proteins:'|<-+1a+->'@0,'<-+1a+->|'@13209&m=8834&f=1a", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:251-13495&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		NA	Yes	Yes	Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.
1ab	ORF1ab	ORF1ab polyprotein	P0DTD1	R1AB_SARS2		ORF	266	21552	266-13468+13468-21552	7096	12.35	1.79348421652	0.914462883055	1.4	3.5	1.1	2.8	4983	0.702226606539	727	0.102452085682	0.119567182292	3.12849071852e-06	429	0.0860927152318	298	0.141031708471	1062	0.149661781285	421	0.059329199549	46	0.0433145009416	375	0.0621478289692	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;265;13203,8085;0,13202&v=1-21291&p=15&e=22&w=0&m=7170&mp=ORFs+and+Mature+Proteins:'|<-+1ab+->'@0,'<-+1ab+->|'@21281,'|<-+S+->'@21298&m=14220&f=1ab", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:251-21574&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		NA	Yes	Yes	Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.
S	S	Spike	P0DTC2	SPIKE_SARS2		ORF	21563	25381	21563-25381	1273	19.32	0.457403142757	0.505903980848	3.0	6.5	2.6	5.7	702	0.551453260016	161	0.126472898665	0.144373753902	0.0359956212337	51	0.0726495726496	110	0.192644483363	172	0.135113904163	86	0.0675569520817	8	0.046511627907	78	0.0708446866485	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21562;3819;0&v=1-3822&p=22&e=23&w=0&m=1349&mp=ORFs+and+Mature+Proteins:'|<-+S+->'@0,'<-+S+->|'@3814,'<-+1ab+->|'@-17,'|<-+3a+->'@3830&m=2580&f=S", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21541-25404&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	See description of mature proteins Spike protein S1, S2, and S2'.
2b	ORF2b	ORF2b			S.iORF1	ORF	21744	21860	21744-21860	39	-37.78	-1.26227811197	0.037283797094	5.5	4.7	4.9	4.3	6	0.153846153846	14	0.358974358974	0.209791610435	0.0229225903375	4	0.666666666667	10	0.30303030303	1	0.025641025641	7	0.179487179487	0	0.0	7	0.184210526316	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21743;117;0&v=1-120&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+2b+->'@0,'<-+2b+->|'@111&f=2b", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21729-21875&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Leaky Scanning	No	Yes	
3a	ORF3a	ORF3a	P0DTC3	AP3A_SARS2		ORF	25393	26217	25393-26217	275	9.01	1.31870647829	0.735089492315	1.9	3.5	1.6	2.9	113	0.410909090909	62	0.225454545455	0.167497330288	0.00791330362153	27	0.238938053097	35	0.216049382716	52	0.189090909091	26	0.0945454545455	8	0.153846153846	18	0.0807174887892	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25392;825;0&v=1-828&p=23&e=39&w=0&mp=ORFs+and+Mature+Proteins:'|<-+3a+->'@0,'<-+3a+->|'@819,'<-+S+->|'@-16,'|<-+E+->'@852&f=3a", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25370-26256&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. Up-regulates expression of fibrinogen subunits FGA, FGB and FGG in host lung epithelial cells. Induces apoptosis in cell culture. Downregulates the type 1 interferon receptor by inducing serine phosphorylation within the IFN alpha-receptor subunit 1 (IFNAR1) degradation motif and increasing IFNAR1 ubiquitination.
3c	ORF3c	ORF3c			ORF3h,3a-iORF1,ORF3a*	ORF	25457	25579	25457-25579	41	-1.21	1.88813503463	0.95192370748	1.1	1.5	0.9	1.3	16	0.390243902439	9	0.219512195122	0.170897350845	0.258683600509	3	0.1875	6	0.24	21	0.512195121951	7	0.170731707317	3	0.142857142857	4	0.2	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25456;123;0&v=1-126&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+3c+->'@0,'<-+3c+->|'@117&f=3c", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25442-25594&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Leaky Scanning	Not In Search Space	Yes	
3d	ORF3d	ORF3d			ORF3b,ORF3c	ORF	25524	25694	25524-25694	57	-27.48	1.01701482667	0.56817242807	2.3	0.3	1.9	0.1	19	0.333333333333	14	0.245614035088	0.18026078371	0.134395172276	4	0.210526315789	10	0.263157894737	12	0.210526315789	4	0.0701754385965	1	0.0833333333333	3	0.0666666666667	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25523;171;0&v=1-174&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+3d+->'@0,'<-+3d+->|'@165&f=3d", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25509-25709&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		No	Not In Search Space	No	
3d-2	ORF3d-2	ORF3d-2			3a-iORF2	ORF	25596	25694	25596-25694	33	-38.84	0.526848615152	0.401097607475	2.9	0.4	2.5	0.1	10	0.30303030303	7	0.212121212121	0.185246507702	0.413269985549	1	0.1	6	0.260869565217	1	0.030303030303	0	0.0	0	0.0	0	0.0	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25595;99;0&v=1-102&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+3d-2+->'@0,'<-+3d-2+->|'@91&f=3d-2", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25581-25709&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		No	Not In Search Space	Yes	
3b	ORF3b	ORF3b				ORF	25814	25879	25814-25879	22	-18.00	1.53817692424	0.830231471212	1.8	1.2	1.5	0.8	14	0.636363636364	5	0.227272727273	0.130403543783	0.149880841735	5	0.357142857143	0	0.0	2	0.0909090909091	0	0.0	0	0.0	0	0.0	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25813;66;0&v=1-69&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+3b+->'@0,'<-+3b+->|'@60&f=3b", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25799-25894&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		No	No	No	
E	E	Envelope	P0DTC4	VEMP_SARS2		ORF	26245	26469	26245-26469	75	3.01	2.41988491156	0.987926506667	0.5	1.2	0.4	1.0	62	0.826666666667	11	0.146666666667	0.0990931971093	0.120595294954	4	0.0645161290323	7	0.538461538462	0	0.0	7	0.0933333333333	0	Undefined	7	0.0933333333333	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26244;225;0&v=1-228&p=39&e=65&w=0&mp=ORFs+and+Mature+Proteins:'|<-+E+->'@0,'<-+E+->|'@220,'<-+3a+->|'@-33,'|<-+M+->'@278&f=E", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:26206-26534&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	No	Yes	Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis.
M	M	Membrane	P0DTC5	VME1_SARS2		ORF	26523	27188	26523-27188	222	11.73	1.97274798604	0.937575387778	1.2	3.3	0.9	2.5	179	0.806306306306	12	0.0540540540541	0.102443064635	0.00766658426129	7	0.0391061452514	5	0.116279069767	36	0.162162162162	14	0.0630630630631	1	0.0277777777778	13	0.0698924731183	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26522;666;0&v=1-669&p=65&e=25&w=0&mp=ORFs+and+Mature+Proteins:'|<-+M+->'@0,'<-+M+->|'@661,'<-+E+->|'@-58,'|<-+6+->'@679&f=M", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:26458-27213&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins.
6	ORF6	ORF6	P0DTC6	NS6_SARS2		ORF	27202	27384	27202-27384	61	-0.31	1.41992173716	0.897379629617	1.4	2.2	0.9	1.8	14	0.229508196721	11	0.180327868852	0.197343018373	0.444029737968	3	0.214285714286	8	0.170212765957	5	0.0819672131148	5	0.0819672131148	1	0.2	4	0.0714285714286	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27201;183;0&v=1-186&p=25&e=21&w=0&mp=ORFs+and+Mature+Proteins:'|<-+6+->'@0,'<-+6+->|'@178,'<-+M+->|'@-18,'|<-+7a+->'@192&f=6", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27177-27405&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	Could be a determinant of virus virulence, since, when expressed in an otherwise attenuated JHM strain of murine coronavirus, it can dramatically increase the lethality of the latter. Seems to stimulate cellular DNA synthesis in vitro.
7a	ORF7a	ORF7a	P0DTC7	NS7A_SARS2		ORF	27394	27756	27394-27756	121	7.19	1.475233327	0.898830852782	1.6	3.2	1.0	2.3	57	0.471074380165	30	0.247933884298	0.157598401925	0.00671677323639	12	0.210526315789	18	0.28125	11	0.0909090909091	9	0.0743801652893	1	0.0909090909091	8	0.0727272727273	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27393;363;0&v=1-366&p=21&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+7a+->'@0,'<-+7a+->|'@357,'<-+6+->|'@-14&f=7a", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27373-27771&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	Non-structural protein which is dispensable for virus replication in cell culture. Mature protein starts on amino acid 16.
7b	ORF7b	ORF7b	P0DTD8	NS7B_SARS2		ORF	27756	27884	27756-27884	43	5.07	1.50835366822	0.902765072868	1.2	3.6	0.8	2.4	20	0.46511627907	9	0.209302325581	0.158578681695	0.233847055596	4	0.2	5	0.217391304348	1	0.0232558139535	6	0.139534883721	0	0.0	6	0.142857142857	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27755;129;0&v=1-132&p=15&e=21&w=0&mp=ORFs+and+Mature+Proteins:'|<-+7b+->'@0,'<-+7b+->|'@123,'|<-+8+->'@138&f=7b", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27741-27905&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Low Level or Leaky Scanning	No	Yes	
8	ORF8	ORF8	P0DTC8	NS8_SARS2		ORF	27894	28256	27894-28256	121	4.61	0.0155149641873	0.199258166226	5.6	8.8	3.9	6.2	24	0.198347107438	19	0.157024793388	0.202469917859	0.127416599051	3	0.125	16	0.164948453608	10	0.0826446280992	7	0.0578512396694	0	0.0	7	0.0630630630631	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27893;363;0&v=1-366&p=21&e=29&w=0&mp=ORFs+and+Mature+Proteins:'|<-+8+->'@0,'<-+8+->|'@358,'<-+7b+->|'@-15,'|<-+N+->'@380&f=8", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27873-28285&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	May play a role in host-virus interaction. Mature protein starts on amino acid 16.
N	N	Nucleocapsid	P0DTC9	NCAP_SARS2		ORF	28274	29530	28274-29530	419	8.32	2.11564253492	0.975801659364	0.9	2.1	0.6	1.4	307	0.732696897375	90	0.214797136038	0.11455393911	3.47550699331e-09	59	0.192182410423	31	0.276785714286	45	0.107398568019	43	0.102625298329	8	0.177777777778	35	0.0935828877005	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28273;1257;0&v=1-1260&p=29&e=39&w=0&mp=ORFs+and+Mature+Proteins:'|<-+N+->'@0,'<-+N+->|'@1252,'<-+8+->|'@-22,'|<-+10+->'@1284&f=N", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28245-29569&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Yes	Yes	Yes	Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication.
9b	ORF9b	ORF9b	P0DTD2	ORF9B_SARS2	ORF9a	ORF	28284	28574	28284-28574	97	-5.91	2.14430157182	0.963362842268	0.9	0.6	0.7	0.4	63	0.649484536082	13	0.134020618557	0.128244776693	0.477564526215	6	0.0952380952381	7	0.205882352941	17	0.175257731959	7	0.0721649484536	3	0.176470588235	4	0.05	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28283;291;0&v=1-294&p=15&e=171&w=0&mp=ORFs+and+Mature+Proteins:'|<-+9b+->'@0,'<-+9b+->|'@285,'|<-+9c+->'@450&f=9b", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28269-28745&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		Leaky Scanning	Yes	Yes	May play a role in host-virus interaction.
9c	ORF9c	ORF9c	P0DTD3	Y14_SARS2	ORF9b,ORF14	ORF	28734	28952	28734-28952	73	-7.84	2.07863699269	0.988854136986	1.0	0.3	0.6	0.2	51	0.698630136986	27	0.369863013699	0.120158905442	3.77755589032e-08	17	0.333333333333	10	0.454545454545	4	0.0547945205479	6	0.0821917808219	0	0.0	6	0.0869565217391	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28733;219;0&v=1-222&p=171&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+9c+->'@0,'<-+9c+->|'@213,'<-+9b+->|'@-165&f=9c", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28563-28967&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		No	No	No	May play a role in host-virus interaction.
10	ORF10	ORF10	A0A663DJA2	A0A663DJA2_SARS2		ORF	29558	29671	29558-29671	38	-3.15	2.43279112105	0.999792789474	0.3	0.2	0.2	0.1	20	0.526315789474	10	0.263157894737	0.148509594072	0.0466532820134	8	0.4	2	0.111111111111	0	0.0	4	0.105263157895	0	Undefined	4	0.105263157895	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;29557;114;0&v=1-117&p=39&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+10+->'@0,'<-+10+->|'@108,'<-+N+->|'@-32&f=10", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:29519-29686&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")		No	No	Questionable	
nsp1	nsp1	nsp1	P0DTC1			Mature protein	266	805	266-805	180	8.83	1.93555724826	0.916754162704	1.3	2.9	1.0	2.3	110	0.611111111111	19	0.105555555556	0.134558313777	0.150577247777	11	0.1	8	0.114285714286	58	0.322222222222	19	0.105555555556	6	0.103448275862	13	0.106557377049	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;265;540;0&v=1-540&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp1+->'@0,'<-+nsp1+->|'@529,'|<-+nsp2+->'@540&f=nsp1", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:251-820&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 1-180 on protein P0DTC1	NA	Yes	NA	Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.
nsp2	nsp2	nsp2	P0DTC1			Mature protein	806	2719	806-2719	638	14.56	1.3883492219	0.786118058777	2.0	4.3	1.6	3.5	275	0.431034482759	102	0.15987460815	0.164186121871	0.40935807169	39	0.141818181818	63	0.173553719008	47	0.0736677115987	44	0.0689655172414	1	0.0212765957447	43	0.072758037225	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;805;1914;0&v=1-1914&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp2+->'@0,'<-+nsp2+->|'@1903,'<-+nsp1+->|'@-11,'|<-+nsp3+->'@1914&f=nsp2", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:791-2734&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 181-818 on protein P0DTC1	NA	Yes	NA	May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.
nsp3	nsp3	nsp3	P0DTC1			Mature protein	2720	8554	2720-8554	1945	11.93	1.48850487105	0.850383459859	1.8	3.9	1.4	3.2	1034	0.531619537275	197	0.101285347044	0.147636974324	9.21829552423e-10	75	0.0725338491296	122	0.133918770582	161	0.0827763496144	106	0.054498714653	5	0.0310559006211	101	0.0566143497758	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;2719;5835;0&v=1-5835&p=15&e=15&w=0&m=2015&mp=ORFs+and+Mature+Proteins:'|<-+nsp3+->'@0,'<-+nsp3+->|'@5824,'<-+nsp2+->|'@-11,'|<-+nsp4+->'@5835&m=3912&f=nsp3", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:2705-8569&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 819-2763 on protein P0DTC1	NA	Yes	NA	Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.
nsp4	nsp4	nsp4	P0DTC1			Mature protein	8555	10054	8555-10054	500	12.48	1.7294561103	0.939393422707	1.4	3.4	1.1	2.7	340	0.68	50	0.1	0.123224101234	0.0622078675675	33	0.0970588235294	17	0.10625	56	0.112	35	0.07	4	0.0714285714286	31	0.0698198198198	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;8554;1500;0&v=1-1500&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp4+->'@0,'<-+nsp4+->|'@1489,'<-+nsp3+->|'@-11,'|<-+nsp5+->'@1500&f=nsp4", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:8540-10069&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 2764-3263 on protein P0DTC1	NA	Yes	NA	Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.
nsp5	3CLpro	3C-like proteinase	P0DTD1			Mature protein	10055	10972	10055-10972	306	12.16	2.02428324453	0.981467323529	1.1	3.2	0.9	2.5	260	0.849673202614	18	0.0588235294118	0.0953079572466	0.0145144255774	15	0.0576923076923	3	0.0652173913043	45	0.147058823529	16	0.0522875816993	1	0.0222222222222	15	0.0574712643678	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;10054;918;0&v=1-918&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp5+->'@0,'<-+nsp5+->|'@907,'<-+nsp4+->|'@-11,'|<-+nsp6+->'@918&f=nsp5", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:10040-10987&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 3264-3569 on protein P0DTD1	NA	Yes	NA	Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN] (PubMed:32198291). Also able to bind an ADP-ribose-1''-phosphate (ADRP).
nsp6	nsp6	nsp6	P0DTC1			Mature protein	10973	11842	10973-11842	290	9.05	1.94812351251	0.980810312644	1.0	2.8	0.8	2.2	212	0.731034482759	28	0.0965517241379	0.114827454344	0.189621063442	17	0.0801886792453	11	0.141025641026	59	0.203448275862	18	0.0620689655172	2	0.0338983050847	16	0.0692640692641	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;10972;870;0&v=1-870&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp6+->'@0,'<-+nsp6+->|'@859,'<-+nsp5+->|'@-11,'|<-+nsp7+->'@870&f=nsp6", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:10958-11857&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 3570-3859 on protein P0DTC1	NA	Yes	NA	Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.
nsp7	nsp7	nsp7	P0DTC1			Mature protein	11843	12091	11843-12091	83	14.03	1.9645552496	0.965669215663	1.3	3.7	1.0	2.9	72	0.867469879518	6	0.0722891566265	0.0923798897187	0.344906377729	6	0.0833333333333	0	0.0	9	0.10843373494	6	0.0722891566265	0	0.0	6	0.0810810810811	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;11842;249;0&v=1-249&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp7+->'@0,'<-+nsp7+->|'@238,'<-+nsp6+->|'@-11,'|<-+nsp8+->'@249&f=nsp7", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:11828-12106&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 3860-3942 on protein P0DTC1	NA	Yes	NA	Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.
nsp8	nsp8	nsp8	P0DTC1			Mature protein	12092	12685	12092-12685	198	10.49	2.17396185236	0.991415386869	0.9	3.0	0.7	2.4	175	0.883838383838	16	0.0808080808081	0.0896867978431	0.389153456821	15	0.0857142857143	1	0.0434782608696	48	0.242424242424	6	0.030303030303	1	0.0208333333333	5	0.0333333333333	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;12091;594;0&v=1-594&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp8+->'@0,'<-+nsp8+->|'@583,'<-+nsp7+->|'@-11,'|<-+nsp9+->'@594&f=nsp8", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:12077-12700&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 3943-4140 on protein P0DTC1	NA	Yes	NA	Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.
nsp9	nsp9	nsp9	P0DTC1			Mature protein	12686	13024	12686-13024	113	10.65	2.18214905546	0.967291989381	1.0	2.8	0.8	2.2	101	0.893805309735	8	0.070796460177	0.0880469505712	0.328274904452	7	0.0693069306931	1	0.0833333333333	34	0.300884955752	7	0.0619469026549	1	0.0294117647059	6	0.0759493670886	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;12685;339;0&v=1-339&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp9+->'@0,'<-+nsp9+->|'@328,'<-+nsp8+->|'@-11,'|<-+nsp10+->'@339&f=nsp9", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:12671-13039&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 4141-4253 on protein P0DTC1	NA	Yes	NA	May participate in viral replication by acting as a ssRNA-binding protein.
nsp10	nsp10	nsp10	P0DTC1			Mature protein	13025	13441	13025-13441	139	11.22	2.26905474101	0.989050976259	0.9	2.6	0.8	2.1	122	0.877697841727	11	0.0791366906475	0.0906970944316	0.385947683404	9	0.0737704918033	2	0.117647058824	42	0.302158273381	7	0.0503597122302	3	0.0714285714286	4	0.0412371134021	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13024;417;0&v=1-417&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp10+->'@0,'<-+nsp10+->|'@405,'<-+nsp9+->|'@-11,'|<-+nsp11+->'@417&f=nsp10", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:13010-13456&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 4254-4392 on protein P0DTC1	NA	Yes	NA	Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.
nsp11	nsp11	nsp11	P0DTC1			Mature protein	13442	13480	13442-13480	13	6.34	2.44338498154	0.997579666667	0.8	2.3	0.6	1.7	10	0.769230769231	1	0.0769230769231	0.108543061661	0.579972271431	0	0.0	1	0.333333333333	10	0.769230769231	1	0.0769230769231	1	0.1	0	0.0	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13441;39;0&v=1-39&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp11+->'@0,'<-+nsp11+->|'@27,'<-+nsp10+->|'@-12&f=nsp11", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:13427-13495&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 4393-4405 on protein P0DTC1	NA	No	NA	
nsp12	RdRp	RNA-directed RNA polymerase	P0DTD1			Mature protein	13442	16236	13442-13468+13468-16236	932	10.22	2.16029889398	0.983959390132	0.9	2.4	0.7	1.8	833	0.893776824034	84	0.0901287553648	0.0880516372919	0.428032146557	65	0.078031212485	19	0.191919191919	241	0.258583690987	52	0.0557939914163	9	0.0373443983402	43	0.0622286541245	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13441;27,2769;0,26&v=1-2796&p=15&e=15&w=0&m=1002&mp=ORFs+and+Mature+Proteins:'|<-+nsp12+->'@0,'<-+nsp12+->|'@2784,'<-+nsp10+->|'@-12,'|<-+nsp13+->'@2796&f=nsp12", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:13427-16251&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 4393-5324 on protein P0DTD1	NA	Yes	NA	Responsible for replication and transcription of the viral RNA genome.
nsp13	Hel	Helicase	P0DTD1			Mature protein	16237	18039	16237-18039	601	12.54	2.08697871164	0.987947471492	1.0	3.2	0.8	2.4	548	0.911813643927	65	0.108153078203	0.0850840593042	0.0284832487818	56	0.102189781022	9	0.169811320755	115	0.191347753744	36	0.0599001663894	6	0.0521739130435	30	0.0617283950617	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;16236;1803;0&v=1-1803&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp13+->'@0,'<-+nsp13+->|'@1791,'<-+nsp12+->|'@-12,'|<-+nsp14+->'@1803&f=nsp13", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:16222-18054&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 5325-5925 on protein P0DTD1	NA	Yes	NA	Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium.
nsp14	ExoN	Proofreading exoribonuclease	P0DTD1			Mature protein	18040	19620	18040-19620	527	15.55	1.92977498669	0.949343073118	1.3	3.9	1.1	3.2	439	0.833017077799	52	0.0986717267552	0.0980483710035	0.502171769375	39	0.0888382687927	13	0.147727272727	73	0.138519924099	31	0.0588235294118	5	0.0684931506849	26	0.057268722467	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;18039;1581;0&v=1-1581&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp14+->'@0,'<-+nsp14+->|'@1569,'<-+nsp13+->|'@-12,'|<-+nsp15+->'@1581&f=nsp14", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:18025-19635&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 5926-6452 on protein P0DTD1	NA	Yes	NA	Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Acts as a proofreading exoribonuclease for RNA replication, thereby lowering The sensitivity of the virus to RNA mutagens.
nsp15	NendoU	nsp15	P0DTD1			Mature protein	19621	20658	19621-20658	346	14.51	1.75572868603	0.92763948316	1.5	4.1	1.3	3.5	239	0.690751445087	39	0.112716763006	0.121455177889	0.345363924697	20	0.0836820083682	19	0.177570093458	44	0.127167630058	18	0.0520231213873	1	0.0227272727273	17	0.0562913907285	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;19620;1038;0&v=1-1038&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp15+->'@0,'<-+nsp15+->|'@1026,'<-+nsp14+->|'@-12,'|<-+nsp16+->'@1038&f=nsp15", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:19606-20673&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 6453-6798 on protein P0DTD1	NA	Yes	NA	Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
nsp16	O-MT	nsp16	P0DTD1			Mature protein	20659	21552	20659-21552	298	16.32	1.67997429519	0.868220354877	1.5	4.8	1.3	4.1	223	0.748322147651	32	0.107382550336	0.111983133998	0.445665670712	22	0.0986547085202	10	0.133333333333	30	0.10067114094	20	0.0671140939597	1	0.0333333333333	19	0.0708955223881	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;20658;894;0&v=1-894&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+nsp16+->'@0,'<-+nsp16+->|'@882,'<-+nsp15+->|'@-12&f=nsp16", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:20644-21567&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 6799-7096 on protein P0DTD1	NA	Yes	NA	Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system.
S1	S1	S1	P0DTC2			Mature protein	21599	23617	21599-23617	673	21.07	-0.386527099851	0.274291876474	4.0	7.7	3.6	6.9	261	0.387815750371	87	0.12927191679	0.171296852014	0.00168044900788	20	0.0766283524904	67	0.162621359223	43	0.0638930163447	50	0.074294205052	1	0.0232558139535	49	0.0777777777778	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21598;2019;0&v=1-2019&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+S1+->'@0,'<-+S1+->|'@2010,'|<-+S2+->'@2019&f=S1", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21584-23632&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 13-685 on protein P0DTC2	NA	Yes	NA	attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.
S2	S2	S2	P0DTC2			Mature protein	23618	25381	23618-25381	588	18.42	1.44799165487	0.779625781327	1.7	5.1	1.4	4.2	441	0.75	71	0.12074829932	0.111707078811	0.260856850434	31	0.0702947845805	40	0.272108843537	127	0.215986394558	34	0.0578231292517	7	0.0551181102362	27	0.058568329718	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23617;1764;0&v=1-1764&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+S2+->'@0,'<-+S2+->|'@1755,'<-+S1+->|'@-9&f=S2", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23603-25396&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 686-1273 on protein P0DTC2	NA	Yes	NA	mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.
S2'	S2'	S2'	P0DTC2			Mature protein	24008	25381	24008-25381	458	18.29	1.56421821913	0.828003778559	1.7	5.0	1.4	4.1	357	0.779475982533	56	0.122270742358	0.106857428071	0.160357784265	26	0.0728291316527	30	0.29702970297	113	0.24672489083	26	0.056768558952	6	0.0530973451327	20	0.0579710144928	=hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24007;1374;0&v=1-1374&p=15&e=15&w=0&mp=ORFs+and+Mature+Proteins:'|<-+S2'+->'@0,'<-+S2'+->|'@1364&f=S2%27", "CodAlignView")	=hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23993-25396&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview")	amino acids 816-1273 on protein P0DTC2	NA	Yes	NA	Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.