Strain

BELGIUM_PIG_1977_LT905450 (Region: Belgium; Strain: Porcine epidemic diarrhea virus isolate CV777 genome assembly, complete genome: monopartite.; Date: 1977)

Gene

nucleocapsid protein

Description

Annotated in NCBI, nucleocapsid protein

Location

LT905450(+):26367-27692

GenBank Accession

SNU46340.1

Full name

Nucleoprotein

CDS

ATGGCTTCTGTCAGCTTTCAGGATCGTGGCCGCAAACGGGTGCCATTATCTCTCTATGCCCCTCTTAGGGTTACTAATGACAAGCCCCTTTCTAAGGTACTTGCAAACAACGCTGTACCCACTAACAAGGGGAATAAGGACCAGCAAATTGGGTACTGGAATGAGCAAATTCGCTGGCGCATGCGCCGTGGTGAGCGAATTGAACAACCTTCCAATTGGCATTTCTACTACCTCGGAACAGGACCTCACGGCGACCTCCGTTATAGGACTCGTACTGAGGGTGTTTTCTGGGTTGCTAAAGAAGGCGCAAAGACTGAACCCACTAATTTGGGTGTCAGAAAGGCGTCTGAAAAGCCAATCATTCCAAAATTCTCTCAACAGCTCCCCAGTGTAGTTGAGATTGTTGAACCTAACACACCTCCTGCTTCACGTGCAAATTCGCGTAGCAGGAGTCGTGGCAATGGCAACAATAGGTCTAGATCTCCAAGTAACAACAGAGGCAATAACCAGTCCCGTGGTAATTCACAGAATCGTGGAAATAACCAGGGTCGTGGAGCTTCTCAGAACAGAGGAGGCAATAATAATAACAATAACAAGTCTCGTAACCAGTCCAATAACAGGAACCAGTCAAATGACCGTGGTGGTGTAACATCACGCGATGATCTGGTGGCTGCTGTCAAGGATGCACTTAAATCTTTGGGTATTGGAGAAAATCCTGACAGGCATAAGCAACAGCAGAAGCCTAAGCAGGAAAAGTCTGACAACAGCGGCAAAAATACACCTAAGAAGAACAAATCCAGGGCCACTTCGAAGGAACGTGACCTCAAAGACATCCCAGAGTGGAGGAGAATTCCCAAGGGCGAAAATAGCGTAGCAGCTTGCTTCGGACCCAGAGGGGGCTTCAAAAACTTTGGAGATGCGGAATTTGTCGAAAAAGGTGTTGATGCGTCAGGCTATGCTCAGATCGCCAGTTTAGCACCAAATGTTGCAGCATTGCTCTTTGGTGGTAATGTGGCTGTTCGTGAGCTAGCGGACTCTTACGAGATTACATACAACTATAAAATGACTGTGCCAAAGTCAGATCCAAATGTTGAGCTTCTTGTTTCACAGGTGGATGCATTTAAAACTGGGAATGCAAAACTCCAGAGAAAGAAGGAAAAGAAGAACAAGCGTGAAACCACGCTGCAGCAGCATGAAGAGGCCATCTACGATGATGTGGGTGCGCCATCTGATGTGACCCATGCCAATCTGGAATGGGACACAGCTGTTGATGGTGGTGATACGGCCGTTGAAATTATCAACGAGATCTTCGATACAGGAAATTAA

Protein

MASVSFQDRGRKRVPLSLYAPLRVTNDKPLSKVLANNAVPTNKGNKDQQIGYWNEQIRWRMRRGERIEQPSNWHFYYLGTGPHGDLRYRTRTEGVFWVAKEGAKTEPTNLGVRKASEKPIIPKFSQQLPSVVEIVEPNTPPASRANSRSRSRGNGNNRSRSPSNNRGNNQSRGNSQNRGNNQGRGASQNRGGNNNNNNKSRNQSNNRNQSNDRGGVTSRDDLVAAVKDALKSLGIGENPDRHKQQQKPKQEKSDNSGKNTPKKNKSRATSKERDLKDIPEWRRIPKGENSVAACFGPRGGFKNFGDAEFVEKGVDASGYAQIASLAPNVAALLFGGNVAVRELADSYEITYNYKMTVPKSDPNVELLVSQVDAFKTGNAKLQRKKEKKNKRETTLQQHEEAIYDDVGAPSDVTHANLEWDTAVDGGDTAVEIINEIFDTGN

Function

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.

Subunit

Homooligomer. Both monomeric and oligomeric forms interact with RNA. Interacts with protein M. Interacts with NSP3; this interaction serves to tether the genome to the newly translated replicase-transcriptase complex at a very early stage of infection.

Uniprot

G8GMY2

EMBL

JN173292 JN255979 AET71266.1 AEW46029.1

Pfam

PF00937 Corona_nucleoca

Interpro

IPR042548   ALPHA_CORONA_NCAP
IPR037195   Nucleocapsid_N
IPR001218   Corona_nucleocap
IPR037179   Nucleocapsid_C

SUPFAM

SSF103068 SSF103068
SSF110304 SSF110304

ProteinModelPortal

G8GMY2

PDB

5N4K E-value=6.04631e-36, Score=379

Ontologies

GO

GO:0019013  C:viral nucleocapsid
GO:0044172  C:host cell endoplasmic reticulum-Golgi intermediate compartment
GO:0003723  F:RNA binding
GO:0044177  C:host cell Golgi apparatus

Subcellular Location

From MSLVP

Capsid

From Uniprot

Host Golgi apparatus
Host endoplasmic reticulum-Golgi intermediate compartment
Virion

Topology

Length:

441

Number of predicted TMHs:

0

Exp number of AAs in TMHs:

0.13531

Exp number, first 60 AAs:

0

Total prob of N-in:

0.00423

outside

1 - 441

Population Genetic Test Statistics

Pi

0.1848946

Theta

0.4022826

Tajima's D

-1.9884

CLR

10.960013

Interpretation

No evidence of Selection

Genomic alignment in the CDS region

Multiple alignment of Orthologues

Gene Tree

Orthologous in Strains

Strain	Status	Gene
CHINA_HS_2019_MN908947
CHINA_AVIAN_2008_NC_016995
CHINA_AVIAN_2007_NC_016991
CHINA_MURINE_2015_NC_035191
CANADA_AVIAN_2007_NC_010800
USA_PIG_2000_NC_038861
CHINA_AVIAN_2007_NC_011549
ITALY_PIG_2009_NC_028806
GERMANY_PIG_2012_LT545990
CHINA_AVIAN_2007_NC_016992
CHINA_BAT_2005_NC_009657
CANADA_HS_2003_NC_004718
CHINA_BAT_2014_NC_030886
CHINA_BAT_2005_NC_018871
USA_MURINE_2009_NC_012936
CHINA_RABBIT_2006_NC_017083
UK_PIG_2000_NC_003436	Protein	NP_598314.1
ROMANIA_PIG_2015_LT898435	Protein	SNQ28049.1
ROMANIA_PIG_2015_LT898436	Protein	SNQ28020.1
GERMANY_PIG_2015_LT898444	Protein	SNQ28080.1
GERMANY_PIG_2015_LT898414	Protein	SNQ27916.1
GERMANY_PIG_2015_LT898439	Protein	SNQ28042.1
GERMANY_PIG_2015_LT898413	Protein	SNQ27903.1
GERMANY_PIG_2015_LT898412	Protein	SNQ27959.1
GERMANY_PIG_2015_LT898411	Protein	SNQ27921.1
GERMANY_PIG_2015_LT898416	Protein	SNQ27928.1
GERMANY_PIG_2015_LT898443	Protein	SNQ28061.1
GERMANY_PIG_2015_LT898420	Protein	SNQ27953.1
GERMANY_PIG_2015_LT898408	Protein	SNQ27891.1
GERMANY_PIG_2015_LT898423	Protein	SNQ27939.1
GERMANY_PIG_2015_LT898432	Protein	SNQ27971.1
GERMANY_PIG_2015_LT898409	Protein	SNQ27945.1
GERMANY_PIG_2015_LT898425	Protein	SNQ27979.1
GERMANY_PIG_2015_LT898446	Protein	SNQ28068.1
GERMANY_PIG_2014_LT898438	Protein	SNQ28026.1
GERMANY_PIG_2014_LT898440	Protein	SNQ28036.1
GERMANY_PIG_2014_LT900501	Protein	SNT95681.1
GERMANY_PIG_2014_LT898427	Protein	SNQ27989.1
GERMANY_PIG_2014_LT898415	Protein	SNQ27897.1
GERMANY_PIG_2014_LT898421	Protein	SNQ27912.1
GERMANY_PIG_2014_LT898431	Protein	SNQ27983.1
GERMANY_PIG_2014_LT898410	Protein	SNQ27965.1
GERMANY_PIG_2014_LT900498	Protein	SNT95657.1
GERMANY_PIG_2014_LT898430	Protein	SNQ27995.1
GERMANY_PIG_1978_LT897799	Protein	SNC44849.1
GERMANY_PIG_2014_LT898447	Protein	SNQ28092.1
GERMANY_PIG_2014_LT898426	Protein	SNQ28015.1
GERMANY_PIG_2014_LT898417	Protein	SNQ28086.1
GERMANY_PIG_2014_LT900500	Protein	SNT95669.1
GERMANY_PIG_2014_LT898445	Protein	SNQ28074.1
AUSTRIA_PIG_2015_LT898418	Protein	SNQ27938.1
AUSTRIA_PIG_2015_LT898441	Protein	SNQ28055.1
AUSTRIA_PIG_2015_LT898433	Protein	SNQ28001.1
AUSTRIA_PIG_2015_LT900502	Protein	SNT95675.1
GERMANY_PIG_2015_LT900499	Protein	SNT95663.1
BELGIUM_PIG_1980_LT906620	Protein	SNX30668.1
BELGIUM_PIG_1977_LT905450	Protein	SNU46340.1
SWITZERLAND_PIG_2003_LT905451	Protein	SNU46346.1
BELGIUM_PIG_1978_LT906581	Protein	SNW64194.1
UK_PIG_1987_LT906582	Protein	SNW64188.1
CHINA_PIG_2009_NC_016990
CHINA_PIG_2010_NC_039208
KENYA_BAT_2010_KY073745
KENYA_BAT_2010_NC_032107
CHINA_AVIAN_2007_NC_016994
EUROPE_MURINE_2004_AY700211
CHINA_AVIAN_2007_NC_011550
USA_MURINE_1997_NC_001846
USA_MURINE_1998_NC_023760
MID_EAST_HS_2012_NC_019843
CHINA_AVIAN_2007_NC_016993
CHINA_MURINE_2013_NC_032730
USA_HS_2004_AY585228
NETHERLAND_HS_2004_NC_005831
CHINA_HS_2004_NC_006577
EUROPE_HS_2000_NC_002645
NETHERLAND_FERRET_2010_NC_030292
JAPAN_FERRET_2013_LC119077
USA_FELINE_2005_NC_002306
CHINA_MURINE_2011_NC_034972
CHINA_AVIAN_2007_NC_016996
ARABIA_CAMEL_2015_NC_028752
CHINA_AVIAN_2007_NC_011547
CHINA_BAT_2012_NC_028824
CHINA_BAT_2013_NC_028814
CHINA_BAT_2013_NC_028833
CHINA_BAT_2011_NC_028811
USA_BOVIN_2001_NC_003045
CHINA_MURINE_2012_NC_026011
GERMANY_ERINACEINAE_2012_NC_022643
GERMANY_ERINACEINAE_2012_NC_039207
UK_HS_2012_NC_038294
AMERICA_WHALE_2007_NC_010646
CHINA_BAT_2013_NC_025217
UGANDA_BAT_2013_NC_034440
CHINA_BAT_2006_NC_009021
CHINA_BAT_2008_NC_010438
CHINA_BAT_2006_NC_009020
CHINA_BAT_2006_NC_009019
CHINA_BAT_2006_NC_009988
USA_BAT_2006_NC_022103
BULGARIA_BAT_2008_NC_014470
CHINA_BAT_2008_NC_010437
USA_AVIAN_2004_NC_001451

Sequence

Summary