Schema for Protein Alignments - UCSC alignment of full-length SwissProt proteins to genome
  Database: wuhCor1    Primary Table: unipCov2AliSwissprot Data last updated: 2020-11-30
Big Bed File: /gbdb/wuhCor1/uniprot/unipAliSwissprotCov2.bb
Item Count: 14
Format description: bigPsl pairwise alignment
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart265Start position in chromosome
chromEnd21552End position in chromosome
nameP0DTD1-1Name or ID of item, ideally both human readable and unique
score1000Score (0-1000)
strand++ or - indicates whether the query aligns to the + or - strand on the reference
thickStart265Start of where display should be thick (start codon)
thickEnd21552End of where display should be thick (stop codon)
reserved12,12,120RGB value (use R,G,B string in input file)
blockCount2Number of blocks
blockSizes13200,8085Comma separated list of block sizes
chromStarts0,13202Start positions relative to chromStart
oChromStart0Start position in other chromosome
oChromEnd21288End position in other chromosome
oStrand++ or -, - means that psl was reversed into BED-compatible coordinates
oChromSize21288Size of other chromosome.
oChromStarts0,13203,Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand
oSequenceSequence on other chrom (or edit list, or empty)
oCDSCDS in NCBI format
chromSize29903Size of target chromosome
match7095Number of bases matched.
misMatch0 Number of bases that don't match
repMatch0 Number of bases that match but are part of repeats
nCount0 Number of 'N' bases
seqType00=empty, 1=nucleotide, 2=amino_acid
accP0DTD1UniProt main accession
uniprotNameR1AB_SARS2UniProt main record name
statusManually reviewed (Swiss-Prot)UniProt status
accListP0DTD1UniProt all accessions
isoIdsUniProt isoform accessions
protFullNamesReplicase polyprotein 1abUniProt protein name
protShortNamespp1abUniProt protein short name
protAltFullNamesORF1ab polyproteinUniProt alternative names
protAltShortNamesUniProt alternative short names
geneNamerepUniProt gene name
geneSynonymsORF1a-1bUniProt gene synonyms
functionText
  • Molecule 'Replicase polyprotein 1ab': Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.
  • Molecule 'Host translation inhibitor nsp1': Inhibits host translation by interacting with the 40S ribosomal subunit (PubMed:32680882). Nsp1 C terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:32680882). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:32680882). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). 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 similarity). By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response (By similarity).
  • Molecule 'Non-structural protein 2': 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.
  • Molecule 'Non-structural protein 3': Responsible for the cleavages located at the N-terminus of the replicase polyprotein. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication (By similarity). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Prevents also host NF-kappa-B signaling (By similarity). In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates (PubMed:32726803). Cleaves preferentially ISG15 from substrates in vitro (PubMed:32726803). Can play a role in host ADP-ribosylation by binding ADP-ribose (PubMed:32578982).
  • Molecule 'Non-structural protein 4': Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.
  • Molecule '3C-like proteinase': Cleaves the C-terminus of replicase polyprotein at 11 sites (PubMed:32321856). Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN] (PubMed:32198291, PubMed:32272481). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (By similarity) (PubMed:32198291, PubMed:32272481).
  • Molecule 'Non-structural protein 6': 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.
  • Molecule 'Non-structural protein 7': Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, PubMed:32438371, PubMed:32526208). 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 (By similarity).
  • Molecule 'Non-structural protein 8': Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, PubMed:32438371, PubMed:32526208). 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 (By similarity).
  • Molecule 'Non-structural protein 9': May participate in viral replication by acting as a ssRNA-binding protein.
  • Molecule 'Non-structural protein 10': 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.
  • Molecule 'RNA-directed RNA polymerase': Responsible for replication and transcription of the viral RNA genome.
  • Molecule 'Helicase': 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.
  • Molecule 'Proofreading exoribonuclease': 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.
  • Molecule 'Uridylate-specific endoribonuclease': Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
  • Molecule '2'-O-methyltransferase': 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.
UniProt function
hgncSymHGNC Gene Symbol
hgncIdHGNC ID
refSeqNC_045512.2RefSeq IDs
refSeqProtYP_009724389.1RefSeq Protein IDs
entrezGene43740578NCBI Entrez Gene
ensGeneEnsembl Gene IDs
ensTransEnsembl Transcript IDs
ensProtEnsembl Protein IDs

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsoChromStartoChromEndoStrandoChromSizeoChromStartsoSequenceoCDSchromSizematchmisMatchrepMatchnCountseqTypeaccuniprotNamestatusaccListisoIdsprotFullNamesprotShortNamesprotAltFullNamesprotAltShortNamesgeneNamegeneSynonymsfunctionTexthgncSymhgncIdrefSeqrefSeqProtentrezGeneensGeneensTransensProt
NC_045512v226521552P0DTD1-11000+2652155212,12,120213200,80850,13202021288+212880,13203,2990370950000P0DTD1R1AB_SARS2Manually reviewed (Swiss-Prot)P0DTD1Replicase polyprotein 1abpp1abORF1ab polyproteinrepORF1a-1bMolecule 'Replicase polyprotein 1ab': Multifunctional protein involved in the transcription and replication of viral RNA ...NC_045512.2YP_009724389.143740578
NC_045512v22156225381P0DTC21000+215622538112,12,12013819003819+38190,2990312730000P0DTC2SPIKE_SARS2Manually reviewed (Swiss-Prot)P0DTC2Spike glycoproteinS glycoproteinE2; Peplomer proteinSORF2Molecule 'Spike protein S1': attaches the virion to the cell membrane by interacting with host receptor, initiating the ...NC_045512.2YP_009724390.143740568
NC_045512v22539226217P0DTC31000+253922621712,12,120182500825+8250,299032750000P0DTC3AP3A_SARS2Manually reviewed (Swiss-Prot)P0DTC3ORF3a proteinORF3aAccessory protein 3a; Protein 3a; Protein U274; Protein X1ORF3aForms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. Up-regulates expressio ...NC_045512.2YP_009724391.143740569
NC_045512v22624426469P0DTC41000+262442646912,12,120122500225+2250,29903750000P0DTC4VEMP_SARS2Manually reviewed (Swiss-Prot)P0DTC4Envelope small membrane proteinE; sM proteinEORF4Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes formi ...NC_045512.2YP_009724392.143740570
NC_045512v22652227188P0DTC51000+265222718812,12,120166600666+6660,299032220000P0DTC5VME1_SARS2Manually reviewed (Swiss-Prot)P0DTC5Membrane proteinME1 glycoprotein; Matrix glycoprotein; Membrane glycoproteinORFMComponent of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with ...NC_045512.2YP_009724393.143740571
NC_045512v22720127384P0DTC61000+272012738412,12,120118300183+1830,29903610000P0DTC6NS6_SARS2Manually reviewed (Swiss-Prot)P0DTC6ORF6 proteinORF6Accessory protein 6; Non-structural protein 6; Protein X3ns6ORF6Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane. ...NC_045512.2YP_009724394.143740572
NC_045512v22739327756P0DTC71000+273932775612,12,120136300363+3630,299031210000P0DTC7NS7A_SARS2Manually reviewed (Swiss-Prot)P0DTC7ORF7a proteinORF7aAccessory protein 7a; Protein U122; Protein X4ORF7aPlays a role as antagonist of host tetherin (BST2), disrupting its antiviral effect. Acts by binding to BST2 thereby int ...NC_045512.2YP_009724395.143740573
NC_045512v22775527884P0DTD81000+277552788412,12,120112900129+1290,29903430000P0DTD8NS7B_SARS2Manually reviewed (Swiss-Prot)P0DTD8ORF7b proteinORF7bAccessory protein 7bORF7bNC_045512.2YP_009725318.143740574
NC_045512v22789328256P0DTC81000+278932825612,12,120136300363+3630,299031210000P0DTC8NS8_SARS2Manually reviewed (Swiss-Prot)P0DTC8ORF8 proteinORF8Non-structural protein 8ns8ORF8May play a role in host-virus interaction.NC_045512.2YP_009724396.143740577
NC_045512v22827329530P0DTC91000+282732953012,12,12011257001257+12570,299034190000P0DTC9NCAP_SARS2Manually reviewed (Swiss-Prot)P0DTC9NucleoproteinNNucleocapsid proteinNC; Protein NNPackages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during ...NC_045512.2YP_009724397.243740575

Protein Alignments (unipCov2AliSwissprot) Track Description
 

Description

This track shows protein sequence annotations from the UniProt/SwissProt database, mapped to genomic coordinates. It shows how the protein sequences in this database map to the genome. This mapping was used to "lift" the UniProt protein annotations to the SARS-CoV-2 genome. The protein annotation themselves have been curated from scientific publications by the UniProt/SwissProt staff.

Display Conventions and Configuration

Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. "glyco", "disulf bond", "Signal peptide" etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details.

Mouse-over a feature to see the full UniProt annotation comment. For variants, the mouse-over will show the full name of the UniProt disease acronym.

Methods

UniProt sequences were aligned to UCSC/Gencode transcript sequences first with BLAT, filtered with pslReps (93% query coverage, within top 1% score), lifted to genome positions with pslMap and filtered again. UniProt annotations were obtained from the UniProt XML file. The annotations were then mapped to the genome through the alignment using the pslMap program. This mapping approach draws heavily on the LS-SNP pipeline by Mark Diekhans. For human and mouse, the alignments were filtered by retaining only proteins annotated with a given transcript in the Genome Browser table kgXref. Like all Genome Browser source code, the main script used to build this track can be found on GitHub.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/uniprot/unipAliSwissprotCov2.bb -chrom=NC_045512v2 -start=0 -end=29903 stdout

Please refer to our mailing list archives for questions or our Data Access FAQ for more information.

Credits

This track was created by Maximilian Haeussler at UCSC, with help from Chris Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff and Alejo Mujica, Regeneron Pharmaceuticals. Thanks to UniProt for making all data available for download.

References

UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278