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
|chrom||NC_045512v2||Reference sequence chromosome or scaffold|
|chromStart||265||Start position in chromosome|
|chromEnd||21552||End position in chromosome|
|name||P0DTD1-1||Name or ID of item, ideally both human readable and unique|
|strand||+||+ or - indicates whether the query aligns to the + or - strand on the reference|
|thickStart||265||Start of where display should be thick (start codon)|
|thickEnd||21552||End of where display should be thick (stop codon)|
|reserved||12,12,120||RGB value (use R,G,B string in input file)|
|blockCount||2||Number of blocks|
|blockSizes||13200,8085||Comma separated list of block sizes|
|chromStarts||0,13202||Start positions relative to chromStart|
|oChromStart||0||Start position in other chromosome|
|oChromEnd||21288||End position in other chromosome|
|oStrand||+||+ or -, - means that psl was reversed into BED-compatible coordinates|
|oChromSize||21288||Size of other chromosome.|
|oChromStarts||0,13203,||Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand|
|oSequence||Sequence on other chrom (or edit list, or empty)|
|oCDS||CDS in NCBI format|
|chromSize||29903||Size of target chromosome|
|match||7095||Number of bases matched.|
|misMatch||0|| Number of bases that don't match |
|repMatch||0|| Number of bases that match but are part of repeats |
|nCount||0|| Number of 'N' bases |
|seqType||0||0=empty, 1=nucleotide, 2=amino_acid|
|acc||P0DTD1||UniProt main accession|
|uniprotName||R1AB_SARS2||UniProt main record name|
|status||Manually reviewed (Swiss-Prot)||UniProt status|
|accList||P0DTD1||UniProt all accessions|
|isoIds||UniProt isoform accessions|
|protFullNames||Replicase polyprotein 1ab||UniProt protein name|
|protShortNames||pp1ab||UniProt protein short name|
|protAltFullNames||ORF1ab polyprotein||UniProt alternative names|
|protAltShortNames||UniProt alternative short names|
|geneName||rep||UniProt gene name|
|geneSynonyms||ORF1a-1b||UniProt gene synonyms|
- 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.
|hgncSym||HGNC Gene Symbol|
|refSeqProt||YP_009724389.1||RefSeq Protein IDs|
|entrezGene||43740578||NCBI Entrez Gene|
|ensGene||Ensembl Gene IDs|
|ensTrans||Ensembl Transcript IDs|
|ensProt||Ensembl Protein IDs|
|NC_045512v2||265||21552||P0DTD1-1||1000||+||265||21552||12,12,120||2||13200,8085||0,13202||0||21288||+||21288||0,13203,||29903||7095||0||0||0||0||P0DTD1||R1AB_SARS2||Manually reviewed (Swiss-Prot)||P0DTD1||Replicase polyprotein 1ab||pp1ab||ORF1ab polyprotein||rep||ORF1a-1b||Molecule 'Replicase polyprotein 1ab': Multifunctional protein involved in the transcription and replication of viral RNA ...||NC_045512.2||YP_009724389.1||43740578|
|NC_045512v2||21562||25381||P0DTC2||1000||+||21562||25381||12,12,120||1||3819||0||0||3819||+||3819||0,||29903||1273||0||0||0||0||P0DTC2||SPIKE_SARS2||Manually reviewed (Swiss-Prot)||P0DTC2||Spike glycoprotein||S glycoprotein||E2; Peplomer protein||S||ORF2||Molecule 'Spike protein S1': attaches the virion to the cell membrane by interacting with host receptor, initiating the ...||NC_045512.2||YP_009724390.1||43740568|
|NC_045512v2||25392||26217||P0DTC3||1000||+||25392||26217||12,12,120||1||825||0||0||825||+||825||0,||29903||275||0||0||0||0||P0DTC3||AP3A_SARS2||Manually reviewed (Swiss-Prot)||P0DTC3||ORF3a protein||ORF3a||Accessory protein 3a; Protein 3a; Protein U274; Protein X1||ORF3a||Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. Up-regulates expressio ...||NC_045512.2||YP_009724391.1||43740569|
|NC_045512v2||26244||26469||P0DTC4||1000||+||26244||26469||12,12,120||1||225||0||0||225||+||225||0,||29903||75||0||0||0||0||P0DTC4||VEMP_SARS2||Manually reviewed (Swiss-Prot)||P0DTC4||Envelope small membrane protein||E; sM protein||E||ORF4||Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes formi ...||NC_045512.2||YP_009724392.1||43740570|
|NC_045512v2||26522||27188||P0DTC5||1000||+||26522||27188||12,12,120||1||666||0||0||666||+||666||0,||29903||222||0||0||0||0||P0DTC5||VME1_SARS2||Manually reviewed (Swiss-Prot)||P0DTC5||Membrane protein||M||E1 glycoprotein; Matrix glycoprotein; Membrane glycoprotein||ORFM||Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with ...||NC_045512.2||YP_009724393.1||43740571|
|NC_045512v2||27201||27384||P0DTC6||1000||+||27201||27384||12,12,120||1||183||0||0||183||+||183||0,||29903||61||0||0||0||0||P0DTC6||NS6_SARS2||Manually reviewed (Swiss-Prot)||P0DTC6||ORF6 protein||ORF6||Accessory protein 6; Non-structural protein 6; Protein X3||ns6||ORF6||Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane. ...||NC_045512.2||YP_009724394.1||43740572|
|NC_045512v2||27393||27756||P0DTC7||1000||+||27393||27756||12,12,120||1||363||0||0||363||+||363||0,||29903||121||0||0||0||0||P0DTC7||NS7A_SARS2||Manually reviewed (Swiss-Prot)||P0DTC7||ORF7a protein||ORF7a||Accessory protein 7a; Protein U122; Protein X4||ORF7a||Plays a role as antagonist of host tetherin (BST2), disrupting its antiviral effect. Acts by binding to BST2 thereby int ...||NC_045512.2||YP_009724395.1||43740573|
|NC_045512v2||27755||27884||P0DTD8||1000||+||27755||27884||12,12,120||1||129||0||0||129||+||129||0,||29903||43||0||0||0||0||P0DTD8||NS7B_SARS2||Manually reviewed (Swiss-Prot)||P0DTD8||ORF7b protein||ORF7b||Accessory protein 7b||ORF7b||NC_045512.2||YP_009725318.1||43740574|
|NC_045512v2||27893||28256||P0DTC8||1000||+||27893||28256||12,12,120||1||363||0||0||363||+||363||0,||29903||121||0||0||0||0||P0DTC8||NS8_SARS2||Manually reviewed (Swiss-Prot)||P0DTC8||ORF8 protein||ORF8||Non-structural protein 8||ns8||ORF8||May play a role in host-virus interaction.||NC_045512.2||YP_009724396.1||43740577|
|NC_045512v2||28273||29530||P0DTC9||1000||+||28273||29530||12,12,120||1||1257||0||0||1257||+||1257||0,||29903||419||0||0||0||0||P0DTC9||NCAP_SARS2||Manually reviewed (Swiss-Prot)||P0DTC9||Nucleoprotein||N||Nucleocapsid protein||NC; Protein N||N||Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during ...||NC_045512.2||YP_009724397.2||43740575|
Protein Alignments (unipCov2AliSwissprot) Track 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.
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
The raw data can be explored interactively with the
Table Browser or the
For automated analysis, the genome annotation is stored in a bigBed file that
can be downloaded from the
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
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.
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.
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.