Schema for Precurs. Proteins - UniProt Precursor Proteins (before cleavage into protein products) |
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Database: wuhCor1 Primary Table: unipCov2FullSeq Data last updated: 2021-03-22
Big Bed File Download: /gbdb/wuhCor1/uniprot/unipFullSeqCoV2.bb
Item Count: 16
The data is stored in the binary BigBed format.
Format description: Browser extensible data (12 fields), eight fields for bigGenePred support, plus extra fields (dbName-pmids, not used by all UniProt subtracks) with UniProt-specific information
| field | example | description |
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| chrom | NC_045512v2 | Chromosome (or contig, scaffold, etc.) | | chromStart | 265 | Start position in chromosome | | chromEnd | 21552 | End position in chromosome | | name | P0DTD1-1 | Name of item | | score | 1000 | Score from 0-1000 | | strand | + | + or - | | 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 | Used as itemRgb as of 2004-11-22 | | blockCount | 2 | Number of blocks | | blockSizes | 13200,8085 | Comma separated list of block sizes | | chromStarts | 0,13202 | Start positions relative to chromStart | | name2 | | Alternative/human readable name | | cdsStartStat | cmpl | Status of CDS start annotation (none, unknown, incomplete, or complete) | | cdsEndStat | cmpl | Status of CDS end annotation (none, unknown, incomplete, or complete) | | exonFrames | 0,0 | Exon frame {0,1,2}, or -1 if no frame for exon | | type | swissprot | Transcript type | | geneName | | Primary identifier for gene | | geneName2 | | Alternative/human-readable gene name | | geneType | | Gene type | | 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 | | geneNameDupl | rep | UniProt gene name | | geneSynonyms | ORF1a-1b | UniProt 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 binds to the host 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome (PubMed:32680882,PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:32680882,PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:32680882,PubMed:32979938). 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 less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316). 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 (By similarity). Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes (By similarity). Binds to host TBK1 without affecting TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).
- 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 (By similarity). Binds to host TBK1 and inhibits TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).
- 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 | | hgncSym | | HGNC Gene Symbol | | hgncId | | HGNC ID | | refSeq | NC_045512.2 | RefSeq IDs | | refSeqProt | YP_009724389.1 | RefSeq Protein IDs | | entrezGene | 43740578 | NCBI Entrez Gene | | ensGene | | Ensembl Gene IDs | | ensTrans | | Ensembl Transcript IDs | | ensProt | | Ensembl Protein IDs |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | name2 | cdsStartStat | cdsEndStat | exonFrames | type | geneName | geneName2 | geneType | acc | uniprotName | status | accList | isoIds | protFullNames | protShortNames | protAltFullNames | protAltShortNames | geneNameDupl | geneSynonyms | functionText | hgncSym | hgncId | refSeq | refSeqProt | entrezGene | ensGene | ensTrans | ensProt |
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| NC_045512v2 | 265 | 21552 | P0DTD1-1 | 1000 | + | 265 | 21552 | 12,12,120 | 2 | 13200,8085 | 0,13202 | | cmpl | cmpl | 0,0 | swissprot | | | | 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 | | cmpl | cmpl | 0 | swissprot | | | | 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 | | cmpl | cmpl | 0 | swissprot | | | | P0DTC3 | AP3A_SARS2 | Manually reviewed (Swiss-Prot) | P0DTC3 | | ORF3a protein | ORF3a | Accessory protein 3a; Protein 3a; Protein U274; Protein X1 | | | ORF3a | Plays a role in virus egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion chan ... | | | NC_045512.2 | YP_009724391.1 | 43740569 | | | |
| NC_045512v2 | 25456 | 25579 | P0DTG1 | 1000 | + | 25456 | 25579 | 12,12,120 | 1 | 123 | 0 | | cmpl | cmpl | 0 | swissprot | | | | P0DTG1 | ORF3C_SARS2 | Manually reviewed (Swiss-Prot) | P0DTG1 | | ORF3c protein | ORF3c | ORF3h protein | ORF3h | | | May play a role in host modulation. | | | | | | | | |
| NC_045512v2 | 25523 | 25694 | P0DTG0 | 1000 | + | 25523 | 25694 | 12,12,120 | 1 | 171 | 0 | | cmpl | cmpl | 0 | swissprot | | | | P0DTG0 | ORF3D_SARS2 | Manually reviewed (Swiss-Prot) | P0DTG0 | | ORF3d protein | ORF3d protein | | | | | May play a role in host modulation. | | | | | | | | |
| NC_045512v2 | 26244 | 26469 | P0DTC4 | 1000 | + | 26244 | 26469 | 12,12,120 | 1 | 225 | 0 | | cmpl | cmpl | 0 | swissprot | | | | 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 | | cmpl | cmpl | 0 | swissprot | | | | 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 | | cmpl | cmpl | 0 | swissprot | | | | 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 | | cmpl | cmpl | 0 | swissprot | | | | 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 | | cmpl | cmpl | 0 | swissprot | | | | P0DTD8 | NS7B_SARS2 | Manually reviewed (Swiss-Prot) | P0DTD8 | | ORF7b protein | ORF7b | Accessory protein 7b | | | ORF7b | | | | NC_045512.2 | YP_009725318.1 | 43740574 | | | |
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Precurs. Proteins (unipCov2FullSeq) Track Description
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Description
This track shows protein sequence annotations from the UniProt/SwissProt database,
mapped to genomic coordinates.
The data has been curated from scientific publications by the UniProt/SwissProt staff.
The annotations are spread over multiple tracks, based on their "feature type" in UniProt:
| Track Name |
Description |
| UCSC Alignment, SwissProt |
Protein sequences from SwissProt mapped onto the genome. All other
tracks are (start,end) annotations mapped using this track. |
| UCSC Alignment, TrEMBL |
Protein sequences from TrEMBL mapped onto the genome. All other tracks
are (start,end) annotations mapped using this track. This track is
hidden by default. To show it, click its checkbox on the track description
page. |
| UniProt Signal Peptides |
Regions found in proteins destined to be secreted, generally cleaved from mature protein. |
| UniProt Extracellular Domains |
Protein domains with the comment "Extracellular". |
| UniProt Transmembrane Domains |
Protein domains of the type "Transmembrane". |
| UniProt Cytoplasmic Domains |
Protein domains with the comment "Cytoplasmic". |
| UniProt Polypeptide Chains |
Polypeptide chain in mature protein after post-processing. |
| UniProt Domains |
Protein domains, zinc finger regions and topological domains. |
| UniProt Disulfide Bonds |
Disulfide bonds. |
| UniProt Amino Acid Modifications |
Glycosylation sites, modified residues and lipid moiety-binding regions. |
| UniProt Amino Acid Mutations |
Mutagenesis sites and sequence variants. |
| UniProt Protein Primary/Secondary Structure Annotations |
Beta strands, helices, coiled-coil regions and turns. |
| UniProt Sequence Conflicts |
Differences between Genbank sequences and the UniProt sequence. |
| UniProt Repeats |
Regions of repeated sequence motifs or repeated domains. |
| UniProt Other Annotations |
All other annotations |
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. TrEMBL annotations are always shown in
light blue, except in the Signal Peptides,
Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.
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.
The subtracks for domains related to subcellular location are sorted from outside to inside of
the cell: Signal peptide,
extracellular,
transmembrane, and cytoplasmic.
In the "UniProt Modifications" track, lipoification sites are highlighted in
dark blue, glycosylation sites in
dark green, and phosphorylation in
light green.
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. 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/unipStructCov2.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 Phil Berman, UCSC.
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
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