Schema for Protein Alignments - UCSC alignment of full-length SwissProt proteins to genome
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Database: wuhCor1 Primary Table: unipCov2AliSwissprot Data last updated: 2023-06-21
Big Bed File Download: /gbdb/wuhCor1/uniprot/unipAliSwissprotCov2.bb Item Count: 16 The data is stored in the binary BigBed format.
Format description: bigPsl pairwise alignment
field | example | description |
chrom | NC_045512v2 | Reference sequence chromosome or scaffold | chromStart | 265 | Start position in chromosome | chromEnd | 21552 | End position in chromosome | name | P0DTD1-1 | UniProt isoform seq. ID | score | 1000 | Score (0-1000) | 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 | MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN | 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 | 2 | 0=empty, 1=nucleotide, 2=amino_acid | transList | no transcript: direct BLAT to genome | Mapped to genome through these transcripts | acc | P0DTD1 | UniProt record accession | uniprotName | R1AB_SARS2 | UniProt record name | status | Manually reviewed (Swiss-Prot) | UniProt status | accList | P0DTD1 | UniProt previous and alternative accessions | isoIds | | All UniProt sequence 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 | 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 associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, 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, PubMed:33080218).
- Molecule 'Non-structural protein 2': Enhances mRNA repression of the 4EHP-GYF2 complex in the host, thereby inhibiting the antiviral response and facilitating SARS-CoV-2 replication. Possibly acts in cooperation with nsp1, which induces ribosome stalling on host mRNA, triggering mRNA repression by the host 4EHP-GYF2 complex which is enhanced by nsp2.
- Molecule 'Papain-like protease nsp3': 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 (PubMed:35551511). 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 antiviral protein IFIH1 (MDA5), but not RIGI (PubMed:33727702). Can play a role in host ADP-ribosylation by ADP-ribose (PubMed:32578982). Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511).
- Molecule 'Non-structural protein 4': Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511).
- Molecule '3C-like proteinase nsp5': 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). May cleave human NLRP1 in lung epithelial cells, thereby activating the NLRP1 inflammasome pathway (PubMed:35594856). May cleave human GSDMD, triggering alternative GSDME-mediated epithelial cell death upon activation of the NLRP1 inflammasome, which may enhance the release interleukins 1B, 6, 16 and 18 (PubMed:35594856). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (PubMed:32198291, PubMed:32272481).
- Molecule 'Non-structural protein 6': Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511). LDs are consumed during DMV formation (PubMed:35551511). 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). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP9, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).
- Molecule 'RNA-capping enzyme subunit nsp9': Catalytic subunit of viral RNA capping enzyme which catalyzes the RNA guanylyltransferase reaction for genomic and sub-genomic RNAs (PubMed:35944563). The kinase-like NiRAN domain of NSP12 transfers RNA to the amino terminus of NSP9, forming a covalent RNA-protein intermediate (PubMed:35944563). Subsequently, the NiRAN domain transfers RNA to GDP, forming the core cap structure GpppA-RNA (PubMed:35944563). The NSP14 and NSP16 methyltransferases then add methyl groups to form functional cap structures (PubMed:35944563). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP8, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).
- Molecule 'Non-structural protein 10': Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease (By similarity) and nsp16 2'-O-methyltransferase activities (PubMed:35944563). Therefore plays an essential role in viral mRNAs cap methylation.
- Molecule 'RNA-directed RNA polymerase nsp12': RNA-directed RNA polymerase that catalyzes the transcription of viral genomic and subgenomic RNAs. Acts in complex with nsp7 and nsp8 to transcribe both the minus and positive strands of genomic RNA (PubMed:32277040, PubMed:32358203, PubMed:32438371, PubMed:32526208). Subgenomic RNAs (sgRNAs) are formed by discontinuous transcription: The polymerase has the ability to pause at transcription-regulating sequences (TRS) and jump to the leader TRS, resulting in a major deletion (PubMed:35706445). This creates a series of subgenomic RNAs that are replicated, transcribed and translated (PubMed:35706445). In addition, Nsp12 is a subunit of the viral RNA capping enzyme that catalyzes the RNA guanylyltransferase reaction for genomic and sub-genomic RNAs (PubMed:35944563). The kinase-like NiRAN domain of NSP12 transfers RNA to the amino terminus of NSP9, forming a covalent RNA-protein intermediate (PubMed:35944563). Subsequently, the NiRAN domain transfers RNA to GDP, and forms the core cap structure GpppA-RNA (PubMed:35944563).
- Molecule 'Helicase nsp13': Plays a role in viral RNA synthesis (PubMed:33232691). 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 'Guanine-N7 methyltransferase nsp14': Plays a role in viral RNA synthesis through two distinct activities. The N7-guanine methyltransferase activity plays a role in the formation of the cap structure GpppA-RNA (PubMed:35944563). The proofreading exoribonuclease reduces the sensitivity of the virus to RNA mutagens during replication (By similarity). This activity acts on both ssRNA and dsRNA in a 3'-5' direction (By similarity).
- Molecule 'Uridylate-specific endoribonuclease nsp15': Plays a role in viral transcription/replication and prevents the simultaneous activation of host cell dsRNA sensors, such as MDA5/IFIH1, OAS, and PKR (By similarity). Acts by degrading the 5'-polyuridines generated during replication of the poly(A) region of viral genomic and subgenomic RNAs (PubMed:33504779, PubMed:33564093). Catalyzes a two-step reaction in which a 2'3'-cyclic phosphate (2'3'-cP) is first generated by 2'-O transesterification, which is then hydrolyzed to a 3'-phosphate (3'-P) (PubMed:33504779, PubMed:33564093). If not degraded, poly(U) RNA would hybridize with poly(A) RNA tails and activate host dsRNA sensors (By similarity). May bind genomic dsRNA in association with the replication-transcription complex (RTC), and play a role in nsp12 discontinous transcription (PubMed:34562452, PubMed:35706445).
- Molecule '2'-O-methyltransferase nsp16': Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs (PubMed:35944563). N7-methyl guanosine cap is a prerequisite for binding of nsp16 (PubMed:35944563). Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system (PubMed:35944563). May disrupt host mRNA splicing in nucleus by interacting with pre-mRNA Recognition Domains ofthe U1 and U2 snRNAs (PubMed:33080218).
| UniProt function | hgncSym | | HGNC Gene Symbol | hgncId | | HGNC IDs | refSeq | | RefSeq Transcript IDs | refSeqProt | | RefSeq Protein IDs | entrezGene | | NCBI Gene IDs | ensGene | | Ensembl Gene IDs | ensProt | | Ensembl Protein IDs | ensTrans | | Ensembl Transcript IDs | isMain | primary sequence | Is this sequence the primary isoform? |
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Sample Rows
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chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | oChromStart | oChromEnd | oStrand | oChromSize | oChromStarts | oSequence | oCDS | chromSize | match | misMatch | repMatch | nCount | seqType | transList | acc | uniprotName | status | accList | isoIds | protFullNames | protShortNames | protAltFullNames | protAltShortNames | geneName | geneSynonyms | functionText | hgncSym | hgncId | refSeq | refSeqProt | entrezGene | ensGene | ensProt | ensTrans | isMain |
NC_045512v2 | 265 | 21552 | P0DTD1-1 | 1000 | + | 265 | 21552 | 12,12,120 | 2 | 13200,8085 | 0,13202 | 0 | 21288 | + | 21288 | 0,13203, | MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGN ... | | 29903 | 7095 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | 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 ... | | | | | | | | | primary sequence |
NC_045512v2 | 21562 | 25381 | P0DTC2 | 1000 | + | 21562 | 25381 | 12,12,120 | 1 | 3819 | 0 | 0 | 3819 | + | 3819 | 0, | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVI ... | | 29903 | 1273 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | 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 ... | | | | | | | | | primary sequence |
NC_045512v2 | 25392 | 26217 | P0DTC3 | 1000 | + | 25392 | 26217 | 12,12,120 | 1 | 825 | 0 | 0 | 825 | + | 825 | 0, | MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINFVRIIMRLW ... | | 29903 | 275 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | 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 viral egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion chan ... | | | | | | | | | primary sequence |
NC_045512v2 | 25456 | 25579 | P0DTG1 | 1000 | + | 25456 | 25579 | 12,12,120 | 1 | 123 | 0 | 0 | 123 | + | 123 | 0, | MLLLQILFALLQRYRYKPHSLSDGLLLALHFLLFFRALPKS | | 29903 | 41 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | P0DTG1 | ORF3C_SARS2 | Manually reviewed (Swiss-Prot) | P0DTG1 | | ORF3c protein | ORF3c | ORF3h protein | ORF3h | | | May play a role in host modulation. | | | | | | | | | primary sequence |
NC_045512v2 | 25523 | 25694 | P0DTG0 | 1000 | + | 25523 | 25694 | 12,12,120 | 1 | 171 | 0 | 0 | 171 | + | 171 | 0, | MAYCWRCTSCCFSERFQNHNPQKEMATSTLQGCSLCLQLAVVVCNSLLTPFARCCWP | | 29903 | 57 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | P0DTG0 | ORF3D_SARS2 | Manually reviewed (Swiss-Prot) | P0DTG0 | | Putative ORF3d protein | Putative ORF3d protein | | | | | | | | | | | | | | primary sequence |
NC_045512v2 | 26244 | 26469 | P0DTC4 | 1000 | + | 26244 | 26469 | 12,12,120 | 1 | 225 | 0 | 0 | 225 | + | 225 | 0, | MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV | | 29903 | 75 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | 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 ... | | | | | | | | | primary sequence |
NC_045512v2 | 26522 | 27188 | P0DTC5 | 1000 | + | 26522 | 27188 | 12,12,120 | 1 | 666 | 0 | 0 | 666 | + | 666 | 0, | MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTI ... | | 29903 | 222 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | 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 ... | | | | | | | | | primary sequence |
NC_045512v2 | 27201 | 27384 | P0DTC6 | 1000 | + | 27201 | 27384 | 12,12,120 | 1 | 183 | 0 | 0 | 183 | + | 183 | 0, | MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEID | | 29903 | 61 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | P0DTC6 | NS6_SARS2 | Manually reviewed (Swiss-Prot) | P0DTC6 | | ORF6 protein | ORF6 | Accessory protein 6; Non-structural protein 6; Protein X3 | ns6 | | ORF6 | Disrupts bidirectional nucleocytoplasmic transport by interacting with the host RAE1-NUP98 complex (PubMed:33360543, Pub ... | | | | | | | | | primary sequence |
NC_045512v2 | 27393 | 27756 | P0DTC7 | 1000 | + | 27393 | 27756 | 12,12,120 | 1 | 363 | 0 | 0 | 363 | + | 363 | 0, | MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE | | 29903 | 121 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | 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 (PubMed:33930332). Acts by binding t ... | | | | | | | | | primary sequence |
NC_045512v2 | 27755 | 27884 | P0DTD8 | 1000 | + | 27755 | 27884 | 12,12,120 | 1 | 129 | 0 | 0 | 129 | + | 129 | 0, | MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA | | 29903 | 43 | 0 | 0 | 0 | 2 | no transcript: direct BLAT to genome | P0DTD8 | NS7B_SARS2 | Manually reviewed (Swiss-Prot) | P0DTD8 | | ORF7b protein | ORF7b | Accessory protein 7b | | | ORF7b | | | | | | | | | | primary sequence |
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Protein Alignments (unipCov2AliSwissprot) Track Description
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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
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