Strain

USA_PIG_2000_NC_038861 (Region: USA:Indiana; Strain: Transmissible gastroenteritis virus complete genome, genomic RNA.; Date: 2000)

Gene

replicase

Description

Annotated in NCBI, replicase

Location

NC_038861(+):315-12368

GenBank Accession

NP_058423.1

Full name

Replicase polyprotein 1a

Alternative Name

ORF1a polyprotein

CDS

ATGAGTTCCAAACAATTCAAGATCCTTGTTAATGAGGACTATCAAGTCAACGTGCCTAGTCTTCCTATTCGTGACGTGTTACAGGAAATTAAGTACTGCTACCGTAATGGATTTGAGGGCTATGTTTTCGTACCAGAATACTGTCGTGACCTAGTTGATTGCGATCGTAAGGATCACTACGTCATTGGTGTTCTTGGTAACGGAGTAAGTGATCTTAAACCTGTTCTTCTTACCGAACCCTCCGTCATGTTGCAAGGCTTTATTGTTAGAGCTAACTGCAATGGCGTTCTTGAGGACTTTGACCTTAAAATTGCTCGCACTGGCAGAGGTGCCATATATGTTGATCAATACATGTGTGGTGCTGATGGAAAACCAGTCATTGAAGGCGATTTTAAGGACTACTTCGGTGATGAAGACATCATTGAATTTGAAGGAGAGGAGTACCATTGCGCTTGGACAACTGTGCGCGATGAGAAACCGCTGAATCAGCAAACTCTCTTTACCATTCAGGAAATCCAATACAATCTGGACATTCCTCATAAATTGCCAAACTGTGCTACTAGACATGTAGCACCACCAGTCAAAAAGAACTCTAAAATAGTTCTGTCTGAAGATTACAAGAAGCTTTATGATATCTTCGGATCACCCTTTATGGGAAATGGTGACTGTCTTAGCAAATGCTTTGACACTCTTCATTTTATCGCTGCTACTCTTAGATGCCCGTGTGGTTCTGAAAGTAGCGGCGTTGGAGATTGGACTGGTTTTAAGACTGCCTGTTGTGGTCTTTCTGGCAAAGTTAAGGGTGTCACTTTGGGTGATATTAAGCCTGGTGATGCTGTTGTCACTAGTATGAGCGCAGGTAAGGGAGTTAAGTTCTTTGCCAATTGTGTTCTTCAATATGCTGGTGATGTTGAAGGTGTCTCCATCTGGAAAGTTATTAAAACTTTTACAGTTGATGAGACTGTATGCACCCCTGGTTTTGAAGGCGAATTGAACGACTTCATCAAACCTGAGAGCAAATCACTAGTTGCATGCAGCGTTAAAAGAGCATTCATTACTGGTGATATTGATGATGCTGTACATGATTGTATCATTACAGGAAAATTGGATCTTAGTACCAACCTTTTTGGTAATGTTGGTCTATTATTCAAGAAGACTCCATGGTTTGTACAAAAGTGTGGTGCACTTTTTGTAGACGCTTGGAAAGTAGTAGAGGAGCTTTGTGGTTCACTCACACTTACATACAAGCAAATTTATGAAGTTGTAGCATCACTTTGCACTTCTGCTTTTACGATTGTAAACTACAAGCCAACATTTGTGGTTCCAGACAATCGTGTTAAAGATCTTGTAGACAAGTGTGTGAAAGTTCTTGTAAAAGCATTTGATGTTTTTACGCAGATTATCACAATAGCTGGTATTGAGGCCAAATGCTTTGTGCTTGGTGCTAAATACCTGTTGTTCAATAATGCACTTGTCAAACTTGTCAGTGTTAAAATCCTTGGCAAGAAGCAAAAGGGTCTTGAATGTGCATTCTTTGCTACTAGCTTGGTTGGTGCAACTGTTAATGTGACACCTAAAAGAACAGAGACTGCCACTATCAGCTTGAACAAGGTTGATGATGTTGTAGCACCAGGAGAGGGTTATATCGTCATTGTTGGTGATATGGCTTTCTACAAGAGTGGTGAATATTATTTCATGATGTCTAGTCCTAATTTTGTTCTTACTAACAATGTTTTTAAAGCAGTTAAAGTTCCATCTTATGACATCGTTTATGATGTTGATAATGATACCAAAAGCAAAATGATTGCAAAACTTGGTTCATCATTTGAATATGATGGTGATATTGATGCTGCTATTGTAAAAGTCAATGAACTACTCATTGAATTTAGGCAGCAAAGCTTGTGCTTCAGAGCTTTTAAGGACGACAAAAGCATTTTTGTTGAAGCCTATTTTAAAAAGTATAAAATGCCAGCATGCCTTGCAAAACATATTGGTTTGTGGAACATCATAAAGAAAGATTCATGTAAGAGGGGTTTTCTTAATCTCTTCAATCACTTGAATGAATTGGAAGATATCAAAGAAACTAATATTCAGGCTATTAAAAACATTCTTTGCCCTGATCCTCTTCTTGATCTGGATTATGGTGCCATTTGGTACAATTGCATGCCAGGTTGCTCTGATCCTTCAGTTTTGGGGAGTGTTCAACTTTTGATCGGTAATGGTGTGAAAGTAGTTTGTGATGGCTGCAAAGGTTTTGCTAACCAACTTTCAAAAGGTTACAACAAGCTCTGTAATGCGGCTCGCAATGATATTGAGATCGGTGGTATACCATTTTCCACTTTTAAAACACCTACAAATACTTTTATTGAAATGACAGATGCTATCTATTCAGTTATTGAACAAGGTAAGGCATTATCCTTTAGAGATGCTGATGTGCCAGTTGTAGACAATGGTACCATTTCTACTGCTGATTGGTCTGAACCCATTCTGCTTGAACCTGCTGAATATGTAAAACCAAAGAACAATGGTAATGTCATTGTTATTGCAGGTTATACATTTTATAAAGATGAGGATGAACATTTTTATCCTTATGGTTTTGGTAAAATTGTGCAGAGAATGTATAATAAAATGGGTGGTGGTGACAAAACTGTCTCATTTTCAGAAGAAGTAGATGTTCAAGAAATTGCACCTGTTACACGTGTTAAACTTGAATTCGAATTTGACAATGAAATTGTAACTGGTGTTCTTGAACGGGCTATTGGTACTAGATACAAATTTACTGGTACAACTTGGGAAGAATTTGAAGAGTCTATTTCTGAAGAACTCGATGCAATCTTTGATACTCTAGCAAACCAAGGTGTCGAACTTGAAGGTTACTTCATTTATGACACTTGTGGTGGCTTTGATATAAAAAATCCAGATGGTATTATGATCTCTCAGTATGATATCAATATTACTGCTGATGAAAAATCAGAAGTTAGTGCATCAAGTGAAGAAGAAGAAGTTGAATCTGTTGAAGAAGATCCTGAGAATGAAATTGTAGAAGCATCTGAAGGTGCTGAAGGGACTTCTTCTCAAGAAGAGGTTGAAACAGTAGAAGTTGCAGATATTACTTCTACAGAAGAAGATGTTGACATTGTTGAAGTATCTGCTAAAGATGACCCTTGGGCTGCAGCTGTTGATGTACAAGAAGCTGAACAATTTAATCCTTCTCTACCACCTTTCAAGACAACGAATCTCAACGGAAAAATTATCCTTAAGCAAGGGGATAATAATTGTTGGATAAATGCTTGTTGCTATCAGCTTCAGGCCTTTGATTTTTTCAACAATGAAGCTTGGGAGAAATTTAAGAAAGGTGATGTCATGGACTTTGTAAACCTTTGTTATGCAGCAACAACACTAGCAAGAGGTCATTCTGGTGATGCAGAGTATCTTCTTGAACTTATGCTCAATGATTATAGCACAGCCAAGATAGTACTTGCAGCTAAGTGTGGTTGTGGTGAAAAAGAAATTGTTTTGGAAAGAGCTGTTTTTAAACTCACCCCACTTAAGGAGAGTTTTAATTATGGTGTTTGTGGTGACTGCATGCAAGTTAACACCTGTAGATTTTTAAGTGTTGAAGGCTCTGGTGTTTTTGTTCATGACATATTAAGCAAGCAAACGCCAGAAGCTATGTTTGTTGTCAAACCTGTTATGCATGCAGTTTACACTGGCACAACTCAAAATGGCCATTACATGGTTGATGATATTGAACACGGTTATTGTGTAGATGGTATGGGTATTAAACCACTTAAGAAACGGTGTTATACATCCACATTGTTCATTAATGCCAATGTAATGACTAGAGCTGAAAAACCAAAACAAGAGTTTAAAGTTGAAAAAGTAGAACAGCAACCGATAGTGGAGGAAAACAAATCCTCTATTGAAAAAGAGGAAATTCAAAGTCCTAAAAACGATGACCTTATACTTCCATTTTACAAAGCTGGTAAACTTTCCTTTTATCAGGGTGCTTTGGATGTTTTGATCAATTTCTTGGAACCTGATGTTATTGTTAATGCTGCTAATGGTGATCTTAAACACATGGGTGGTGTCGCAAGAGCCATCGATGTTTTCACTGGTGGCAAATTAACAGAACGTTCTAAGGATTATCTTAAAAAGAACAAATCTATTGCTCCTGGTAATGCTGTTTTCTTTGAAAATGTCATTGAGCATCTTAGTGTTTTGAATGCAGTTGGACCACGTAATGGTGACAGCCGAGTTGAAGCCAAACTTTGTAATGTTTACAAAGCAATTGCAAAGTGTGAAGGAAAAATATTAACACCACTTATTAGTGTTGGTATCTTTAATGTTAGACTTGAAACATCATTGCAGTGCTTACTTAAGACTGTGAATGACAGGGGATTGAATGTCTTCGTATACACTGACCAGGAGAGGCAAACTATTGAGAATTTCTTCTCTTGTTCTATCCCTGTCAATGTTACTGAGGATAATGTTAACCATGAACGTGTGTCTGTTTCTTTTGACAAAACATACGGTGAACAGCTTAAGGGCACCGTTGTCATCAAAGACAAAGATGTTACAAACCAGTTGCCTAGCGCTTTTGATGTTGGTCAAAAAGTTATTAAGGCTATTGATATAGATTGGCAAGCTCATTATGGTTTCCGTGATGCTGCTGCTTTTAGCGCTAGTAGTCATGATGCTTATAAATTTGAAGTTGTTACACATAGCAATTTCATTGTGCATAAGCAGACTGACAACAACTGTTGGATTAATGCAATTTGTCTTGCATTACAGAGACTCAAGCCACAGTGGAAATTTCCTGGTGTTAGAGGTCTCTGGAATGAATTTCTTGAGCGTAAAACACAAGGTTTTGTACATATGTTGTATCACATTTCTGGAGTAAAGAAAGGTGAGCCAGGTGATGCTGAATTAATGCTGCATAAACTTGGTGACTTGATGGACAATGATTGTGAAATCATTGTCACACACACTACAGCATGTGACAAGTGCGCAAAAGTAGAAAAGTTTGTTGGACCAGTGGTAGCAGCACCTCTTGCAATTCATGGCACTGACGAAACATGTGTGCATGGCGTTAGTGTCAATGTCAAAGTCACCCAAATTAAGGGCACTGTTGCTATTACTTCTTTGATTGGTCCTATTATTGGAGAAGTACTAGAAGCAACTGGTTATATTTGTTATAGCGGTTCTAACAGGAATGGTCATTACACCTATTACGATAACCGTAATGGATTAGTGGTTGATGCAGAAAAGGCTTACCATTTTAATAGAGACTTATTACAGGTCACAACAGCTATTGCAAGTAATTTCGTTGTCAAGAAACCACAAGCAGAGGAAAGACCTAAGAATTGTGCTTTTAACAAAGTTGCAGCATCTCCTAAGATTGTACAAGAACAAAAATTGTTGGCTATTGAAAGTGGTGCTAACTATGCTCTTACTGAATTTGGAAGATATGCTGACATGTTCTTTATGGCTGGAGATAAAATTCTTAGGTTGCTGCTTGAAGTCTTTAAATATTTGCTGGTTTTATTTATGTGTCTTAGAAGTACTAAGATGCCTAAAGTTAAAGTCAAACCACCTCTTGCATTTAAAGATTTTGGTGCTAAGGTCAGAACGCTCAATTACATGAGACAATTGAACAAACCCTCTGTCTGGCGTTACGCAAAACTAGTTTTATTGTTGATAGCAATATATAATTTCTTTTATTTGTTTGTCAGTATACCAGTAGTGCATAAATTAACATGTAACGGTGCTGTACAGGCATATAAAAATTCTAGTTTTATAAAGTCTGCAGTCTGTGGCAACTCTATTTTATGCAAAGCCTGTTTGGCTTCTTATGATGAGTTGGCTGATTTTCAACATCTCCAAGTTACTTGGGATTTCAAATCTGACCCACTATGGAACAGACTGGTACAATTGTCTTACTTTGCATTCTTGGCTGTTTTTGGTAATAACTATGTTAGGTGTTTTCTTATGTATTTTGTATCTCAGTACCTCAACCTTTGGCTTTCTTATTTTGGTTATGTAGAGTACAGTTGGTTTTTGCATGTTGTCAACTTTGAATCCATCTCAGCTGAGTTTGTGATCGTAGTTATAGTGGTTAAGGCAGTTCTCGCCCTTAAACATATTGTTTTCGCATGCTCAAACCCGTCTTGCAAAACGTGCTCTAGGACTGCAAGGCAGACACGTATTCCTATTCAAGTTGTTGTTAATGGTTCAATGAAGACTGTTTATGTTCATGCTAATGGTACTGGTAAATTCTGCAAGAAACACAATTTTTATTGTAAGAACTGTGATTCTTATGGCTTTGAAAACACATTCATCTGTGACGAAATTGTACGTGATCTCAGTAATAGTGTTAAACAAACTGTTTACGCCACTGATAGATCTCATCAAGAAGTCACAAAAGTTGAATGTTCAGATGGCTTTTACAGATTTTATGTTGGTGATGAATTCACTTCATATGACTATGATGTAAAACACAAGAAATACAGTAGTCAAGAGGTTCTCAAGAGCATGCTCTTGCTTGATGACTTCATTGTGTACAGTCCATCTGGTTCTGCTCTTGCAAATGTTAGAAATGCCTGTGTTTACTTTTCACAACTTATTGGTAAGCCTATTAAGATTGTTAACAGTGATTTGCTTGAAGACCTCTCTGTAGATTTTAAAGGGGCACTTTTTAATGCTAAAAAGAATGTAATTAAGAATTCTTTCAATGTTGATGTCTCAGAATGCAAAAATCTTGACGAATGTTACAGGGCTTGCAATCTTAATGTTTCATTTTCTACATTTGAAATGGCTGTCAACAATGCTCATAGGTTTGGTATTCTGATTACTGATCGTTCTTTTAACAATTTCTGGCCATCAAAAGTTAAGCCTGGTTCATCTGGTGTGTCGGCCATGGACATTGGTAAGTGTATGACTTCTGATGCTAAGATTGTTAATGCTAAAGTTTTAACTCAACGTGGTAAAAGTGTTGTTTGGCTTAGCCAGGATTTTGCTGCACTTAGCTCAACTGCTCAGAAAGTTTTGGTTAAAACTTTTGTAGAAGAAGGTGTCAACTTTTCACTCACATTTAATGCTGTAGGTTCAGATGATGATCTTCCTTATGAAAGATTCACTGAATCTGTGTCTCCAAAAAGTGGTTCAGGCTTTTTCGATGTAATTACACAGCTTAAACAAATTGTGATTTTGGTTTTTGTTTTTATCTTTATTTGTGGTTTGTGCTCTGTTTACAGTGTTGCTACACAGTCCTACATTGAATCTGCTGAAGGCTATGACTACATGGTTATTAAGAATGGAATTGTTCAACCTTTTGACGATACCATTTCATGTGTTCATAACACTTATAAAGGATTCGGTGACTGGTTTAAAGCTAAGTATGGTTTTATCCCTACTTTTGGTAAATCATGTCCAATTGTTGTAGGAACTGTTTTTGATCTTGAAAATATGAGACCAATTCCTGACGTGCCTGCATATGTTTCTATTGTGGGTAGATCTCTTGTTTTCGCTATTAATGCTGCTTTTGGTGTTACTAATATGTGCTATGATCATACTGGCAATGCAGTTAGTAAGGACTCTTACTTTGATACTTGTGTGTTTAATACTGCGTGCACCACTCTTACAGGTCTTGGTGGTACAATTGTATATTGTGCAAAGCAAGGTTTAGTTGAAGGTGCTAAGCTCTATAGTGATCTTATGCCAGACTATTATTATGAGCATGCTAGTGGTAACATGGTTAAATTGCCAGCAATTATTAGAGGACTTGGTCTACGTTTTGTGAAAACACAGGCTACAACTTATTGTAGAGTGGGAGAGTGCATTGATAGTAAAGCTGGTTTTTGCTTTGGTGGCGATAACTGGTTTGTCTACGACAATGAGTTTGGCAATGGATACATCTGTGGTAATTCTGTGCTAGGATTCTTTAAGAATGTCTTCAAACTCTTTAACTCTAACATGTCTGTGGTAGCTACATCTGGTGCGATGCTTGTTAACATTATTATTGCATGCTTAGCTATTGCAATGTGTTATGGTGTTCTTAAGTTTAAGAAGATTTTTGGTGATTGTACTTTCCTCATTGTTATGATCATTGTCACCCTTGTTGTGAACAATGTGTCTTATTTTGTCACTCAAAACACGTTCTTTATGATCATCTACGCCATTGTTTACTATTTTATAACAAGAAAACTTGCATACCCAGGCATTCTTGATGCTGGGTTTATTATTGCTTATATTAATATGGCTCCATGGTACGTGATTACCGCATATATCCTAGTTTTCCTCTATGACTCACTCCCTTCACTGTTTAAACTTAAAGTTTCAACAAATCTTTTTGAAGGTGATAAATTTGTGGGTAACTTTGAATCTGCTGCTATGGGTACTTTTGTTATTGACATGCGTTCATATGAAACTATTGTTAATTCTACTTCTATTGCTAGAATTAAATCATATGCTAACAGCTTCAATAAATATAAGTACTACACAGGTTCAATGGGAGAAGCTGACTACAGAATGGCTTGCTATGCTCATCTTGGTAAAGCTCTTATGGACTATTCTGTTAATAGAACAGACATGCTTTACACACCTCCTACTGTTAGTGTTAATTCTACACTTCAGTCAGGTTTGCGGAAAATGGCACAGCCTAGTGGTCTTGTAGAGCCTTGCATTGTAAGAGTTTCCTATGGTAACAATGTGCTTAATGGTTTATGGTTAGGAGATGAAGTCATTTGCCCTAGACATGTTATTGCTAGTGATACCACACGTGTTATCAACTATGAAAATGAAATGTCTAGTGTGAGACTTCACAACTTTTCAGTTTCTAAGAATAATGTGTTTTTGGGTGTTGTGTCTGCCAGATATAAGGGTGTGAATCTTGTACTTAAAGTCAACCAGGTTAATCCTAACACACCAGAACATAAATTTAAGTCTATTAAAGCTGGTGAAAGTTTTAACATTCTTGCTTGTTATGAAGGATGTCCTGGCAGTGTTTATGGTGTCAACATGAGAAGTCAAGGTACCATTAAAGGATCTTTTATAGCTGGTACTTGTGGATCAGTAGGTTATGTGTTAGAAAATGGAATTCTCTATTTTGTATACATGCATCACTTAGAACTTGGAAATGGCTCGCATGTTGGTTCCAATTTTGAAGGAGAAATGTACGGTGGTTATGAAGATCAACCTAGCATGCAATTGGAAGGTACTAATGTCATGTCATCAGATAATGTGGTTGCATTCCTATATGCTGCACTTATCAATGGTGAAAGGTGGTTTGTTACAAACACATCGATGTCATTAGAATCATACAATACATGGGCCAAAACTAACAGTTTCACAGAACTTTCTTCAACTGATGCTTTTAGCATGTTGGCTGCAAAAACTGGTCAAAGTGTTGAGAAATTACTAGATAGCATCGTAAGACTCAACAAGGGTTTTGGAGGTCGTACTATACTTTCTTATGGCTCATTGTGTGACGAGTTCACTCCAACTGAAGTCATAAGGCAAATGTATGGTGTAAATCTTCAGGCTGGTAAAGTAAAATCTTTCTTCTACCCTATTATGACTGCAATGACAATTCTCTTTGCCTTTTGGCTTGAATTCTTTATGTACACACCCTTCACTTGGATTAATCCAACTTTTGTTAGCATTGTATTGGCTGTTACAACTTTGATCTCGACGGTTTTTGTCTCTGGCATCAAACATAAGATGTTGTTCTTTATGTCTTTTGTCCTTCCTAGTGTTATCCTTGTGACAGCACACAATTTGTTCTGGGACTTTTCTTACTATGAAAGTCTTCAGTCAATTGTTGAGAATACTAACACTATGTTTTTGCCTGTTGACATGCAAGGTGTCATGCTCACAGTGTTTTGCTTTATTGTCTTTGTTACATATAGTGTTAGATTCTTCACTTGCAAACAATCATGGTTCTCACTTGCTGTGACAACTATTCTTGTGATCTTTAACATGGTTAAAATCTTTGGAACATCTGATGAACCATGGACTGAAAACCAAATTGCTTTCTGCTTTGTGAACATGCTTACTATGATTGTCAGTCTTACTACAAAGGATTGGATGGTTGTCATTGCATCATACAGAATTGCATATTATATTGTTGTATGTGTAATGCCATCTGCTTTTGTATCTGACTTTGGGTTTATGAAGTGTATTAGCATTGTTTACATGGCGTGCGGTTATTTGTTTTGTTGCTATTATGGCATTCTTTATTGGGTTAACAGATTTACATGCATGACTTGTGGTGTTTATCAATTCACTGTGTCTGCAGCTGAACTTAAATACATGACCGCTAACAACCTTTCTGCACCTAAGAACGCATATGACGCTATGATTCTTAGTGCTAAATTGATTGGTGTTGGAGGTAAGAGAAACATCAAAATTTCAACTGTACAGTCAAAACTTACAGAGATGAAATGTACCAATGTTGTCTTGCTTGGTCTTTTATCTAAAATGCATGTCGAGTCTAACTCAAAAGAGTGGAACTATTGTGTTGGACTACACAATGAGATAAACCTTTGTGACGATCCTGAAATCGTTCTTGAGAAACTGTTAGCTCTTATTGCATTCTTCTTGTCCAAACATAACACTTGTGACCTTAGCGAACTTATTGAATCATACTTTGAGAACACCACCATACTCCAGAGTGTGGCTTCAGCTTATGCTGCATTGCCTAGCTGGATTGCACTTGAAAAAGCTCGCGCTGATCTTGAAGAGGCTAAGAAAAATGATGTTAGCCCTCAAATTTTGAAGCAGCTTACTAAAGCATTTAACATTGCCAAGAGTGATTTTGAGCGCGAAGCATCAGTGCAAAAGAAACTCGACAAAATGGCTGAGCAGGCTGCAGCTAGTATGTATAAAGAAGCACGAGCTGTGGACAGAAAGTCAAAGATTGTTTCTGCTATGCATAGCCTACTTTTTGGTATGCTTAAGAAACTTGATATGTCCAGTGTCAACACTATTATTGACCAGGCTCGTAATGGTGTTCTACCTTTAAGTATCATTCCAGCTGCATCAGCTACAAGACTTGTTGTTATTACACCTAGCCTTGAAGTGTTTTCCAAGATTAGGCAAGAAAACAATGTTCATTATGCTGGTGCTATTTGGACTATTGTTGAAGTTAAAGATGCTAATGGTTCACATGTACATCTTAAGGAAGTCACCGCTGCTAATGAATTAAACCTTACTTGGCCATTGAGCATTACTTGTGAGAGAACCACAAAGCTTCAGAACAATGAAATTATGCCAGGTAAACTTAAAGAAAGAGCTGTCAGAGCGTCAGCAACTCTTGATGGTGAAGCTTTCGGCAGTGGAAAGGCTCTTATGGCATCTGAAAGTGGAAAAAGCTTTATGTATGCATTTATAGCCTCAGACAACAATCTTAAGTATGTTAAGTGGGAGAGCAATAATGATATTATACCTATTGAACTTGAAGCTCCATTGCGTTTCTATGTTGACGGCGCTAATGGTCCTGAAGTCAAGTATTTGTATTTTGTCAAGAATTTAAACACTCTTAGACGTGGTGCCGTTCTTGGTTATATCGGTGCAACAGTTCGTCTGCAAGCTGGTAAACCCACTGAACATCCATCTAACAGTAGTTTATTGACATTGTGTGCTTTTTCACCTGATCCTGCTAAAGCATATGTTGATGCTGTTAAGAGAGGCATGCAACCAGTTAATAACTGTGTAAAAATGCTCTCAAATGGTGCTGGTAATGGTATGGCTGTTACAAACGGTGTCGAAGCTAACACACAACAGGACTCTTATGGTGGTGCTTCAGTTTGTATTTATTGCAGATGCCATGTTGAACATCCTGCTATTGATGGATTATGCCGCTACAAAGGTAAGTTCGTGCAAATACCAACTGGCACACAAGATCCAATTCGGTTCTGTATTGAAAATGAAGTTTGTGTTGTCTGTGGTTGTTGGCTTAACAATGGTTGCATGTGCGATCGTACTTCTATGCAGAGTTTTACTGTTGATCAAAGTTATTTAAACGAGTGCGGGGTTCTAGTGCAGCTCGACTAG

Protein

MSSKQFKILVNEDYQVNVPSLPIRDVLQEIKYCYRNGFEGYVFVPEYCRDLVDCDRKDHYVIGVLGNGVSDLKPVLLTEPSVMLQGFIVRANCNGVLEDFDLKIARTGRGAIYVDQYMCGADGKPVIEGDFKDYFGDEDIIEFEGEEYHCAWTTVRDEKPLNQQTLFTIQEIQYNLDIPHKLPNCATRHVAPPVKKNSKIVLSEDYKKLYDIFGSPFMGNGDCLSKCFDTLHFIAATLRCPCGSESSGVGDWTGFKTACCGLSGKVKGVTLGDIKPGDAVVTSMSAGKGVKFFANCVLQYAGDVEGVSIWKVIKTFTVDETVCTPGFEGELNDFIKPESKSLVACSVKRAFITGDIDDAVHDCIITGKLDLSTNLFGNVGLLFKKTPWFVQKCGALFVDAWKVVEELCGSLTLTYKQIYEVVASLCTSAFTIVNYKPTFVVPDNRVKDLVDKCVKVLVKAFDVFTQIITIAGIEAKCFVLGAKYLLFNNALVKLVSVKILGKKQKGLECAFFATSLVGATVNVTPKRTETATISLNKVDDVVAPGEGYIVIVGDMAFYKSGEYYFMMSSPNFVLTNNVFKAVKVPSYDIVYDVDNDTKSKMIAKLGSSFEYDGDIDAAIVKVNELLIEFRQQSLCFRAFKDDKSIFVEAYFKKYKMPACLAKHIGLWNIIKKDSCKRGFLNLFNHLNELEDIKETNIQAIKNILCPDPLLDLDYGAIWYNCMPGCSDPSVLGSVQLLIGNGVKVVCDGCKGFANQLSKGYNKLCNAARNDIEIGGIPFSTFKTPTNTFIEMTDAIYSVIEQGKALSFRDADVPVVDNGTISTADWSEPILLEPAEYVKPKNNGNVIVIAGYTFYKDEDEHFYPYGFGKIVQRMYNKMGGGDKTVSFSEEVDVQEIAPVTRVKLEFEFDNEIVTGVLERAIGTRYKFTGTTWEEFEESISEELDAIFDTLANQGVELEGYFIYDTCGGFDIKNPDGIMISQYDINITADEKSEVSASSEEEEVESVEEDPENEIVEASEGAEGTSSQEEVETVEVADITSTEEDVDIVEVSAKDDPWAAAVDVQEAEQFNPSLPPFKTTNLNGKIILKQGDNNCWINACCYQLQAFDFFNNEAWEKFKKGDVMDFVNLCYAATTLARGHSGDAEYLLELMLNDYSTAKIVLAAKCGCGEKEIVLERAVFKLTPLKESFNYGVCGDCMQVNTCRFLSVEGSGVFVHDILSKQTPEAMFVVKPVMHAVYTGTTQNGHYMVDDIEHGYCVDGMGIKPLKKRCYTSTLFINANVMTRAEKPKQEFKVEKVEQQPIVEENKSSIEKEEIQSPKNDDLILPFYKAGKLSFYQGALDVLINFLEPDVIVNAANGDLKHMGGVARAIDVFTGGKLTERSKDYLKKNKSIAPGNAVFFENVIEHLSVLNAVGPRNGDSRVEAKLCNVYKAIAKCEGKILTPLISVGIFNVRLETSLQCLLKTVNDRGLNVFVYTDQERQTIENFFSCSIPVNVTEDNVNHERVSVSFDKTYGEQLKGTVVIKDKDVTNQLPSAFDVGQKVIKAIDIDWQAHYGFRDAAAFSASSHDAYKFEVVTHSNFIVHKQTDNNCWINAICLALQRLKPQWKFPGVRGLWNEFLERKTQGFVHMLYHISGVKKGEPGDAELMLHKLGDLMDNDCEIIVTHTTACDKCAKVEKFVGPVVAAPLAIHGTDETCVHGVSVNVKVTQIKGTVAITSLIGPIIGEVLEATGYICYSGSNRNGHYTYYDNRNGLVVDAEKAYHFNRDLLQVTTAIASNFVVKKPQAEERPKNCAFNKVAASPKIVQEQKLLAIESGANYALTEFGRYADMFFMAGDKILRLLLEVFKYLLVLFMCLRSTKMPKVKVKPPLAFKDFGAKVRTLNYMRQLNKPSVWRYAKLVLLLIAIYNFFYLFVSIPVVHKLTCNGAVQAYKNSSFIKSAVCGNSILCKACLASYDELADFQHLQVTWDFKSDPLWNRLVQLSYFAFLAVFGNNYVRCFLMYFVSQYLNLWLSYFGYVEYSWFLHVVNFESISAEFVIVVIVVKAVLALKHIVFACSNPSCKTCSRTARQTRIPIQVVVNGSMKTVYVHANGTGKFCKKHNFYCKNCDSYGFENTFICDEIVRDLSNSVKQTVYATDRSHQEVTKVECSDGFYRFYVGDEFTSYDYDVKHKKYSSQEVLKSMLLLDDFIVYSPSGSALANVRNACVYFSQLIGKPIKIVNSDLLEDLSVDFKGALFNAKKNVIKNSFNVDVSECKNLDECYRACNLNVSFSTFEMAVNNAHRFGILITDRSFNNFWPSKVKPGSSGVSAMDIGKCMTSDAKIVNAKVLTQRGKSVVWLSQDFAALSSTAQKVLVKTFVEEGVNFSLTFNAVGSDDDLPYERFTESVSPKSGSGFFDVITQLKQIVILVFVFIFICGLCSVYSVATQSYIESAEGYDYMVIKNGIVQPFDDTISCVHNTYKGFGDWFKAKYGFIPTFGKSCPIVVGTVFDLENMRPIPDVPAYVSIVGRSLVFAINAAFGVTNMCYDHTGNAVSKDSYFDTCVFNTACTTLTGLGGTIVYCAKQGLVEGAKLYSDLMPDYYYEHASGNMVKLPAIIRGLGLRFVKTQATTYCRVGECIDSKAGFCFGGDNWFVYDNEFGNGYICGNSVLGFFKNVFKLFNSNMSVVATSGAMLVNIIIACLAIAMCYGVLKFKKIFGDCTFLIVMIIVTLVVNNVSYFVTQNTFFMIIYAIVYYFITRKLAYPGILDAGFIIAYINMAPWYVITAYILVFLYDSLPSLFKLKVSTNLFEGDKFVGNFESAAMGTFVIDMRSYETIVNSTSIARIKSYANSFNKYKYYTGSMGEADYRMACYAHLGKALMDYSVNRTDMLYTPPTVSVNSTLQSGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNLQAGKVKSFFYPIMTAMTILFAFWLEFFMYTPFTWINPTFVSIVLAVTTLISTVFVSGIKHKMLFFMSFVLPSVILVTAHNLFWDFSYYESLQSIVENTNTMFLPVDMQGVMLTVFCFIVFVTYSVRFFTCKQSWFSLAVTTILVIFNMVKIFGTSDEPWTENQIAFCFVNMLTMIVSLTTKDWMVVIASYRIAYYIVVCVMPSAFVSDFGFMKCISIVYMACGYLFCCYYGILYWVNRFTCMTCGVYQFTVSAAELKYMTANNLSAPKNAYDAMILSAKLIGVGGKRNIKISTVQSKLTEMKCTNVVLLGLLSKMHVESNSKEWNYCVGLHNEINLCDDPEIVLEKLLALIAFFLSKHNTCDLSELIESYFENTTILQSVASAYAALPSWIALEKARADLEEAKKNDVSPQILKQLTKAFNIAKSDFEREASVQKKLDKMAEQAAASMYKEARAVDRKSKIVSAMHSLLFGMLKKLDMSSVNTIIDQARNGVLPLSIIPAASATRLVVITPSLEVFSKIRQENNVHYAGAIWTIVEVKDANGSHVHLKEVTAANELNLTWPLSITCERTTKLQNNEIMPGKLKERAVRASATLDGEAFGSGKALMASESGKSFMYAFIASDNNLKYVKWESNNDIIPIELEAPLRFYVDGANGPEVKYLYFVKNLNTLRRGAVLGYIGATVRLQAGKPTEHPSNSSLLTLCAFSPDPAKAYVDAVKRGMQPVNNCVKMLSNGAGNGMAVTNGVEANTQQDSYGGASVCIYCRCHVEHPAIDGLCRYKGKFVQIPTGTQDPIRFCIENEVCVVCGCWLNNGCMCDRTSMQSFTVDQSYLNECGVLVQLD

Function

The papain-like proteinase 1 (PLP1) and papain-like proteinase 2 (PLP2) are responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PLP2 possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. PLP2 also antagonizes innate immune induction of type I interferon by blocking the nuclear translocation of host IRF-3 (By similarity).
Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.
Nsp9 is a ssRNA-binding protein.

Catalytic Activity

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Subunit

3CL-PRO exists as monomer and homodimer. Eight copies of nsp7 and eight copies of nsp8 assemble to form a heterohexadecamer. Nsp9 is a dimer. Nsp10 forms a dodecamer (By similarity).

Miscellaneous

Produced by conventional translation.

Similarity

Belongs to the coronaviruses polyprotein 1ab family.

Keywords

3D-structure Activation of host autophagy by virus Host cytoplasm Host membrane Host-virus interaction Hydrolase Inhibition of host innate immune response by virus Inhibition of host IRF3 by virus Inhibition of host RLR pathway by virus Membrane Metal-binding Modulation of host ubiquitin pathway by viral deubiquitinase Modulation of host ubiquitin pathway by virus Protease Reference proteome Repeat Ribosomal frameshifting RNA-binding Thiol protease Transmembrane Transmembrane helix Ubl conjugation pathway Viral immunoevasion Zinc Zinc-finger

Feature

chain Replicase polyprotein 1a

Uniprot

P0C6V2

Pubmed

7856095 10805807 11842254 12093723 12746549

EMBL

Z34093 AJ271965

Proteomes

UP000001440

Pfam

PF08715   Viral_protease
PF16348   Corona_NSP4_C
PF09401   NSP10
PF08710   nsp9
PF08717   nsp8
PF16688   CNV-Replicase_N
PF08716   nsp7
PF01661   Macro
PF05409   Peptidase_C30

Interpro

IPR038634   A-CoV_nsp1_sf
IPR037204   NSP7_sf
IPR009003   Peptidase_S1_PA
IPR013016   Peptidase_C30/C16
IPR038123   NSP4_C_sf
IPR014828   NSP7
IPR036333   NSP10_sf
IPR002589   Macro_dom
IPR008740   Peptidase_C30
IPR014829   NSP8
IPR014827   Viral_protease
IPR032039   A-CoV_nsp1
IPR036499   NSP9_sf
IPR037230   NSP8_sf
IPR018995   RNA_synth_NSP10_coronavirus
IPR032505   Corona_NSP4_C
IPR014822   NSP9

SUPFAM

SSF140367   SSF140367
SSF143076   SSF143076
SSF101816   SSF101816
SSF50494   SSF50494
SSF144246   SSF144246

Gene 3D

1.10.150.420 1.10.8.370 2.30.30.1000 2.40.10.250 2.40.10.290

ProteinModelPortal

P0C6V2

PDB

4F49 E-value=0, Score=1641

Ontologies

GO

GO:0019082  P:viral protein processing
GO:0039548  P:suppression by virus of host IRF3 activity
GO:0003723  F:RNA binding
GO:0033644  C:host cell membrane
GO:0008242  F:omega peptidase activity
GO:0004197  F:cysteine-type endopeptidase activity
GO:0016021  C:integral component of membrane
GO:0039520  P:induction by virus of host autophagy
GO:0039648  P:modulation by virus of host protein ubiquitination
GO:0008270  F:zinc ion binding
GO:0036459  F:thiol-dependent ubiquitinyl hydrolase activity
GO:0003968  F:RNA-directed 5'-3' RNA polymerase activity
GO:0044220  C:host cell perinuclear region of cytoplasm
GO:0019079  P:viral genome replication

Subcellular Location

From MSLVP

Capsid

From Uniprot

Host membrane
nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity). With evidence from 4 publications.

Topology

Length:

4017

Number of predicted TMHs:

18

Exp number of AAs in TMHs:

443.216139999999

Exp number, first 60 AAs:

0.0002

Total prob of N-in:

0.00033

outside

1 - 1834

TMhelix

1835 - 1853

inside

1854 - 1890

TMhelix

1891 - 1913

outside

1914 - 1975

TMhelix

1976 - 1998

inside

1999 - 2004

TMhelix

2005 - 2024

outside

2025 - 2028

TMhelix

2029 - 2051

inside

2052 - 2400

TMhelix

2401 - 2423

outside

2424 - 2495

TMhelix

2496 - 2518

inside

2519 - 2658

TMhelix

2659 - 2681

outside

2682 - 2690

TMhelix

2691 - 2713

inside

2714 - 2719

TMhelix

2720 - 2742

outside

2743 - 2745

TMhelix

2746 - 2768

inside

2769 - 3185

TMhelix

3186 - 3208

outside

3209 - 3212

TMhelix

3213 - 3235

inside

3236 - 3241

TMhelix

3242 - 3264

outside

3265 - 3283

TMhelix

3284 - 3306

inside

3307 - 3312

TMhelix

3313 - 3332

outside

3333 - 3363

TMhelix

3364 - 3386

inside

3387 - 3392

TMhelix

3393 - 3415

outside

3416 - 4017

Population Genetic Test Statistics

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	Protein	NP_058423.1
CHINA_AVIAN_2007_NC_011549
ITALY_PIG_2009_NC_028806	Protein	YP_009199240.1
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
ROMANIA_PIG_2015_LT898435
ROMANIA_PIG_2015_LT898436
GERMANY_PIG_2015_LT898444
GERMANY_PIG_2015_LT898414
GERMANY_PIG_2015_LT898439
GERMANY_PIG_2015_LT898413
GERMANY_PIG_2015_LT898412
GERMANY_PIG_2015_LT898411
GERMANY_PIG_2015_LT898416
GERMANY_PIG_2015_LT898443
GERMANY_PIG_2015_LT898420
GERMANY_PIG_2015_LT898408
GERMANY_PIG_2015_LT898423
GERMANY_PIG_2015_LT898432
GERMANY_PIG_2015_LT898409
GERMANY_PIG_2015_LT898425
GERMANY_PIG_2015_LT898446
GERMANY_PIG_2014_LT898438
GERMANY_PIG_2014_LT898440
GERMANY_PIG_2014_LT900501
GERMANY_PIG_2014_LT898427
GERMANY_PIG_2014_LT898415
GERMANY_PIG_2014_LT898421
GERMANY_PIG_2014_LT898431
GERMANY_PIG_2014_LT898410
GERMANY_PIG_2014_LT900498
GERMANY_PIG_2014_LT898430
GERMANY_PIG_1978_LT897799
GERMANY_PIG_2014_LT898447
GERMANY_PIG_2014_LT898426
GERMANY_PIG_2014_LT898417
GERMANY_PIG_2014_LT900500
GERMANY_PIG_2014_LT898445
AUSTRIA_PIG_2015_LT898418
AUSTRIA_PIG_2015_LT898441
AUSTRIA_PIG_2015_LT898433
AUSTRIA_PIG_2015_LT900502
GERMANY_PIG_2015_LT900499
BELGIUM_PIG_1980_LT906620
BELGIUM_PIG_1977_LT905450
SWITZERLAND_PIG_2003_LT905451
BELGIUM_PIG_1978_LT906581
UK_PIG_1987_LT906582
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

Ontologies

Subcellular Location

Topology

Population Genetic Test Statistics

Genomic alignment in the CDS region

Multiple alignment of Orthologues

Gene Tree

Orthologous in Strains