Recode v. 2.0 / Database of translational recoding events.
Details for "r200564"
| Accession number | r200564 [export] |
| Locus name | gag-pol |
| Recode1 name | pro_m_vir_srv1 |
| Description | viral or mobile polyprotein |
| Recode status | Validated |
Organism
| Genomic class | Viral Genome (Virus) |
| Organism | Mason-Pfizer monkey virus [details] |
| Acronym | MPMV |
Sequence
| Variant | Simian type D virus 1 |
| GenBank IDs | M11841 |
| Sequence | RNA of 2738 nucleotides [sequence] |
| Organisation | Pseudoknot structure (1) [see structure]
Sequence (1)
Trans/Interaction (1)
|
Recoding event
| Event type | -1 Frameshifting (position: 1,827) |
| Description | approx. 13% frameshifting with reporter gene in S. cerevisiae. This is the CDS part of the sequence. |
| Models | HMM |
ATGGGGCAGG AATTAAGCCA GCACGAACGT TATGTGGAAC AATTAAAACA GGCTTTAAAG ACACGGGGAG
TAAAGGTTAA ATATGCTGAT CTCTTAAAGT TTTTTGATTT TGTAAAGGAT ACTTGTCCTT GGTTTCCGCA
AGAGGGAACC ATAGATATCA AAAGGTGGCG TAGAGTAGGC GATTGTTTCC AAGATTATTA TAATACTTTT
GGCCCTGAGA AAGTCCCAGT AACTGCCTTC TCATACTGGA ATTTAATTAA AGAATTGATA GATAAGAAAG
AAGTTAACCC ACAAGTAATG GCTGCCGTGG CTCAAACTGA AGAAATCTTA AAAACTAGTT CTCATACAGA
GCTTACAACA AAGCCCTCCC AAAATCCAGA CTTGGACCTT ATTTCTCTTG ATAGTGACGA TGAAGGAGCT
AAAGGTTCCT CCCTAAAAGA TAAAAATTTA TCATGTACTA AAAAGCCAAA AAGATTCCCA GTTCTATTAA
CAGCACAAAC TAGTGCGGAC CCTGAGGACC CCAACCCCTC AGAGGTAGAC TGGGACGGAT TAGAGGATGA
GGCAGCAAAA TATCATAATC CCGATTGGCC TCCCTTCCTA ACCCGTCCAC CTCCTTATAA TAAAGCCACT
CCTTCCGCAC CCACTGTAAT GGCGGTTGTT AATCCAAAAG AGGAATTAAA AGAGAAGATT GCTCAATTAG
AGGAACAGAT TAAATTAGAA GAGTTACATC AAGCACTCAT TTCCAAGTTA CAAAAACTAA AAACAGGAAA
TGAAACTGTC ACTAGTCCAG AAACTGCAGG GGGCTTTTCT CGCACACCTC ACTGGCCGGG GCAACATATC
CCTAAAGGAA AATGCTGCGC CAGTCGAGAA AAGGAAGAAC AAACCCCAAA AGATATTTTC CCAGTAACTG
AAACTGTCGA TGGGCAGGGT CAAGCCTGGA GGCACCATAA TGGTTTTGAT TTTACCGTCA TAAAAGAATT
AAAAACGGCT GCCTCTCAAT ATGGGGCTAC TGCCCCATAC ACATTAGCCA TAGTAGAATC TGTAGCGGAC
AATTGGCTTA CCCCTACAGA TTGGAATACA CTTGTTAGGG CAGTCCTCTC AGGAGGAGAT CATTTACTAT
GGAAATCTGA GTTTTTTGAA AATTGTAGAG AAACGGCTAA AAGAAATCAA CAAGCCGGTA ATGGTTGGGA
TTTTGATATG TTAACAGGCT CAGGTAACTA TTCTAGCACT GATGCACAAA TGCAATATGA TCCGGGATTG
TTTGCTCAAA TTCAAGCGGC TGCTACAAAA GCCTGGAGAA AACTTCCCGT TAAGGGAGAC CCAGGAGCTT
CCCTTACAGG AGTCAAACAA GGACCCGATG AGCCATTTGC AGATTTTGTA CACAGACTTA TAACAACTGC
TGGGAGAATT TTTGGAAGTG CTGAGGCTGG TGTAGACTAT GTAAAACAAC TAGCATATGA AAACGCTAAT
CCAGCCTGTC AGGCAGCCAT CCGCCCCTAT AGAAAGAAAA CAGATTTAAC TGGCTACATC CGCCTTTGTT
CGGACATTGG GCCTTCTTAT CAACAGGGCT TAGCCATGGC CGCCGCCTTT AGCGGACAAA CTGTCAAAGA
TTTTCTTAAC AACAAAAATA AAGAAAAAGG AGGGTGTTGT TTTAAATGCG GGAGGAAAGG ACATTTTGCA
AAAAATTGTC ATGAACATAT ACATAACAAT TCTGAAACAA AGGCTCCTGG ACTCTGTCCC AGGTGTAAAA
GAGGGAAACA TTGGGCCAAT GAATGCAAAT CCAAAACTGA TAGTCAAGGA AACCCACTAC CACCCCATCA
GGGAAACGGA CTGAGGGGCC AGGCCCAGGC CCCGAAACAA GCTTATGGGG CGGTCAGCTT TGTTCCAGCC
AACAAAAACA ACCCATTTCA AAGCTTACCA GAGCCACCCC AGGAAGTGCA GGATTGGACC TCAGTTCCAC
CTCCCACACA GTATTAACAC CGGAAATGGG GCCCCAAGCG TTAAGCACTG GAATATATGG GCCCCTACCT
CCCAACACTT TTGGATTAAT CTTAGGCAGA AGTAGCATTA CTATAAAAGG TCTACAAGTT TATCCAGGAG
TAATTGATAA TGACTATACT GGGGAAATTA AAATAATGGC AAAGGCTGTC AACAATATTG TTACTGTTCC
TCAAGGCAAC AGGATAGCTC AATTAATCCT CCTACCTCTA ATTGAGACAG ACAATAAAGT ACAACAACCC
TATAGAGGAC AAGGAAGTTT TGGATCCTCA GACATATATT GGGTCCAACC TATTACCTGT CAGAAGCCCT
CCTTAACATT ATGGTTAGAT GATAAAATGT TCACAGGATT AATCGATACG GGAGCTGATG TCACTATCAT
CAAGCTAGAG GACTGGCCTC CTAATTGGCC TATAACAGAT ACCTTAACCA ATTTAAGAGG TATAGGACAA
AGCAACAACC CTAAGCAAAG TTCTAAATAT CTTACTTGGA GAGATAAAGA AAATAATTCT GGTCTCATTA
AACCGTTTGT TATTCCTAAT TTACCTGTCA ACCTTTGGGG CAGAGATCTC CTTTCTCAAA TGAAAATTAT
GATGTGTAGT CCTAGTGACA TAGTCACTGC CCAAATGTTA GCCCAAGGCT ACAGCCCCGG AAAAGGATTA
GGAAAAAACG AAAATGGCAT TCTACATCCT ATCCCAAATC AAGGACAATT TGACAAAAAG GGATTTGGAA
ATTTTTAA
Products
| Product | gag |
| Description | gag polyprotein |
MGQELSQHER YVEQLKQALK TRGVKVKYAD LLKFFDFVKD TCPWFPQEGT IDIKRWRRVG DCFQDYYNTF
GPEKVPVTAF SYWNLIKELI DKKEVNPQVM AAVAQTEEIL KTSSHTELTT KPSQNPDLDL ISLDSDDEGA
KGSSLKDKNL SCTKKPKRFP VLLTAQTSAD PEDPNPSEVD WDGLEDEAAK YHNPDWPPFL TRPPPYNKAT
PSAPTVMAVV NPKEELKEKI AQLEEQIKLE ELHQALISKL QKLKTGNETV TSPETAGGFS RTPHWPGQHI
PKGKCCASRE KEEQTPKDIF PVTETVDGQG QAWRHHNGFD FTVIKELKTA ASQYGATAPY TLAIVESVAD
NWLTPTDWNT LVRAVLSGGD HLLWKSEFFE NCRETAKRNQ QAGNGWDFDM LTGSGNYSST DAQMQYDPGL
FAQIQAAATK AWRKLPVKGD PGASLTGVKQ GPDEPFADFV HRLITTAGRI FGSAEAGVDY VKQLAYENAN
PACQAAIRPY RKKTDLTGYI RLCSDIGPSY QQGLAMAAAF SGQTVKDFLN NKNKEKGGCC FKCGRKGHFA
KNCHEHIHNN SETKAPGLCP RCKRGKHWAN ECKSKTDSQG NPLPPHQGNG LRGQAQAPKQ AYGAVSFVPA
NKNNPFQSLP EPPQEVQDWT SVPPPTQY
| Product | gag-pol |
| Description | gag capsid polyprotein, protease. |
| Modifications | 1827..1827:ribosomal_frameshift |
MGQELSQHER YVEQLKQALK TRGVKVKYAD LLKFFDFVKD TCPWFPQEGT IDIKRWRRVG DCFQDYYNTF
GPEKVPVTAF SYWNLIKELI DKKEVNPQVM AAVAQTEEIL KTSSHTELTT KPSQNPDLDL ISLDSDDEGA
KGSSLKDKNL SCTKKPKRFP VLLTAQTSAD PEDPNPSEVD WDGLEDEAAK YHNPDWPPFL TRPPPYNKAT
PSAPTVMAVV NPKEELKEKI AQLEEQIKLE ELHQALISKL QKLKTGNETV TSPETAGGFS RTPHWPGQHI
PKGKCCASRE KEEQTPKDIF PVTETVDGQG QAWRHHNGFD FTVIKELKTA ASQYGATAPY TLAIVESVAD
NWLTPTDWNT LVRAVLSGGD HLLWKSEFFE NCRETAKRNQ QAGNGWDFDM LTGSGNYSST DAQMQYDPGL
FAQIQAAATK AWRKLPVKGD PGASLTGVKQ GPDEPFADFV HRLITTAGRI FGSAEAGVDY VKQLAYENAN
PACQAAIRPY RKKTDLTGYI RLCSDIGPSY QQGLAMAAAF SGQTVKDFLN NKNKEKGGCC FKCGRKGHFA
KNCHEHIHNN SETKAPGLCP RCKRGKHWAN ECKSKTDSQG NPLPPHQGNR TEGPGPGPET SLWGGQLCSS
QQKQPISKLT RATPGSAGLD LSSTSHTVLT PEMGPQALST GIYGPLPPNT FGLILGRSSI TIKGLQVYPG
VIDNDYTGEI KIMAKAVNNI VTVPQGNRIA QLILLPLIET DNKVQQPYRG QGSFGSSDIY WVQPITCQKP
SLTLWLDDKM FTGLIDTGAD VTIIKLEDWP PNWPITDTLT NLRGIGQSNN PKQSSKYLTW RDKENNSGLI
KPFVIPNLPV NLWGRDLLSQ MKIMMCSPSD IVTAQMLAQG YSPGKGLGKN ENGILHPIPN QGQFDKKGFG
NF
Publications
- Giedroc DP, Theimer CA, Nixon PL. (2000) Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol. 298(2):167-185. [abstract]
- ten Dam EB, Verlaan PW, Pleij CW. (1995) Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions. RNA. 1(2):146-154. [abstract]
- Du Z, Holland JA, Hansen MR, Giedroc DP, Hoffman DW. (1997) Base-pairings within the RNA pseudoknot associated with the simian retrovirus-1 gag-pro frameshift site. J Mol Biol. 270(3):464-470. [abstract]
- ten Dam E, Brierley I, Inglis S, Pleij C. (1994) Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1. Nucleic Acids Res. 22(12):2304-2310. [abstract]
- Bekaert M, Rousset JP. (2005) An extended signal involved in eukaryotic -1 frameshifting operates through modification of the E site tRNA. Mol Cell. 17(1):61-68. [abstract]