Overall information

FSDB ID	PM1V0005	Type	-1 frameshifting
Data	PREDICTED	Kingdom	viruses
Definition	Simian retrovirus 2, complete genome. 8105 bp DNA linear VRL 04-SEP-2002
Resource	[1] Thayer RM, Power MD, Bryant ML, Gardner MB, Barr PJ, Luciw PA. Virology. 1987 Apr;157(2):317-29.
Nucleic acid sequence		AF126467
Amino acid sequence
gene	494..2458 /gene="gag"
CDS	Click for details 494..2458 /gene="gag" /codon_start=1 /product="Gag protein" /protein_id="AAD43254.1" /db_xref="GI:5442104" /translation="MGQELSQHELYVEQLKKALKTRGVKVKGNDLLKFFDFVKDTCPW FPQEGTIDIKRWRRVGDCFQDYYNTFGPEKIPVTAFSYWNLIKDLIDKKEADPQVMAA VTQTEKILKVSSQTDLRDKSQNKEMDLISLESDDEEAKAPSEKISMPNKSPKKYPAML TSQNNNMDKDPDSSEVDWDGLKDEAARYHNPDWPPFLSRPPPYNGTTATAPAVMAVVN PKEELKEKISQLEEQIKLEELHQSLIIRLQKLKTGSERVTSSGNMESHSRTPKRPGQH LPIGKYLINKNTEEYPSKDIFPVTETMDGQGQAWRHHNGFDFTVIKELKTAVSQYGAT APYTLAIVESIADNWLTPADWNTLVRAVLSGGDHLIWKSEFFENCRDTAKRNQQAGNG WDFDMLTGSGNYANTDAQMQYDPGLFAQIQAAATKAWRKLPVKGDPGASLTGVKQGPD EPFADFVHRLITTAGRIFGNAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR LCSDIGPSYQQGLAMAAAFSGQTVKDFLNNKNKDRGGCFKCGKRGHFAKDCRDHSNKN PELKVPGLCPRCKRGKHWANECKSKTDSQGNPLPPHQGNGMRGQPQAPKQAYGAVSFV PASSNNPFQNLIEPPQEVQDWTSVPPPTQY"
gene	2275..3219 /gene="prt"
CDS	Click for details 2275..3219 /gene="prt" /note="protein expressed by frameshift mechanism" /codon_start=1 /product="protease" /protein_id="AAD43255.1" /db_xref="GI:5442105" /translation="SRKSLTTPSGKRDEGPAPGPEASLWGSQLCSSQQQQSISKLNRA SPGSAGLDLCSTTHTVLTPEMGPQTLATGVYGPLPPNTFGLILGRGSTTVKGLLIYPG VIDNDYTGEFKIMAKAISSIITIPQGERIAQLILLPLLRTAHKIQHPYRGNKNFGSSD IFWVQPITNQKPSLVLWLDGKAFTGLIDTGADVTIIKQEDWPSHWPTTETLTNLRGIG QSNNPRQSSKYLTWKDKENNSGLIKPFVIPNLPVNLWGRDLLSQMKIMMCSPNDIVTA QMLAQGYSPGKGLGKREDGILQPIPNSGQLNRKGFGNF"
gene	3195..5798 /gene="pol"
CDS	Click for details 3195..5798 /gene="pol" /note="reverse transcriptase; protein expressed by frameshift mechanism" /codon_start=1 /product="polymerase" /protein_id="AAD43256.1" /db_xref="GI:5442106" /translation="QKRIWKFLAAAVDILAPQRYADPITWKSDEPVWVDQWPLTQEKL AAAQQLVQEQLQAGHIIESNSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQP GLPSPVAIPQGYFKIVIDLKDCFFTIPLQPVDQKRFAFSLPSTNFKQPIKRYQWKVLP QGMANSPTLCQKYVAAAIEPIRKSWAQMYIIHYMDDILIAGKIGEQVLQCFAQLKQAL TTTGLQIAPEKVQLQDPYTYLGFQLNGPKITNHKAVIRRDKLQTLNDFQKLLGDINWL RPYLHLTTGDLKPLFDILKGDSNPNSPRFLSEAALTSLKKVETAIAEQFVTQIDYTQP LTLLIFNTTLTPTGLFWQNNPVMWIHLPASPKKVLFPYYDAIADLIILGRDNSKKYFG LEPSTIIQPYSKSQIHWLMQNTETWPIACASYAGNIDNHYPPNKLIQFCKLHAVVFPR IISKTPLDNALLVFTDGSSTGIAAYTFEKTTVKFKTSHTSAQLVELQALIAVLSAFPQ RALNIYTDSAYLAHSIPLLETVSQIKHISDTAKLFLQCQQLIYNRSIPFYLGHIRAHS GLPGPLSQGNHITDLATKVVATTLTTNLTEAQAAHALHHLNAQSLRLMFKITREQARQ IVKQCPTCVTYLPIPHFGVNPKGLIPNMLWQMDVTHYSEFGKLKYVHVSIDTFSGFLV ATLQTGEATKHVIAHLLHCFSIIGQPIHIKTDNGPGYTSSSFRAFCSKLHIKHTFGIP YNPQGQGIVERAHLSLKNTLEKIKKGEWYPTQGSPRNILNHALFILNFLNLDAQNKSA ADRFWHTNSKREYAMVKWKDPLDNSWHGPDPVLIWGRGSVCVYSQTHDAARWLPERLV RQVSNVTQSRE"

Graphical view

2272 TAGTCAAGGAAATCCCTTACCACCCCATCA GGGAAAC GGGATGA GGGGCCAGCCCCAGGCCCCGAAGCAAGCCTATGGGGC
Stop codons	TAG (2272),
Slippery sequence	GGGAAAC (2302 - 2308)
Spacer	GGGATGA (7 nt)
Stimulatory structure	GGGGCCAGCCCCAGGCCCCGAAGCAAGCCTATGGGGC (2316 - 2352)
	PREDICTED STRUCTURE Predicted by pknotsRG with the minimum energy option Visualized by PseudoViewer

3192 TAACAGAAAAGGATTTGG AAATTTT TAGC TGCGGCCGTTGACATACTTGCACCCCAGAGGTATGCTGACCCCATTACATGGAAGTCAGATGAGCCTGTTTGGGTTGATCAATGGCC
Stop codons	TAA (3192),
Slippery sequence	AAATTTT (3210 - 3216)

Model

-1 frameshift signal

FSFinder parameters

Run FSFinder
(You can obtain the above result by running FSFinder with the sequence and parameter values. You may have to alternate frames to get the same result.)

Target gene

genes in viruses

Sequence type

Patial genome

Direction

+ strand

Pattern

Pattern
Match
Exceptions AAA UUU

spacer

nt

RNA structure

Stem Pseudoknot
- Stem1	<
- Stem2	<
- Loop1	<
- Loop2	<
- Loop3	<