Overall information

FSDB ID	EM1V0007	Type	-1 frameshift
Data	EXPERIMENTAL	Kingdom	viruses
Definition	Equine infectious anemia virus complete genome. 8359 bp RNA linear VRL 03-DEC-1998
Resource	[1] ten Dam EB, Pleij CW, Bosch L. Virus Genes. 1990 Jul;4(2):121-36.
Nucleic acid sequence		AF033820
Amino acid sequence
gene	525..1985 /gene="gag"
CDS	Click for details 525..1985 /gene="gag" /codon_start=1 /product="gag protein" /protein_id="AAC82599.1" /db_xref="GI:2801511" /translation="MGDPLTWSKALKKLEKVTVQGSQKLTTGNCNWALSLVDLFHDTN FVKEKDWQLRDVIPLLEDVTQTLSGQEREAFERTWWAISAVKMGLQINNVVDGKASFQ LLRAKYEKKTANKKQSEPSEEYPIMIDGAGNRNFRPLTPRGYTTWVNTIQTNGLLNEA SQNLFGILSVDCTSEEMNAFLDVVPGQAGQKQILLDAIDKIADDWDNRHPLPNAPLVA PPQGPIPMTARFIRGLGVPRERQMEPAFDQFRQTYRQWIIEAMSEGIKVMIGKPKAQN IRQGAKEPYPEFVDRLLSQIKSEGHPQEISKFLTDTLTIQNANEECRNAMRHLRPEDT LEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQTCYNCGKPGHL SSQCRAPKVCFKCKQPGHFSKQCRSVPKNGKQGAQGRPQKQTFPIQQKSQHNKSVVQE TPQTQNLYPDLSEIKKEYNVKEKDQVEDLNLDSLWE"
gene	1766..5182 /gene="pol"
CDS	Click for details 1766..5182 /gene="pol" /codon_start=1 /product="pol polyprotein" /protein_id="AAC82600.1" /db_xref="GI:2801512" /translation="MQKCSKKREARGSREAPETNFPDTTEESAQQICCTRDSSDSKSV PRSERNKKGIQCQGEGSSRGSQPGQFVGVTYNLEKRPTTIVLINDTPLNVLLDTGADT SVLTTAHYNRLKYRGRKYQGTGIIGVGGNVETFSTPVTIKKKGRHIKTRMLVADIPVT ILGRDILQDLGAKLVLAQLSKEIKFRKIELKEGTMGPKIPQWPLTKEKLEGAKEIVQR LLSEGKISEASDNNPYNSPIFVIKKRSGKWRLLQDLRELNKTVQVGTEISRGLPHPGG LIKCKHMTVLDIGDAYFTIPLDPEFRPYTAFTIPSINHQEPDKRYVWKCLPQGFVLSP YIYQKTLQEILQPFRERYPEVQLYQYMDDLFMGSNGSKKQHKELIIELRAILLEKGFE TPDDKLQEVPPYSWLGYQLCPENWKVQKMQLDMVKNPTLNDVQKLMGNITWMSSGIPG LTVKHIAATTKGCLELNQKVIWTEEAQKELEENNEKIKNAQGLQYYNPEEEMLCEVEI TKNYEATYVIKQSQGILWAGKKIMKANKGWSTVKNLMLLLQHVATESITRVGKCPTFK VPFTKEQVMWEMQKGWYYSWLPEIVYTHQVVHDDWRMKLVEEPTSGITIYTDGGKQNG EGIAAYVTSNGRTKQKRLGPVTHQVAERMAIQMALEDTRDKQVNIVTDSYYCWKNITE GLGLEGPQSPWWPIIQNIREKEIVYFAWVPGHKGIYGNQLADEAAKIKEEIMLAYQGT QIKEKRDEDAGFDLCVPYDIMIPVSDTKIIPTDVKIQVPPNSFGWVTGKSSMAKQGLL INGGIIDEGYTGEIQVICTNIGKSNIKLIEGQKFAQLIILQHHSNSRQPWDENKISQR GDKGFGSTGVFWVENIQEAQDEHENWHTSPKILARNYKIPLTVAKQITQECPHCTKQG SGPAGCVMRSPNHWQADCTHLDNKIILTFVESNSGYIHATLLSKENALCTSLAILEWA RLFSPKSLHTDNGTNFVAEPVVNLLKFLKIAHTTGIPYHPESQGIVERANRTLKEKIQ SHRDNTQTLEAALQLALITCNKGRESMGGQTPWEVFITNQAQVIHEKLLLQQAQSSKK FCFYKIPGEHDWKGPTRVLWKGDGAVVVNDEGKGIIAVPLTRTKLLIKPN"

Graphical view

1739 TAAACAGCCTGGACATTTCTCAAAGCAATGCAGAAGTGTTCC AAAAAAC GGGAAGCAA GGGGCTCAAGGGAGGCCCCAGAAACAAACTTTCCC
Stop codons	TAA (1739),
Slippery sequence	AAAAAAC (1781 - 1787)
Spacer	GGGAAGCAA (9 nt)
Stimulatory structure	GGGGCTCAAGGGAGGCCCCAGAAACAAACTTTCCC (1797 - 1831)
	Stimulatory structure from PseudoBase Visualized by PseudoViewer

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	<