Repbase Reports |
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| 2005, Volume 5, Issue 1 |
| January 31, 2005 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 7 |
Gypsy-17-I_DR |
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An internal portion of the Gypsy-17_DR LTR retrotransposon - a consensus sequence. |
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Submitted: 00-Jan-2005 |
Accepted: 31-Jan-2005 |
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Key Words: LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; protease; reverse transcriptase; integrase; Gypsy-17_DR; Gypsy-17-LTR_DR; Gypsy-17-I_DR |
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Source: Danio rerio |
Organism: Danio rerio |
Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio |
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| [1] |
Authors: Kapitonov,V.V. and Jurka,J. |
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Title: Gypsy-17_DR, a family of LTR retrotransposons from zebrafish |
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Journal: Repbase Reports 5:(1) p.7 (2005) |
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Abstract: Gypsy-17-I_DR is an internal portion of the Gypsy-17_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy-17-LTR_DR. The consensus sequence was reconstructed based on multiple alignment of two proviral copies (they are less than 1% divergent from the consensus sequence). Gypsy-17_DR retrotransposons are characterized by 4-bp target-site duplications. The internal portion contains two ORFs encoding the 572-aa Gypsy-17_DR1p gag (pos. 85-1799) and 1578-aa Gypsy-17_DR2p pol proteins (pos. 1794-6527) composed of the protease, reverse transcriptase, and integrase domains. The second protein, including the protease domain, does not start from Met. Presumably, the gag-pol fusion protein is formed originally due to a ribosomal frame shift. This family is likely still active in the genome. One proviral copy is flanked by identical LTRs. Gypsy-17-I_DR1p: MEIVHAENICIRNAVIISGLTHTERDDEVLKHLSDYGSIERLIRIDEPKTEFHGQIIVEFKNDS AMQLLEQSLPTAFQSPTSSDVTYTIKSLTSVYTPAASSSATHTFIEGLREISKVTGKPLEELLQ DELAKLTASAVSPPQTESEFLTTESDPEGSQKRVVEPTQTTMVSAHGDVTPSNESVIFQTKSNN SLPQISASPSRLNADMGTPLKLTVSDVTPAEVQRLVVEHIVRSDTPSHSLTTMRLRPFSGKPSY SANEIDYDTWRTNIEFFCTDSTLTDAQRSQRILDSLLPPAADVVKHLGPHSPPSDYLELLESAF GTVEDGDELFAKFMSTFQDAGEKPSQFLHRLQKVLSTAIKRGGVSAADRDRHLLKQFCRGCWDN ALITELQLEQKRKNPPAFSDLLLLLRIEEDKQSIKAVRMNQHLGAAKHSATPPRRVVTNLHSIS AACSAVKHDEVEDLKRQVVELQNQIASMKPFKKCKEFKPKEPSVPSKSAKTFSPKPSKGTNPQP NKSAKPRPWYCFNCGEDGHIASRCETSPNPSLVGAKNRQLKEKQLQWEVCDGVPDPNDLN Gypsy-17-I_DR2p: FKLTSVPFVGQRGTGESSQSPTDNLAVSVSDDSPTPKHKCCLKLPSGLIGTKCTARVLIADKEI NCLLDTGSQVTTFPLSFYQDVFANQPIQPLHHLLEIEGANGCQVPYLGYIETSITFPKEFVSSD IEVPTLALIVPDTRPNAQVLIGTNTLNSLYSEYISSKPLKHHPVPQGYQAVMQVLEFVHRQGAE GNLGWVNLNCRVPESIPAGKTVVLEGSVRMSTPVTDRWVVVEAPRASSLPGGIMVSSCLLSLTA GGKYLPIVLKNETEHDVVLPPKIRLAEVNSIQCVMPNGQNNVLTSSVNLTKNSEDSKIHFNFDN SPLTSEWRERVTRKLNSMHEVFACHDLDFGHTTKTKHHIRLHDETPFKHKARPIHPKDIQAVRK HLQELLDAGIIRESESPFSSPIVVVRKKNGEVRLCVDYRKLNLQTIKDAYALPNLEETFSALTG SRWFSVLDLKSGYYQIEVEEIDKPKTAFVCPLGFWEFNRMPQGVTNAPSTFQRLMERCMGDINL KEVLVFIDDLIVFSATLEEHEERLLRVLHRLKDYGLKLSPEKCTFFQTSVRYLGHIVSPSGVET DPDKIKALKTWPSPTNLKELRSFLGFAGYYRRFIKDFSKIVKPLNHLTSGYPPLHKSKKTQEIK GHYLNPREPFKQRWTSNCQHAFEEIIDKLTSAPILGFANPKLPYILHTDASTTGLGAALYQEQE GKMRAIAFASRGLSFSESRYPAHKLEFLALKWAVTEKFHDYLYGSQFTVITDSNPLTYILTTAK LDAASYRWLSALSTYSFSLKYRAGKLNLDADGLSRRPHEVAMDVVSRKEQERIDKFLTLHLENL GETSLTQDEVEAICDKHIISSMPEDVVESASDRTVLVHSLAMSSNAVPNSYEEEELGVSLIPRL SVQDLIEKQGADSTISQIISHLNSGEKPSPTVRGELPELSLMMREWNRFVLLDGVLYRKRQNGE VLTHQLVLPKEFRATVLRSLHDEMGHMGIDRTLDLARSRFYWPKMAQEVEQKIKTCPRCVLHKA PPEKAAPLVNIRTTRPLELLCMDFLSLEPDRRNFKDILVITDHFTKYAVAVPTVNQKARTVAQA LWDNFIVHYGFPERLHSDQGRDFESHTIKELCSISGIKKGRTTPYHPRGNPVERFNRTLLNMLG SMNDEQKAHWRDFVKPLVHAYNCTKSEVTGFTPYELMFGRQPRLPIDLAFGLPTTSKRLSHSQY VSKLKKHLEESYQIATRNALKNAERNKIRFDKHVVDSTLEVGDRVLVKQVRLRGKHKLADKWEP SAYIVVRRVHDLPVYTVRPEGDEGPLRTLHRDLLLPCGFLTLPGEKVSNPPSSTSKPRTRQQVS GEDASENGVNDTAESMEDEVPEYWIRIPVTNESHENALGTLTSTFDPPVGCDPQLPFVALGDES HVEMDSAGLEACLDDSHQEKQIKQITTLQGESSEMSESGKSSEGELSEEMPQCPDDGIERSVEE ELEEEIRKPLSNAPDNISSNIEQHETSQEPENPMRRSQRRKEKPDRLQYSELGNPLVIVAQALF HGLTTAFTNSLNGVDFVETSSPSTSDKAVTCQPVRVNATGRA
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Derived: [1] (consensus) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References: |
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