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 5 |
Gypsy-16-I_DR |
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An internal portion of the Gypsy-16_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-16_DR; Gypsy-16-LTR_DR; Gypsy-16-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-16_DR, a family of LTR retrotransposons from zebrafish |
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Journal: Repbase Reports 5:(1) p.5 (2005) |
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Abstract: Gypsy-16-I_DR is an internal portion of the Gypsy-16_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy-16-LTR_DR. The consensus sequence was reconstructed based on multiple alignment of nine proviral copies (they are less than 1% divergent from the consensus sequence). Gypsy-16_DR retrotransposons are characterized by 4-bp target site duplications. The internal portion contains two ORFs encoding the 645-aa Gypsy-16_DR1p gag (pos. 109-2043) and 1601-aa Gypsy-15_DR2p pol proteins (pos. 1971-2043) 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. Each of all nine proviral copies is flanked by identical LTRs. Gypsy-16_DR1p: MDIIEKENVDISKAVIVGGMTLTETDSDLESWLLRYGSINRHLLIDDPDCEFHRHAIIEFTHNS AMKTLMPLLPLTVVSMSNPSTTFMVRALSCVYPHIASDSATNGYLEELQNIASFSGKSIEEVLQ TELLKIKFGPSHAESLPVLDKKLEFPNAARSQILDRSTVSSPNRLLSPVISQSMITEQTAFPSS RISPFHEVESTNSKNLSKESLNHRSTKPTVTVSSHPALTMDIIDPPSVQKVVVEHIVRTNDTAP MHHTSFRLRSFSGKIPRPVNEPDFDTWRASVDLLLTDPSISDLNRARKIIDSLLPPAADIVKHV SPNSLPAVYLELLESVYGSVEDGDELLARFMNSFQNNGEKPSTYLHRLQVLLSTAIRRGGIFEE ERNRYLLKQFCRGCWDSSLIADLQLERRKATPPSFAELVVLIRTEEDKNASKEERMRKHLGLNK HYPAPSKFRLSAHQISAHQSETQDDQTDTSLAKQVCELQAQVVALQKPSSQKEKKKNAKPDEVS ELRNVVTELQAQITAMQTTATPKIKSDVEATEIADLKRQIADLKVQLTAPDMYRNRTRNLLPEP RATDCYRASKLPESRPRPGYCFRCAEDGHLASSCSNAPDPTKVAEKKRKLRERQAQWDTQQVAI MNPLN Gypsy-16_DR2p: EKTQVKGATSPVGYPTSSNHESFKLRTVSVEGHTETKRNNNCPEKRKQLFNQNACDAPPLRNLP RGLVGVKCTAQITVGNKRVSCLLDTGSQVTTVPWSFYQENLSNCPLKSLDNLLEVEGANGQTVP YLGYVELTLKFPREFLGTETEVPTLALVVPDLMNTPQVLIGTNSLDALYSNYVQQSASFPQSNF HGYRAVQKVLEARYKQASADVVGCIKFKGHVPEVVPAGCTVVLDGHVLVNCPHVGKCVALESPT SPALPGGLLVASCLHSLPSKRHQQLPVVLRNETQTDITIYPRTIIAEMRAVQEVIKSGQVNSST VNKELSACSNLKFDFENSPLTPEWKKRITDQLNSMPEVFALHDLDYGHTNKVTHRIKLNDETPF KHRPRPIHPQDIDAVRKHLQDLLAAGIIRESESPFASPIVVVRKKDNSVRLCIDFRKLNSQTIK DAYALPNLEEVFSALTGSKWFSVLDLKSGYYQIEMEEADKSKTAFVCPLGFWEFNRMPQGITNA PSTFQRLMERCMGDLNRKEVLVFIDDLIIFSESLEEHESRLMHVLKRLKEYGLKLSPEKCKFFQ TSVRYLGHIVSENGVETDPVKIEALKTWPRPRNLKELRSFLGFSGYYRRFIQDYSKIIKPLNDL TVGYPPLQKRHLQENKNKQYLDPKKEFGDRWNQPCQQAFDMIIEKLTSAPVLGFADPKLPYVLH TDASTTGLGAALYQKQEGQMRVIAFASRGLTRSESRYPAHKLEFLALKWAVTSKFSDYLYGTEF VVVTDSNPLTYILTSAKLDATSYRWLSSLSTYNFKLQYRAGSQNCDADGLSRRPHGELLDDPAS QKERERIKQFTLHHLDEFGVEDSLILPEAIKAICDRHQIGNSSHKCKFSNPSIALVESLALHAD VLPNEFEQENEHGLPVIPYLSNEELKRQQRMDPDLKFIIDCLQRNEKPSSSKDQSLAVTLWIRE WSRLELRDGLLYRKKQDQESTHYQLALPVALRGTVLKSLHNDMGHMGMERTLDLVRTRFFWPKM SSSVEEKIKTCERCVRRKAFPEKAAEMMNIKTTRPLELVCMDFLSLEPDQSNTKDILVITDHFT KYAVAVPTRNQKAQTVARCLWENFLVHYGFPERLHSDQGRDFESSLIKELCLVAGIHKVRTTPY HPRGNPVERFNRTLLQMLGTLENKKKSCWKEFVKPLVHAYNCTRNDVTGYTPYELMFGRQPRLP VDLAFGLPVDRSTKSHSQYVKDLKEGLRESYEIAIKNSAKVAQRNKRRFDKHVVVSTLDVGDKV LVRNLRLRGKNKLADKWEPDVYVVIRKAGDLPVYVVQPDGKTGPVRTLHRDLLRPCGYLSENEI EEMSPPNVQRKPRTRSSSALEYAPKEHQMSDQSESEDDSLYIRNAGRQLESITTTVLPSSQSPV LVRNLPGIEPIEPLPVVVNPEKETLPDSRLEEDLTENQRDDVNENFLPVLNPADIDPKEIEPER SGNSVEVQIHRRALELDPVDVPHSNDQNPHVRNVSSNQPIVDEDLDTSGPRRSKRQCRPPNKLE YHKLGNPLTLVIQSLLQGLSSAFTTSLEEPILTRDQPFVVPDPFPIAVTTQPRTCPRTCLNSGG E
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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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