Repbase Reports

2005, Volume 5, Issue 1
January 31, 2005
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 5

Gypsy-16-I_DR

An internal portion of the Gypsy-16_DR LTR retrotransposon - a consensus sequence.

Submitted:
00-Jan-2005
Accepted:
31-Jan-2005
Key Words:
LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; protease; reverse transcriptase; integrase; Gypsy-16_DR; Gypsy-16-LTR_DR; Gypsy-16-I_DR
Source:
Danio rerio
Organism:
Danio rerio
Taxonomy:
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy-16_DR, a family of LTR retrotransposons from zebrafish
Journal:
Repbase Reports 5:(1) p.5 (2005)
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
Derived:
[1] (consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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