Repbase Reports

2003, Volume 3, Issue 7
July 31, 2003
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 120

Copia1-I_TP

Copia1-I_TP is an internal portion of the Copia1_TP LTR retrotransposon - a consensus sequence.

Submitted:
31-Jul-2003
Accepted:
31-Jul-2003
Key Words:
LTR retrotransposon; Copia clade; 6-bp TSD; protease; integrase; reverse transcriptase; RNaseH; Copia1_TP; Copia1-LTR_TP; Copia1-I_TP
Source:
consensus
Organism:
Thalassiosira pseudonana
Taxonomy:
Eukaryota; stramenopiles; Bacillariophyta; Coscinodiscophyceae; Thalassiosirophycidae; Thalassiosirales; Thalassiosiraceae; Thalassiosira
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Copia1_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana.
Journal:
Repbase Reports 3:(7) p. 120 (2003)
Abstract:
Copia1_TP is a young family of copia-like LTR retrotransposons. Copia1-I_TP, an internal portion of Copia1_TP is flanked by 100% identical Copia1-LTR_TP LTRs. The consensus sequence encodes the 1506-aa Copia1_TPp polyprotein (positions 89-4606) composed of the protease, integrase, reverse transcriptase and ribonuclease H domains. Copia1_TP is characterized by unusual 6-bp target site duplications (5-bp in standard copia-like elements). There is no tRNA-like primer binding site in Copia1_TP. Instead, this retrotransposon uses self-priming by the 12-bp CGTTTATAAACG palindrome present at the very 5'-end of its internal portion. Copia1_TPp: MSTEEKSIRVITFSGKKKDYRVWSIKFTARSHKKGYKSILDGKETVPTESEYENAIAIDEDKRNKKDCKV IKCYEANAVAYDDLILSIDGLSSTGKVAFNIVETAKSTDYPEGNARLAWLHLANKYAPKTGTSYIQLMRS FVNSKLDLGTDPDDWITELESLRTEMDKVKISGKTDMSDVDLIIHIIASVPEEYEVAVSDLEDRLTSGAD KIDIEIVREKLSARFDRLKKNDVKDAVNETALSALGVLLEDEDLHPDELAAFVKQFKGRCNKCGTYGHKA ATCPSVKNDGGDPGTSALDDAKPKALTYLRGKKCFLCGKYGHLKSDCKLNKKQSAEQANMAIGESDDDNE SIDELGLYAFGLEVTKDDLAFHVIDGVEYPSFTDNTWIGDTGSSCHIVNDDTGLYDITPISEVVGGIGGQ SIRATKMGRLNVVIKQADGTQVKRVLYPVKYCLGATERIWSLNQEVNDARLSTDDKHRYVLTYNDEQQTK IVFDRRAKTNNGWVPGVEVIQDTAEIGMFTKQTKTINEYHEELGHPNMVATRSTAKARHENVVGPIQQCE DCAVGKAHQKRVPKQPVARAKNPGERLFLDISHPKQQSIGGSNDWILVADDATDNCWSWFTRRKDQLSDV IVPFIIDLKASYGITVKCIRCDNSGENHSLERRCNQEGLGIKFEYTAPNTPQQNGRVERKFQTLYGRVRA MLVGSGIKQPLRNKLWAEAANTATMLDNELVKEGETLTSHQKFFGKGVKSPIPIGSTKKFGEMCIVSNRE KIMSKLADRGKPCIWLGYAANHAQCTYRVYNPKTRRVILTRDVVFLRKSYGEWNADKDEATAVKPTTLPD DDDSDDEEEPININHHPIVSESEDEEPDTFFSAPSHESTDDNEESDISEGDTSEAENQTNPKLLREMRKL DASYNPDAHKVIESTKLNEEPIDNGTGRVSDVEGTDELSNLLIATDELSNLLMDITKVASSEKPTLLQLP YDEPKTWEQAWYHPDPYQRKMWRAAIMKEWNDMKKRNVWIVQRRCDMPKDRRCVKSKWVFKLKRNGVFRA RIVACGYSQIPGVDFEESYSPVMNDITLRILLVIWIVMTLKAIIADVETAFLYGKLLEVIFMECPPGMMG TTKDDVLRLLMCIYGLVQAAARYYAYMAKTLRSMGFKGGDVDPCLFVKWINGRVCFVGLYVDDNLIIGHP ELVDDTIKQLRQKGLILKISDLDDYLSCHIVLSKDKRRAWLGQPHLIASIVNKFGSQIKGLRQYKTPGTP GLSLVRDVERVNPLSTEKHSMYRSGVGLLGYLVKHSRPDLANMQRELSKSLDCPTEASYKELLRGLKYVV DTKEFGLKIEPSLSNVNEPWRIVVYSDSDYATDPDTRRSTSGYILYLRDVPIAWKSKAQQSVSLSSTEAE WIALSEAVKEIKFVVNLLESMKIKVNYPIKCRVDNIGAIFMSQNVTTTSRAKHIDIRTKFVREYVEDGKI KIVFVRSGDNDSDIMTKNVQGDLHDKHSKKLIGKQH
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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