Repbase Reports |
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| 2003, Volume 3, Issue 7 |
| July 31, 2003 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 120 |
Copia1-I_TP |
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Copia1-I_TP is an internal portion of the Copia1_TP LTR retrotransposon - a consensus sequence. |
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Submitted: 31-Jul-2003 |
Accepted: 31-Jul-2003 |
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Key Words: LTR retrotransposon; Copia clade; 6-bp TSD; protease; integrase; reverse transcriptase; RNaseH; Copia1_TP; Copia1-LTR_TP; Copia1-I_TP |
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Source: consensus |
Organism: Thalassiosira pseudonana |
Taxonomy: Eukaryota; stramenopiles; Bacillariophyta; Coscinodiscophyceae; Thalassiosirophycidae; Thalassiosirales; Thalassiosiraceae; Thalassiosira |
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| [1] |
Authors: Kapitonov,V.V. and Jurka,J. |
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Title: Copia1_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana. |
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Journal: Repbase Reports 3:(7) p. 120 (2003) |
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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
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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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