Repbase Reports |
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| 2003, Volume 3, Issue 8 |
| August 31, 2003 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 144 |
Copia6-I_TP |
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Copia6-I_TP is an internal portion of the Copia6_TP LTR retrotransposon - a consensus sequence. |
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Submitted: 31-Aug-2003 |
Accepted: 31-Aug-2003 |
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Key Words: LTR retrotransposon; Copia clade; 5-bp TSD; protease(?); integrase; reverse transcriptase; RNaseH(?); Copia6_TP; Copia6-LTR_TP; Copia6-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: Copia6_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana. |
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Journal: Repbase Reports 3:(8) p. 144 (2003) |
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Abstract: Copia6_TP is a young family of copia-like LTR retrotransposons. Copia6-I_TP, an internal portion of Copia6_TP is flanked by 100% identical Copia6-LTR_TP LTRs. The internal sequence is not perfectly reconstructed because of unsufficient sequence data. The consensus sequence encodes the 1442-aa Copia6_TPp protein (positions 28-4351, conceptual translation). Copia6_TPp: MARTRKTAGRADDEAKQADDVDVDAENSASEDEDAEAVADGDDAGGAQGDERQPTVAELAAMELSSDEDD DEADGNSGDVSSIVTDTRQEPSLQAPMVHTPIVDGEVTFESVRVLIDGPRPASLTGDDGAYGQSMYYALM SIGFSLEAAHAMMHRESLNTADKCADLDGSTIKAALKGLSTDLKGAIKDKYGLLIKPVYVPAVTQTNFYA LCRKFKFVKLTEGMVYPKDVGHKIGTIPEFVQLNKILGKFEYSETSMFTNKPELDKHDHAKNLADLDDFL RGIRTTSGTSVAYLARRNKKVPIVKARLSCDSIDDYMITHTLIVPRRENDTFMNHRIEEEYARLLSQEVG EANRLLYRALEYFYKDTDSMVIIKAYKKTADGMGAHIALKKRYMGAEWLSHSTEDAISNIEHARYKGESR SGRHSWDAYCKVFDKNWQIVQNNIASGHNRTFPPEYLGEKFIRGIDEGISTKMDAALAAAQGDKKLLSDI NALQNRIYTALPAASGNRRDKRNVAAVAGKGSSPGGKKKARFTGTLDPDVHYKPKEYRKMTQGQKNKLYA MRPPKDEDGTSGSAASVPNSKYESVRKERNEYKRKVAELTSEQKSGRSNSRSRSSSVSPSPAKRSSSKSR AIRRKSADGEGRLMVVIKIVGIVLVWETKWSxxxMWSPPFVVYDxMLASEHKQxxPRGNAMQRGRVVKRK RDDDGNIVGTANANPILDTRVYEVMFPDGEVTELAANTIATSMYAQCDVDGNEYLLLEAFVDHQKSDAAL TLEQQKTNHNGRPSIRKSTAGWKLCCQWLDGSTSWVRLSELKESHPVQVAEYAVAAGIDHEPAFNWWVRH VLKKRDRIIAQVKQRNARYLKKTHKFGIEMPKSVQEALELDKKNGNNLWGDAIKKEMQNVRIAFDILPDG TTAPIGYQHVQCHMIFDVKMEDFRRKALLVAGGHTTEAPPTLTYASVVSRETVRIALTMAALHGLPIMAA DVMNAYVTAPNKEKIWMTLGPKFGSNCGKKAIIVRALYGLKSAGAAFRSHLGECTRNLGYKPCLADPDLW MKPEYDPSDSFKYWSYILCYVDDILVIHHQPEDVIKKIDKYFPLKPGSVGKPDMYLGTKLREITFTNGEK AWAMSPSKYVQESVSNCVKHVKANMSDMFSLPKKAINPFPTDYEPMEDGTPELDAEHASYYQQLIGIMRW MVEIGRIDIDTQVSMLASHVALPRQGHMSAALHIMAYLRDHHNSRMVFDAHEPEIVKSDFKKYDWQEFYR DAKEALPPNMPPARGRAVDLRLYVDSDHAGDKVTRRSRTGYIIYLNSAPIQWLSKKQSTVETSVFGAEFV AMKHGIETVRGIRYKLRMMGIEVDNPTYVYGDNMSVVTNSSKPESQLKKKCNSICYHAVRESVAMGESLV SHISTDKNPADLMTKTLVGVKRRFLVSKLLYDIYDDHGIAKQ The 800-aa N-terminal portion of Copia8_TPp is not similar to proteins encoded by known copia elements detected in other species. Copia6_TP is characterized by standard 5-bp target site duplications. Primer binding site is not complementary to tRNA and it does not form a self-priming palindrome present in Copia1-4_TP families.
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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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