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 149 |
Copia9-I_TP |
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Copia9-I_TP is an internal portion of the Copia9_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; protease(?); integrase; reverse transcriptase; RNaseH(?); Copia9_TP; Copia9-LTR_TP; Copia9-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: Copia9_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana. |
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Journal: Repbase Reports 3:(8) p. 149 (2003) |
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Abstract: Copia9_TP is a young family of copia-like LTR retrotransposons. Copia9-I_TP, an internal portion of Copia9_TP is flanked by 100% identical Copia9-LTR_TP LTRs. Copia9-I_TP encodes (pos. 777-3041) a hypothetical 755-aa Copia9_TP1p protein of unknown function. The consensus sequence also encodes the 1560-aa Copia9_TP2p polyprotein (positions 3135-7814) composed of the protease (putative, pos. 130-280), integrase (pos. 420-580), reverse transcriptase and RNaseH (putative) domains. Copia9_TP1p: MTTPSDSTPSRQSRRKAGLSPEHPTLSGEKATRLKASPNEGAILPPTSLGMAEEEVHPVDKLKEMEQSVD SKFKEMEQSVDSKFKEMEQSVDSKFKEMEQSVDSKFKEMEHSVDVKFKSVDSKFKAMDKRFDDIENLLKK VLSRQRTGESNKSRSSVSIDPVDNMMGSFEASLLGTTDKDTVDEGGDEVVFNGSVSTKGMEPSGSVHSGS VVSVRHPLKSTGKISRHSSLVTPVKVKTTAENAREAWSKAPKKMNDWPTGNDRNGVEDISDAGGVKQIPT AQPPPMSPQEASTYYEPQLDHFLPPLYFAGGSGRNDNFNGVDVLAYHHLKSLGILNNYVWSDIMNAHGTV MAKWNLYNGPRDKDIHDASKFPTLENCRVDTLVSWYQSLQPRLASYCIGLTPFDGIELSFGYQGLCIPGL GIKRYRPMALALYEILITKLPREHQTLLGLFDVGTKDGYHLFWSFFCLTLPIFNTDMELKYPKFADHSGD VEQFARATVIYHKFERMDGRNMNQRHKVMKYLTTLSKAVDWPIVHVKLDCVSRCPGDLSLPVDSQYGTLP PSLSLAQVTADIMQYLRNRQHDPTLGNVDTYRRTNMLEAQLVNKGTVWKDAKPMDFHMQGYEDLYETDIS VFDPVANAVQRRSFPRKSTAPERARVRSPPVACDACGGNHKAITCFWLARALRIQDFIKDPRNKRRIDEA IQYWKDKRAAQVEHKGPERDPKRILAAYVDTFGLSPEQVAEEMDMEEVLESVKDE Copia9_TP2p: MDPPRHALYSISASTTDTTVDRPPAEPPPPKQPDPIQTSKLTATPASTMQSLESPPPGSIFQQTPRREAS IPYIMDSARVNFGWMHDQSTSLTCRGMDSIIYNEHEPCFLGLANDNESEWATPRVLTTYQSQQNLVGGTH QPLPRVIRDAMWDPGANICMTPYLHLLTNIVKITPFAVGVAVGPSSFPHKEVSTSMCTMKGDLMLPLVDG SYHAQECYYNPQATDTLVSPQAICEDSHDRFSQWSMEANTTGQPGRITFKSAQGDALMSIPLHLKNGLWH CKNENFLQRSPNPIPCTPMIGMEQVQEPLEEIEFSPHAAMNRRRPTSKAKQLEADLWSARLGFPSDWQLD VLPLNAAGLPTKFCPHPFSHYEWKTSARMHRNPRGKDPERVIERGMRFYLDYGFMRASATDYSRPSKATD RVVQSFDGYNCYLLIVDEVSHHVWVFLCQSKEPPVEIVSDFLLVYGHKRGGVLRTDQGGELARSAKFREA MRIRNFELDDGPTAAFPQHSAFYAIEPTGAGAASQNGGVEKWNDTLATTVRALLYSAGLPPKYWSVALVH AVYLHNRRVHKSIQRTPFEAWYGLKPNLRHLKVFGSRVCVKVPATRRAKLDRGDFRGIFLGYTATNSNIR YLDLDSGLVKSSADAIFDEAWYTQSRRPPAAQLLYDLGVMNDVEDSPGSMMYPPAPTVYPPLPSKSQILT KPLMASKLPLPLREYSPSIVSAKAAKSSAVWNSIIAHHDESPPIHSIIEEYGINKTDMAMVYISPDPYNS AFEEHLDIRDFTNERHPTAGMSLIEQDGGRLILAHMMPGTPAAKIPYWRSRLKQAWLISVNGIEVHTRAD VQEAIASAILQKKTNCTLLFAHPEIKHGLTNQGIPQVNMDQLNPRLLLRPSVQDLINNMPTFDSNIDDTS IPLNNNDILWQPRACVTRGNSEDDVFTYRTRAMKLTRGKLRQQKDWDEWHRAEWTQLDQYEDQGMFGDPV RINDERLIFYLVWTYVEKVLDKRKKARCTCDGSTRAGKVRILDHTYANCVDQTGARIFYAASAAENLLMF GADVSNAFGEAPSPKQGFYIRPDKAFNEWWTIHKQRPPIPPGHVIPILKAMQGHPESPRLWERHVDGILR KALNFKPTIHEPCLYSGAVEGERVLFLRQVDDFNVAAPTERIANIVYDTIDEHLTMPLKRMGLVTLFNGM DITQSRHYIKLHCTTYIERICEKYLNDWLKDAKISADRPLPFPTKDEFLKQLLEEVGDPDLTKQAKLRTQ HNVGYRNLMGEIIYAMVTCRPDISYHTVKLAQSSARPADIHYRAAKSVLRYLYATRNDGIHYWRSKPNDI LNDLPLPAISSNISDLMTDGRPVHDPLHPHGFVDSDWATCPRTRRSFTGICFCLAGGTIAYKTKLQPTVA MSSTEAEFMAASDGGKMSLYIRSVLYDLGIPQWAAHELYEDNDACNAMANAGKPTTRTRHMDIRYHALRD WVERDLIVLERVPTSLNQADHFTKSLPRILFHRHVDYILGHVPPPHSPLHDNIASIGIQTEYHPPVTTTK TCTTTRTTPYHPYVSVLNNE 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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