Repbase Reports |
|---|
| 2003, Volume 3, Issue 8 |
| August 31, 2003 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 147 |
Copia8-I_TP |
|||
|---|---|---|---|
Copia8-I_TP is an internal portion of the Copia8_TP LTR retrotransposon - a consensus sequence. |
|||
|
Submitted: 31-Aug-2003 |
Accepted: 31-Aug-2003 |
||
|
Key Words: LTR retrotransposon; Copia clade; 5-bp TSD; protease(?); integrase; reverse transcriptase; RNaseH(?); Copia8_TP; Copia8-LTR_TP; Copia8-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: Copia8_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana. |
|||
|
Journal: Repbase Reports 3:(8) p. 147 (2003) |
|||
Abstract: Copia8_TP is a young family of copia-like LTR retrotransposons. Copia8-I_TP, an internal portion of Copia8_TP is flanked by 100% identical Copia8-LTR_TP LTRs. The internal sequence is not perfectly reconstructed because of unsufficient sequence data. The consensus sequence encodes the 1173-aa Copia8_TPp protein (positions 576-4038, conceptual translation). The ~550-aa N-terminal portion of Copia8_TPp is not evidently similar to proteins encoded by known copia elements detected in other species. Copia8_TPp: SGGTLQFTAAIGCTTAVACDTACQLFTAVTVSATHAEAPKGVSPELLSKIWRINQQTAKRTLEVTSQLNK QDGDSSLARNFSTNDRMQRYRRLKSFFFSDTFFVTKEAKSTRGFTCMQLFVSDKGFIFVVPMKSVAEFPH ALRMFAKEVGVPQALIVDPHRAQTSKEVQQFCHKIGTTLRVLEESTQFANRAELYIGLMKESIRKDIRET HSPLVLWDYCAERRALIFNLTAKNLFQLQGQNPYTATFGEEGDISNLCQFGWYEWVYFRDGSQAFPTMRE CLARCLGPAKNEGNEMAMDTEDDAQIVPRRSLHRLSEAELNPTNEIELRKRKAFDNAIAAKLGDSFSLPP TPLTSHLDDDNAAFVPYEDDEESPIEMPDADAVDAAGTPVMQQSLADTLINAEVLLPQGESKQLAKVIRR SVDADGHVIGMFNKNPILNTLLYDVEFPDGVTKQYAANLKTYFAKSTRMDDTLASSGILEYRRNKSAVTK ENQYVVTKRGRRKLRQTTVGWDFLVQWKDGTTQWLPLKLLKESNPVDVAEFVTARGIADEPAFCWWVPYT LRKRDRIIASVNSRIKKRNRKYGIEVPTSIEDARRLDKENGNTLWQDAIAKEMYNVSIAFQILEPGESVP PGWTKSSGHIIFDVKMDFTRKARWVKDGHRTPDPESSSYAGVVSRESVRIALTYAALNDVDIIAADIRNA YLQAPSSEKHFIICGTEFGLEHVGKKALIRRALYGGKVAGRDFWHHLRDCMGHLGFRSSKADPDVWMXPT VRTDKSEYYEYVLLYVDDCLVLSEKAEDIIRKEIGKYSELKEESIGPPDIYLGGKMRRVVLDHGSKAWAF GSSQYVQHAVKNVEEYLKGRGESLPARASSPISNNYRPEVDVTEELEGETASYYHSLIGVLRWIVELGRV DIDVEVSMMSSHLALPRKGHLQQLFHIFAYLKKHHNAEMVFDPSDPVVEPSQFERQDWSHTVYGDDLVEE LPPDMPPPRGQGFRMRVFVDSDHAGDTVTRRSRTGFLVYLNCAPIYWLSKKQTSCETSTFGSEFVAMKQA TEYVRGLRYKLRMKGIPVEEPTLVYGDNQSVLANTTLPSSTLKKKSNSIAYHFVREGCARDEWSDEWRTT YINTHLNPADMLTKPLPPGEKRSKFVRMVLHHL Copia8_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.
|
|||
|
Derived: [1] (Consensus) |
|||
|
Download Sequence - Format: IG, EMBL, FASTA |
|||
|
References: |
|||