Repbase Reports |
|---|
| 2003, Volume 3, Issue 8 |
| August 31, 2003 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 141 |
Copia5-I_TP |
|||
|---|---|---|---|
Copia5-I_TP is an internal portion of the Copia5_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(?); Copia5_TP; Copia5-LTR_TP; Copia5-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: Copia5_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana. |
|||
|
Journal: Repbase Reports 3:(8) p. 141 (2003) |
|||
Abstract: Copia5_TP is a young family of copia-like LTR retrotransposons. Copia5-I_TP, an internal portion of Copia5_TP is flanked by 100% identical Copia5-LTR_TP LTRs. Copia5-I_TP encodes (pos. 286-1731) a hypothetical 482-aa Copia5_TP1p protein of unknown function. The consensus sequence also encodes the 1404-aa Copia5_TP2p polyprotein (positions 1849-6060) composed of the protease(?), integrase, reverse transcriptase and RNaseH(?) domains. Copia5_Tp1p: MAENPNPDVFQDAQEQVDAIAQLTQLVIQQTNTVNALLAALGNAQVGAPVAASASTFALTPGKVGVEAVI DYSTKHGSSVYKEYKAALPTVWDLKGKGLVVFIQEFLTRAQDAGWTQGTMQVTKFNNADGTPIDLITEYG KIDVDTLKAQCDVFLLPGGANFQTRATQNNKLMAECLLSSVTASATQALIADRGQYTFDGTIYAPVLFKH MMKIATLDNKATSKWLRDQLKQMPAVMLEVKGNIDDFFNTFDKWHTQLIGRGEDLDDALDCLWDGLKAAP CEKFSKWIQDKYDLHIEDDPTWGPITVEELTKRVKAKYNLMVTNKEYGSASKEQAEIIALRAQIDALKGD LKLSVAPKGNSKGDKKDKKGGEKGGKEKKTKNTKAKGDKQRQKQEESWKKTPPKDGEPTTKTVGDHTFNW CVHHMAWVWHRSENCDLGKKRAAEQNHVSYAAAVNSSPIETGTSSNFRALMSTLAQAALDEE Copia5-Tp2p: MHFFCFAEVPYHRSKGRPPSKRKESRLRRRYRARHQYHPPRVRKKKKWKTPPSPSASIALDPPLSCHYVW LFKIFKIFASIEILVRRALVVLAPRVLASCIAYRASALHDAVEVRFDSDSFKIGIDNHASRTMSPSKDHF EDLILHNTTTTVGGIGSGLSIKGVGTFVFKIEDDDGGVHCIKIPNSLYVPGLKTVLLSPQHWAQEARDHH PKPEGTVCSNTSKACVLYWNQLRYKRTVYFHRSTNTPVFRTAPGALSHRAFVSTFEAMEAPLQRKKEQLR FRPALNATFLREQPDAATFLREQPDEAEFVAEETLLEKATQQPDPNADDDTVQISNTAPKEHEQQTIGCL TFDPAPRGELHDDQHYSAEDPQAELMRWHYRLGHLPFPRLKLLAETGEIPKRLAKVIPPRCAGCLFGAMT KVPWRAKGKQDTTIFSATKAGQVVSVDQMISTQVGFVAQLKGRLTTQRYRAATVFVDHFSRLKFIYLMTG LSSEETVAAKKAFERFASNNGVRIQQYHCDNGRFADKAFISHCEQQQQHITYCGVNAHFQNGIAEKAIRD IQEQARKQLLHARSRWPEVIHLALWPYALRMAVHLHNTVPSLADGRSPLEVFASLAVGSKMRDNHTFGCP VFALQNALAAGNTIPKWSPRARLGVNLGPSPSHARNVALVLNLSTGLVSPQYHCRFDDFFETTRYAKRDL SVGSTWQRLAGLIRVDRLPSLELHDNNAVSLAEATNIAETVLPPSENDAIEEEELFDADNQQHNDFDDVT TEPGDPNNPAETQTADSDSDTTTQTPTAGISSRGRRRKLSRRMAESVSQREFFGDRNMHYMASQSTVGLN EAEDDRLHEEHLALQSLMSNPIAFHAEMMGDIMYFHQAMKQPDSEEFVKAVVKEVNGHIENNHWQLVPRS EVPPDAEVVPSVWAMRRKRNLTTNEITKYKARLNMHGGKQTYGVNYYETFAPVVSWFGIRLLVVFAIVFK WSLRQVDFVMAYTQAPIEMDMYMELPAGLSTKHGDSKSHVLKLLANLYGQKQAGRVWNEYLVGKLRSIGF EQSKVDDCVFYRGDVVFIVYVDDGMFLGRCDRQLTSIIKELVDLGLDIEDQGHPADYVGVNIRKLQDGSY EFTQRAIIDSVIADVGLDGPNIATKPVPAKSTVHLHAHKSSPAFNGRFNYRSVVGKLNYLAQTTRPDIMY ATHQIAKYSSDPRKEHGEAIIYLVRYLKGTRHLGLKFKVDRTKGFECYVDADFSGAWNRAFAATDPSTAK SRGGWIVFYAGCPIIWASKLQTQVALSTTEAEYIAMSMALRDVIPIMELVREMKNRKFEVICTEPLVYCK VFEDNSGALELARLPKLRPRSKHINVCYHHFREHVRKGLIKIFPVSTDAQVADALTKALPQNSFVRHRRH YCGG Copia5_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: |
|||