Repbase Reports |
|---|
| 2003, Volume 3, Issue 7 |
| July 31, 2003 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 130 |
Gypsy2-I_TP |
|||
|---|---|---|---|
Gypsy2-I_TP is an internal portion of the Gypsy2_TP LTR retrotransposon - a consensus sequence. |
|||
|
Submitted: 31-Jul-2003 |
Accepted: 31-Jul-2003 |
||
|
Key Words: LTR retrotransposon; Gypsy clade; 4-bp TSD; gag; protease; reverse transcriptase; RNAseH; intergrase; Gypsy2_TP; Gypsy2-LTR_TP; Gypsy2-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: Gypsy2_TP, a family of gypsy-like LTR retrotransposons from diatom Thalassiosira pseudonana. |
|||
|
Journal: Repbase Reports 3:(7) p. 130 (2003) |
|||
Abstract: Gypsy2_TP is a young family of gypsy-like LTR retrotransposons. Gypsy2-I_TP, an internal portion of Gypsy2_TP is flanked by 100% identical Gypsy2-LTR_TP LTRs. The consensus sequence encodes the 389-aa gag-like Gypsy2_TP1p protein (pos. 61-1227) and 1193-aa Gypsy2_TP2p polyprotein (pos. 1231-4809) composed of the protease, reverse transcriptase, ribonuclease H, and integrase domains. Gypsy2_TP is characterized by 4-bp target site duplications. There is no tRNA-like primer binding site in Gypsy2_TP. Instead, this retrotransposon uses self-priming by the 12-bp CTGTAATTACAG palindrome present at the very 5'-end of its internal portion. Gypsy2_TP1p: MSYLDSEPCINYERSWDTTETERTVALVQVWDNGTKSKVEVPIDDNTKGIEHLVMVTNEEFKLACEELQF EDEDLYIQYAKCLKGNTKFYWDNVMGEVEDADKTTVNFPTHQIDLIQAIVGEDQRDVLHEWMETRYKKPP NVHPIQHHARTLEIFRFMDAVPGIAPQADEATKKKWLFKSYPLKFRDEYHTSGRSLTTDTMLQVTTFMKK LYEIEERNRRIAGRKRGRSPSNYRGGGSKRQRNCGGESNNSRDSHNDGGRSNNGNNNKQRHSRKGNNHGH GGKHNDHRNDNNRNKSRVQDDEKCPLHPNLEPGHTWLECRQNQYGPNFRPKSDSKGNGRRTNEHRSGKRD NENGTNYFVDRKANDNMEAESSNDVHHFDLIGSMSNAGS Gypsy2_TP2p: LQQRTADGLHAESYDLMQQDEESEEISNNIKSIVEHVNEVDDTNLSTFPETDCDASKDGDASAGIANGDA SDNGEDDIGMIDMLAFEPIIYQVPTPKQLQSQSKDIVPATLMIAQKVQGQQCPRLLKVLLDSGGGATLFH RSCLPRGATPRMLPEKKEMKTILGTFTPNNEVLLEDIQLPEFDKSRKVDFVNAFIFDEPCRYDVILGRDF LSKAGITICFKSNVMTWLENVVPMRCPTTDKETLEAVLDACYMHDEEYELEIDWLDGYLSNPIPILDAKY EKADIDEVTTMQKHLTKEQQRELATLLRKHEKLFNGTLGLYPHKKVHIDVEPNAKPVHSRAYPIPRVQLE TFKRELMHLVRIGVLSPQGASEWASPSFIIPKKDGRVRWISDLRALNKVIKRKQYPLPIITEIIRRRTGY SFFTKLDISMQYYTFELDDESKELCTIVTPFGKFKYNRLPMGLKCSPDIAQEAMDNLFRDIDEAEVYIDD VGAFSNTWAQHIDLLDTILGRLEDNGFTINPLKCEWGIKETDWLGYWLTPHGVKPWKKKIQGILDMQRPT TLKEMRTFLGAVNYYRDLWPRRAHILKPLTDRVGKKEFIWTPEMEKSFKTMKAVVAADALMHYPNHNLPF EIYTDASDYQLGACIMQNKAPVVYFSRKLTGAQRNYTTMEKELLSVVMVCKEYRSMLLGADLHFFTDHKN LTYHNLNSQRVLRWRCYLEEYSPNFHYLPGKDNVLADAFSRLPCLHDEGVEGKSNDELDDLGTEELHSQF RAKRNDNVESFASLLDEPSVFDCFVNLPQIPQQQNPLNYAVLQQNQIADAQLQTLLRDNPQRYQLRDFGD VQLICYVKDGDDPLTQWKIALPENMIQHTMIWFHHVIGHPGNNRLRDTIQARYYHPSLRKKIDEFQCGIC EQHKLSGAGYGYLPEREARLAPWTEVAIDLIGPWKLELNGREYEFNALTCIDTVTNLVELIRVDKKTASH IRSKFEQVWLARYPWPQRCVHDNGGEFVGASFQELLEAANIRDVPTSSRNPQSNAICERMHQTVGNILRT LIYSNPPQTEEQAANLVDEALATTMHAMRSAVSRTLGSSPGALAFNRDMFLDVPLLADWHLLQQRREHLI NENLRRQNMKRRRWDYVPGQRVWLKTVDPTKLGLRTIGPFFIEQVHTNGTITIERRRGVLERVNIRRVVP SRE
|
|||
|
Derived: [1] (Consensus) |
|||
|
Download Sequence - Format: IG, EMBL, FASTA |
|||
|
References: |
|||