Repbase Reports |
|---|
| 2005, Volume 5, Issue 1 |
| January 31, 2005 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 15 |
Gypsy-21-I_DR |
|||
|---|---|---|---|
An internal portion of the Gypsy-21_DR LTR retrotransposon - a consensus sequence. |
|||
|
Submitted: 00-Jan-2005 |
Accepted: 31-Jan-2005 |
||
|
Key Words: LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; protease; reverse transcriptase; integrase; Gypsy-21_DR; Gypsy-21-LTR_DR; Gypsy-21-I_DR |
|||
|
Source: Danio rerio |
Organism: Danio rerio |
Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio |
|
| [1] |
Authors: Kapitonov,V.V. and Jurka,J. |
||
|
Title: Gypsy-21_DR, a family of LTR retrotransposons from zebrafish |
|||
|
Journal: Repbase Reports 5:(1) p.15 (2005) |
|||
Abstract: Gypsy-21-I_DR is an internal portion of the Gypsy-21_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy-21-LTR_DR. The consensus sequence was reconstructed based on multiple alignment of five proviral copies (they are less than 1% divergent from the consensus sequence). Gypsy-21_DR retrotransposons are characterized by 4-bp target site duplications. The internal portion contains two ORFs encoding the 562-aa Gypsy-21_DR1p gag (pos. 86-1771) and 1585-aa Gypsy-21_DR2p pol proteins (pos. 1672-6426) composed of the protease, reverse transcriptase, and integrase domains. The second protein, including the protease domain, does not start from Met. Presumably, the gag-pol fusion protein is formed originally due to a ribosomal frame shift. Gypsy-21_DR1p: MEIIEQENIKVPNSLIVSGTTDTESDIDLTEHLGKYGCINRIVRIDSPGSPHHKNVIVEYESGS AVKILEPQLPFIFENPHQADIQYEIKALSSIYVETVTTSATKGYMEKLKSIAKLSGRRFEDLLQ EELSKCREPVAQADDDTTDVASDLRSGIPQVNPAQGSQEMPMGAAFVPLVGTNVPNVNPPEIQR VVVEHIVKSEEATSHMHAPLKLRFFSGRSPRPANEVDYEIWHNSVELMLQDPAVSDLVRSRKII DSLLPPASDIVRTLGLHATPRAYLDLLDSAFGTVEDGDELFAKFLSTMQNAGEKPSQFLQRLQV ALAQAIRRGGVPSSEADRHLVRQFCRGCWDDALISELQLEQKKANPPSFSELLLLLRTAEDKIS TKELRMRKHLGASKLRTSSYSVCASSDEVVSTQTIVSDLKKQIAELQNQVEGLTKAKKQAQCAP EGRVCDLQKQVVGLKGQIVEAKPSKSAKTQSATRMNKTQSVQTNLSEVVSSVPLKQLSKPKPWY CFHCGEDSHIASTCDRDANPALVAAKRKLLKERQSSWEAQMGSSHRTPLK Gypsy-21_DR2p: CKSCLGSCQKKAFKRAAVVLGGTNGVIPSHSFKIESAPVVGQTGAEKCSRRPKNSKFCNHHASS RSKPFILPKGLVGAKCTAEVSIAGQKCSVLFDTGSQVTTVSQTYYEQNLSHLEIKPLEHLEVEA ANGQFVPYLGYVEIDVVFPKEFLGAEITLTTLALVTADTSSNVQSPVLIGTNTLDLAYEAQFDS EVAQPSHVLPYGFKVVMNVLRHRFKLKTNSMIGLVRAQGTKPEVVPAGQTLVLEGSINSRELSS DKWVLMEAPLQSSLPGGLLCASSLVTLSQRSFQKIPVILKNETEHDILVPAKSVIAELYSLQSV NVKEPATESNSQGKELPPYTLDFGDSPIPNEWKERISQKLCAMSDVFALHDLDFGKTDKVTHRI RLHDQTPFKQRARPIHPQDFDAVRKHLQELLDAGVIRESESPFSSPIVVVRKKNGDVRLCVDYR KLNLQTIKDAYALPNLEETFSALTGSRWFSVLDLKSGYYQIEVEESDKHKTAFVCPLGFWEFNR MPQGVTNAPSTFQRLMERCMSDVHLKEVVVFLDDLIVFSDTLEEHERRLLRVLHRLREFGLKLS LEKCRFFQTSVKYLGHIVSSSGVETDPDKVAALKTWPVPKNLKELRSFLGFSGYYRRFIRDYAA IVKPLNDLTSGYPPHRKSSKVRERRDYHNPKEPFGSRWSANCQKAFEAIIEALTTAPVLGFADP KLPYVLHTDASTVGLGAALYQEQEGQLKVIAYASRGLSRSEARYPAHKLEFLALKWAVTEKFYD YLYGNQFTVVTDSNPLTYVLTSAKLDSTSYRWLSALSAFSFKLQYRAGKQNIDADSLSRLPHGA LKNDVASQKEQERIRQFALNHLFDDVQTMSPEVIQAICDKHIVYCKSVDCGVTPMTLVESLAIH VDAIPGSFDHDENNFGCPVVPTFGENDLKEKQRSDPIIREVIVQLETGETIPPLVRKELPMLSL LMRELSKLELQNGILYRRRHDGDTITYQLVLPESLRSMVLTCLHDDMGHLGVDRTLDLVRSRFY WPKMLVDIERKIRTCPRCVCRKSLPDHAAPLVNIQVTRPLELVCMDFLSIEPDSRNTKDVLVIT DFFTKYAVAVPTCNQKSRTVAKALWENFIVHYGIPEKLHSDQGADFESKTIKELCELMGIHKIR TTPYHPRGNPVERFNRTLLNMLGTLKKCDKVHWSSFVKPLVHAYNCTKHDSTGFSPYELMFGRQ PRLPIDLAFDVPLNREEYKTHSQFVHDLKCRLKKTYDLAMKSTAKVGERNKARFDKHVVESVLD IGDRVLVKNVHLRGKQKLADKWESLVYVVVKRAGDLPVYTVKPEGKEGPLRTLHRDLLLPCDLL QLPEEVLALPSTRKRPPTRKNPCNKVQDQVDFDSDDDDSSLELMHSDLLIPTNITFTEVYEAGT GPQTEVPSIPIVQDTVGHISTENLPVSADSPIECLPEIENFQIDNAPTLNVLPVDDPDVVESDE NLPAEVPVNLGDQQIPVEETVKVSEHETETKKHENDGNVIRKSDRVRQKPRIFTYPELGNPLVS IVQSLFQSLSTAVTDSIIENNSFTKAADAVVTQPVSFMHRDVHRVNGGGA
|
|||
|
Derived: [1] (consensus) |
|||
|
Download Sequence - Format: IG, EMBL, FASTA |
|||
|
References: |
|||