Repbase Reports

2004, Volume 4, Issue 1
January 31, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 27

Gypsy2-I_ST

Internal portion of Gypsy2_ST retrotransposon.

Submitted:
31-Jan-2004
Accepted:
31-Jan-2004
Key Words:
LTR; Gypsy retrotransposon; Tf1 group; 5-bp TSD; gag; protease; reverse transcripatase; RNase H; chromodomain; Gypsy2-LTR_ST; Gypsy2-I_ST
Source:
Silurana tropicalis (Xenopus tropicalis)
Organism:
Silurana tropicalis
Taxonomy:
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Silurana
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy2_ST, a self-primed Gypsy LTR retrotransposon from the frog Silurana tropicalis.
Journal:
Repbase Reports 4:(1) p. 27 (2004)
Abstract:
Gypsy2-I_ST is an internal portion of a young Gypsy2_ST LTR retrotransposon. The internal sequence is flanked by identical Gypsy2-LTR_SR long terminal repeats. Gypsy2_ST belongs to the Tf1 group of self-primed Gypsy LTR retrotransposons. Its reverse transcription is primed by a heteroduplex formed between a 10-bp portion of PBS (Gypsy2-I_ST, pos. 3-12) and the 10-bp 5' end of the Gypsy2_ST mRNA (Gypsy2-LTR_ST, pos. 193-202). Gypsy2_ST encodes a 1499-aa Gypsy2_STp polyprotein (Gypsy2-I_ST, pos. 23-4321, and Gypsy2-LTR_ST, pos. 1-198) composed of gag (pos. 100-200), protease (pos. 350-450), reverse transcriptase (pos. 560-730), RNase H (pos. 820-950), integrase (pos. 1060-1220) and chromodomain (pos. 1360-1410). Gypsy2_STp: MDPAEESAASPFDQISQQLASLTQAVRDLQGSYQHLQTQVQGLSDPSNPVPPAAPAMSASPSAEYTGRPF EPKVPLPDKFSGDRRQFRTFINSCRLLFSLQPYTFSSEQTKVGVMISLLSGEPQTWAHRLLERRSSILID ANTFIHAMAQLYDDPHREVTAEAALRSLTQGKRPVEEYVSDFRRYAADTEWNTQALKHQFRIGLSETLKD ELAHVGVPQGLEELIDLSVQIDRRLRERRAERLQPSSMSWLSPRTSGNLQAAAHAGDTSEPMQIGLVRSA LSSEERTRRRQLNLCLYCGQPGHFLKDCPTRPKGKTRCPAMSPCVTFREPTSLSFPVVLQWPQDCLKSTV VIDSGACGCFMDLDFIKEHAVPTRPKMQPLSLRTADGSPITSGPVTLETLPLEVFLDSKHIETISFDVVA SPLFPILLGFPWLRLHNPSINWNTGDIHFDSKTCSSHLLEKSHSMAVAPATDTQFAVVPNYLHEFKDVFD EKGADTLPPHRVYDCPIDLLPGAAIPFGRIYPLSEPELIVLKKYIDENLEKGFICPSTSPAGAGIFFVEK KDHSLRPCIDYRQLNLITVKNRYPLPLIPELFQNLREAKIFSKLDLRGAYNLVRIRKGDEWKTAFRSRYG HFEYLVMPFGLCNAPATFQHLVNDIFRDFLDQFVIVYLDDILVFSSSIKEHEIHMRKVFSRLREHSLFAK LEKCEFHKTSIEFLGFVISTDGILMDPKKVSAVLNWPVPTSRKATQRFIGFSNFYRRFIRNFSKIISPIT DLTSTTKRFQWSSQAQSAFDKLKELFTSAPILKHPDPSLPFVVEVDASETAVGAVLSQRSGLQNFLHPVA FFSKKLSPSEKNYDVSDRELLAIKVAFEEWRQYLEGSSHPILIFSDHRNLEYLRTAKRLRPRQARWALFF SRFNFHITYRPGSQNHKADALSRMFHDENVETQSDTILRPQNFLLLQTDLVAKMLEQSSSVVPSDQLRNK DGLLFFKDRIFVPEALRLDVLRLIHDHPLAGHMGGRKTVDLAKRSFYWPGMIRDCNQYVLSCEVCARFKE SRTKHLGLLHPLPIPDRLWGSVSLDFIVELPHSHGFNTIFVVVDRLSKMAHFIPLTSIPSAVTTAEVFIR EVVRLHGVPDEIISDRGVQFTSRFWRTLCNALKIKLALSTAFHPESNGQTERTNQTLEQYLRCFSSFLQD NWYELLPLAEFAYNNSVHSSIKQTPFYANFGFHPQVLPNFPKEVSVPAVQDRLSFISNNVQLIQSAMKQA QRNFKFFADRKRRSDPEFKLGDSVWLSTRHIKLPCPTKKLGQKFVGPFPITKQVNEVAFKLKLPSSYKIH PVFHAALLKPVVKNRFVRRSAKPPDPVPIEGVEEFEVQSILDSRIRRGRLQYLIQWKGYSPEENSWESAS DVHAPLLVRSFHKKHPEKPASTCARRSHLGGGQCQAIRTARAKPPVQRMRDYSRAPVRICARALTRSRRR AHASAHFRAKTGACASRLKRRRGLQSSAR Gypsy2_ST and Gypsy1_ST are highly diverged from each other, there is only 46% identity between the Gypsy2_ST and Gypsy1_ST pol proteins. Surprisingly, in both retrotransposons, the ~63-aa C terminal portions of the pol proteins are encoded by the 3' proviral LTRs, and the stop codons are in the regions complementary to the PBSs.
Derived:
Positions 90354 86034 Accession No AC146867 GenBank
Download Sequence - Format:
IG, EMBL, FASTA
References:

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