Repbase Reports

2001, Volume 1, Issue 4
April 30, 2001
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 15

ATLINE1_6

ATLINE1_6, non-LTR retrotransposon - a fossil.

Submitted:
30-Apr-2001
Accepted:
30-Apr-2001
Key Words:
non-LTR retrotransposon; L1 superfamily; poly(A) tail; ORF1; ORF2; reverse transcriptase; ATLINE1_6
Source:
thale cress
Organism:
Arabidopsis thaliana
Taxonomy:
Eukaryota; Plantae; Embryobionta; Magnoliophyta; Magnoliopsida; Dilleniidae; Capparales; Brassicaceae
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
ATLINE1_6, a family of non-LTR retrotransposons.
Journal:
Repbase Reports 1:(4) p.15 (2001)
Abstract:
ATLINE1_6 belongs to the L1 superfamily of non-LTR retrotransposons. It is a one-copy family; there are no other genomic retroelements that are more than 75% identical to ATLINE1_6. ATLINE1_6 has been inserted in the A. thaliana genome relatively recently, a few millions of years ago. It is flanked by a perfect 15-bp TSD. Two proteins, ATLINE1_6p1 and ATLINE1_6p2, are encoded by ORF1 (position 604-1416) and ORF2 (position 1537-5480, conceptual translation), respectively. ATLINE1_6p1 (271 aa): MGRLTNPSVQRLWSMFPFLSNRCNLRGKALGSDLGKGCFQFKFDYEEDLLKVLDNRPYHYDQWMVILQRW EPIISESFPCKIPFWIELQGLPKHFWQPEMLKTIGEELGEILDMEITSSAAKLRVLVDGLQPLTKETIVD FRDGSETTVFLVYKNLKNHCHHCFRLSHETKLCPGLTESRGKDSVSVQPAVSQDSRGGSRNYYTPKDNFT APRLSHHDCERTHYSQEVSNRQRNSHPSSPVLSNHFSADRGRTQRERRGPLVEVTLWQFLR Presumably ORF1 is incomplete because of a ~1-kb deletion that has happened after insertion of the retrotransposon in the genome. ORF2 is saturated by 4 false stop codons and one short indel; they are marked by X in the next protein sequences. ATLINE1_6p2 (1322 aa): MTVQRIKEIRKKIFPDLLFLMETKNSSETVLQSLQWLDYPSHHLVPPESPAAGGLGLFWKSSVEVEIIHS SLHYIDTKIKAKGRTFYSTFLYGEPDRTKRLQIWNALQELSSSREGPWFITGDFNDIVNSAEKSGGPDRP EGSFTDLRSFMSSCDLYDLKHTGNFLSWRGRRHSHLVRCRLDRAMANSDWIIAYPSGRSEYLRFEGSDHR PLVTSFDHVQKKTKNIFRYDRTLKDNPEISKLMNETWKSNPSAKVDYRLHLCRAALLNWSKEHHLNSQKE ILSLRVQLEEALTDDAATQDSVDLLNQNLLLAYRKEETFWKQRSRNLWLALGDKNSCFFHAATNSRRAIN TISVIENSAGTSVYEDSEIIETISDYFQDIFTSQEGDRTSVVAEALSPCITTDMNNTLISLPTVAEIKQA CLSIHPDKAPGRDGFSASFFQSNWSTVSEEITAEVQAFFISEILPQKINHTHVRLIPKIPAPQKVSDYRP IALCSVYYKIIAKLLAKRLQPILHSCISENQSAFVPQRAISDNVLITHEALHYLKNSGALVNCYMAVKTD MSKAYDRLEWDFVKAALEEMGFHHHFVGWIMXCISTISYSFLLNGQAKGLVVPERGIRQGDPLSPYIFII CSEVLSRMCLKAQENGSLPGIRVAMGCPRVNHLLFADDTMFFCRVDPKSCLKLKSILHKYELASGQKINQ AKYSITFSAKTPPAVRERVKQILLIQKEGGQGKYLGLPELFGRKKKDLFTAIVDRIKQRALSWSSRFLSS AGKLTMLKSVLSTMPTYTMSCFQLPLSLCKRIQSTLTRFWWDSKPDQRKMSWISWQKMTLSFKSGGLGFR DVQTFNKALLAKLSWRLLQNPSCLLAKLLLGKYCKHSTLLDCKVSNSASHGWRSICLGRDVLSLQLGRLI GNGLTTPIWRAPWLSLTKSXAPMGPPTEASHLLVVSDLLIAGTTNWNKELIRQLLPVYEKDILLLKPSLL GAADRWAWLPTSSGLYAANSGYFEALKETASLENPPNHDLVKNFNWRSNIWGLQTSPKTKLYLWXXXALP VGSNLLLRHISDTAKCPRCEQAESTLHLFFHCSFARRIWDLAPFSIRPNFDGIRSFKEGLVLANTLICLP PTGIGSGPLFPWLLWTIWTASXSSINAKFWKKKPFTWLSXGQRNGKRPKPPKIFTAGLPRNPLHHRLVTG DQICYTDVAWLPDCRAGFGWIFKSAQDFQLFAGNSSASDVGSPLIAETLVTLADVRVACESDIKAISFAS DSQIIVKALNQKLQVKELHGILHDILSLSSSFDACTFTFINREFNHQADALAKRALVCCMEP ATLINE1_6p2 contains the reverse transcriptase and endonuclease domains.
Derived:
Positions 34318 39842 Accession No AL161499 GenBank (rel. 126.0)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Kapitonov,V.V. and Jurka,J.
    ATLINE1_6, a family of non-LTR retrotransposons.
    Direct submission (December 13, 2001)

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