Repbase Reports |
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| 2001, Volume 1, Issue 4 |
| April 30, 2001 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 15 |
ATLINE1_6 |
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ATLINE1_6, non-LTR retrotransposon - a fossil. |
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Submitted: 30-Apr-2001 |
Accepted: 30-Apr-2001 |
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Key Words: non-LTR retrotransposon; L1 superfamily; poly(A) tail; ORF1; ORF2; reverse transcriptase; ATLINE1_6 |
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Source: thale cress |
Organism: Arabidopsis thaliana |
Taxonomy: Eukaryota; Plantae; Embryobionta; Magnoliophyta; Magnoliopsida; Dilleniidae; Capparales; Brassicaceae |
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Authors: Kapitonov,V.V. and Jurka,J. |
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Title: ATLINE1_6, a family of non-LTR retrotransposons. |
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Journal: Repbase Reports 1:(4) p.15 (2001) |
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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.
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Derived: Positions 34318 39842 Accession No AL161499 GenBank (rel. 126.0) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References:
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