Repbase Reports

2001, Volume 1, Issue 3
March 31, 2001
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 34

ATLINE1_5

ATLINE1_5, non-LTR retrotransposon - a fossil.

Submitted:
31-Mar-2001
Accepted:
31-Mar-2001
Key Words:
non-LTR retrotransposon; L1 superfamily; poly(A) tail; ORF1; ORF2; reverse transcriptase; ATLINE1_5
Source:
thale cress
Organism:
Arabidopsis thaliana
Taxonomy:
Eukaryota; Plantae; Embryobionta; Magnoliophyta; Magnoliopsida; Dilleniidae; Capparales; Brassicaceae
[1] Authors:
Kapitonov,V. and Jurka,J.
Title:
ATLINE1_5, a non-LTR retrotransposon.
Journal:
Repbase Reports 1:(3) p. 34 (2001)
Abstract:
ATLINE1_5 is a non-LTR retrotransposon. Its individual copies are ~88% identical to each other. There are only 3 copies of ATLINE1_5 present in the genome. ATLINE1_5 belongs to the L1 superfamily of non-LTR retrotransposons, its copies are flanked by ~15-bp target site duplications. Two proteins, ATLINE1_5p1 and ATLINE1_5p2, are encoded by ORF1 (position 431-2546) and ORF2 (position 2691-6710), respectively. Both ORFs are saturated by several false stop codons. Stop codons at positions 1019 and 5675 are replaced by R in the corresponding protein sequences, based on their comparison with other homologous proteins. ATLINE1_5p1 (771 aa): MSKRMRPSWYRDSPPKQLPYAFVPEEDDDVVILPQVDNSALLGRLQLSLVGRMFHQGGRSTEALLSFLPN IWDVEGRVRGVSLGDSRFQFFFESETDLQKVLNKRPCHFSKWSFALERWKSHIGISFPDTMTFWIKTEGI PTEFWEEEVLRNFGASIGAVRRVDSSKGRLQISVKADVPFRFNKNAQLPNGEVVKVKLFYEKLFGWCTYC RRICHELDQCPLLDENQRVALMAEDQRHSHLDGSVDGRS*SLSLSQGGTVVPRNGPGERVVSLPEGPQI* KSNPSYGPNRLAANNPPLSKSSSRFGGSRSRRHPHPPSSRRLPTDRAPPPNRASGSVRRSSPPEGRKRRY GVSFSQEKIVEKPSKGNQDLARVVPSSSLPPSTIPGELRSSPHLSDSQITISDPLLAPSRAKQRTSSPAY VRERPFRLNLSKKHSASEKGKGKVGDPPMSLGDTTPGSSPSAKKSLNFDLDPSSKITTTPSSVNHVVQVP SPPGKRLSWYEMKVEEDEANARALGAGPDTILAAKFSQVVSFASPVVDVPALPDRQSHSPPLSGGSPQAE WDKNLNPLSEALNLDWTAEDEAAYHALEPPFTTGEEDVAGKNTLRIESHVSSLERLETQSSISLASTQRP TPSKVLEGATENGGDVENRDQLLSLDGLLSLEIDFVSTLGGPKKGVKKKRAETHSRKGNTTSGKVQSSLG LLVNLASKKIQNVKGRSPSKRLLLKGGASKSRAAKRPSSAPRSSIFPSSKVKSPGSIGGSVGSMEPPDTN P ATLINE1_5p2 contains the reverse transcriptase and endonuclease domains. ATLINE1_5p2 (1402 aa): MSKDVLRVSVSCSKVGLPSQELLNVRLRLLVQASSRHPKSNLRGLLVARWGPWNPPTLTHEDLSVEDMCR MYSPGFLFLSETKNDLLYLQNMQVSLGFDCLQTVDPIGNSGGLALLYSNEFPVTVVFLNDQLIDIETIID GNRVCITFVYGDPNVQYRELVWERLTRIGIIRSDPWFMIGDFNEITGNHEKKGGKSWSESSFLPFRCMIE NCGMIEIPSHDNLFSWVGRRSCGVTGRRVRKVIKARLDRAMANEEWHNIFSHSNVEYVKLWGSDHRPLLG SIQNSPQRNFKQFSFDKRWFGKSGFKESVYEGWNLSSHDGDFFSQKVKSCRKSISTWKKASSTNSEKKIV DLQDQIDRAQEDEAISAEDLLALKWKLCDAYREEEIFWRQKSRELWYKSGDNNTNFFHAITKQRRAKNKI IGLLNQDGLWIDNEVGIENLEVDYFKDLVTTSNPQDFHSAIRDVPVIISEEINKNLTKDISPAEVKRALF SLNPDKAPGPDGMTSFFYQKFWDLTGPDLVIIVQNFLSSGAFDKQLNETNICLIPKVDRPRKMVEFRPIS LCNVSYKVISKVLSFRLKKLLPDLISETQSAFVAGRLITDNILIAQENFHALRNNPACRKKFMAIKTDMS KAYDRVEWCFLQALMLKMGFSQKWVDLITFCISSVTYKVLVNGSPRGFIKPSRGIRQGDPISPFLFILCT EALVASLKDAEWHGRIQGLQISRASPSTSHLLFADDSLFFCRADPVQGQEIIKILRTYGEASGQQLNSAK SSILFGHDVENTIRNNIKVAIGIHKDGGMGSYLGLPEKIHGSKVQVFSFVRDRLQKRLNTWTAKFLSKGD KEVLIKSVAQALPTYVMSCFLLPKAIRSKLSNAIANVWWKTNENSNGIHWIAWDTLCKPHSEGGIGFRTL EEFNLALLAKQLWRLIRFPNSLLSRILRGRYFRFSDPLHIGASFRPSYGWRSIMAAKPLLLLGLRRTIGS GMLTRVWEDPWIPSIPARPAKSILDTRDPHLYVNDLIDQNTQSWKIDRLTSLIDPVDIPLILGIRPSRTY LSDGYSWPYTKSGNYSVKSGYWAARDLSRPICDPPSQGPGVTALQAQVWKLKTTRKLKHFAWQCISGCLS TCQRLAYRHMGTDKSCPRCGASEESINHLLFHCPPSRQIWALSPIPSSGSLFPRNSLFYNFDFFLWRGRE FDIEEDVIALFPWIIWYIWKSRNRFIFENVREPPPETLALALQEAAAWKQAMLIDEDHVDAPPPPSFAEA PPAELVECQFDASWHAEDSLSGFGWVFVRHDVVLHLGLKSERRSLSPLHAEFDSLLWAMESLISIGMTTG AFASDCANLISILDNQDEWPSFAAEIVSYRSLVCLFSSFSIRFVPRSFNFRADCLAKKARVRNCIFSHAV GS There are no elements in the genome that are more than 81% identical to ATLINE1_5. Given the well preserved ORF1 and ORF2, ATLINE1_5 is a relatively young retrotransposon, which is represented just by one copy in the genome.
Derived:
Positions 83766 90600 Accession No AC007047 GenBank (rel. 124.0)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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