Repbase Reports |
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| 2004, Volume 4, Issue 9 |
| September 30, 2004 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 227 |
GYPSY2-I_CB |
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Caenorhabditis briggsae family of LTR retrotransposons - a consensus. |
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Submitted: 00-Sep-2004 |
Accepted: 30-Sep-2004 |
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Key Words: LTR; Gypsy clade; CER; 4bp TSDs; Cb000348; gag; AP protease; reverse transcriptase; RNase-H; integrase; GYPSY2-LTR_CB; GYPSY2-I_CB |
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Source: consensus |
Organism: Caenorhabditis briggsae |
Taxonomy: Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Pseudocoelomata; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis |
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| [1] |
Authors: Pavlicek,A. and Jurka,J. |
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Title: GYPSY2_CB - a family of autonomous LTR retrotransposons. |
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Journal: Repbase Reports 4:(9) p.227 (2004) |
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Abstract: Individual GYPSY2-I_CB copies are 97% identical to the consensus. GYPSY2-I_CB is similar to CER3-I_CE and CER2-I_CE from C. elegans. The LTRs are listed as GYPSY2-LTR_CB and flanked by 4bp target duplications. The consensus is taken from the single elements with long ORFs found in the genome. GYPSY2-I_CB_ORF: 442-1993 (517 aa) gag-like MTEQIIFEVATAMNTVASVKQCVVSDLQSVHQKIQEIASLSIDRLEAVEDRVAENTDRINTLFANRADNS GTPSTHNSAQTSHPPSRRASPTPPNEILGSSINVLGLKIGSRIPIFSGAPAENFSTFVRSFMDHVKAVNP ALEESSVRAVFLTYLTEFARDKAEELLEKHPSYTCQQLVEEMRKTFEDPNRAEMERQQLRQCSQRTDESV DDFCTRVRKLALSAHAGNSRDFIQEKAKEAFIDGLLFNLKFLVKGESPTNFQEAQNSAMKFELLLKEAAR SNTIAPQGLAVIPAPAPAQNSPWSKPKRECFYCGIPGHFARECRRKIADQAKGIFQKTNKVSNLRSQTRS FPQRNPVDNHQIFSNNPGVQAIQPVVSTIHAQMEAMQTELEVRQNQINALIKRNDELTTNPGNHQVPNRR VSCLRWSQTYLLILITFMSLFTQVAAISPLVCMPHTPQSYLRLPAPLDCSRATGHEPHPVTQKELTIFRP NTIAYEANGTLCKIVKRITKYSVNFSE GYPSY2-I_CB_ORF: 2052-3102 (350 aa) pol? MKKFLHCSHGDLVPFNGIYKTLNDHILTWPSAPFSAFLGTQTAESTNCVMMPTRVMTRFGKETPESPAGS MVGCRFSSGFCNTREGAAFQWTPNPKQECKYLELRTMKGFMTKNIWVSTEKEFAISFDQNNTRLLDCGRK LVISDQGYGIALPNRNKRSNSVDELTNFVTSNQLAAQLLAVEEVVLETTAAWFAGNFMSWCSSFNAVAAA TRAAVASNPTLAARQMLKKENIFAKYIGNDVLSLQVCSPVPQDSYEFVPFTKTCYSKPALRVRLPKNTSI VTFVDLTTRVITNRAHPVDCSLVTSFQYVSNKTLYSLNPFTLELKTDTNFQTMTIPSRSWICYSRTSNLP GYPSY2-I_CB_ORF: 3366-6717 (1117 aa) pol-like MILVSNVLTPYLPFRQPAQPQFERPQSPDGQVCDYVTLTERLRSPRINALAHPTEYFSAVVPLKANGINC WALIDTGASFTVAGQGILHLLGIPRLQEPLSYMAVGLGNNEVKMAGSAVVKFQIGSHVLFQNTHFTTGQC TPGGPRDYDFIIGNDAHYMVTDVELPSEPAQRISESTTLQMIQDFRNETTKWMTIDTPITSVPNGKRNPN VATLSRFDCDRIFALYIVKESAGGNLHLNPAHRELVSYDRPDLYTVHLTRHSEDILNPGPPNPANYYIGD LLVVLSLKRRPGAKLNEIKRDFVDILDMNKCHFWQVNKFALVQRKVEKDQPLWKMDDLKEPIDPRRKLKM PWKAECIGYNQNQVVEAKIALFKELHPQDQKCTAADILVPVLEPASTLRSLLPGDARHAVITATNVQPPI VPLKPTVTAVRVLPGKFRKYISIAPNAFKGAESDPDYDLGGKALLWTARFGLAATLAIANKGRDTTTYST TITESETTGRRSTVTFTIRRPSTAAPVSSWTRSTAFKMDISPGGTCDLEVESATLINTQLTIRAKFTFES QSRINEKNLLNQNAVVWQQLDDNLHQLRTFPEPEDWLKVPVDSPSGNVLIALTGGPEIDGIMPWDKTDVV DFAGSAVKLSEEQSYYANTLAKTKIAGVIANAPPGVGKTLMVAGAAIHAIRETNDLRSIQTLTGMTNVSV LPMVKTLRTLDPETRYPPVRLISESHREHLDPALRTEIDYPILWIKVFKDLLHRIDPSTAVATIRENPDL MSAIQHLHAKKIDPEEFAHHFIRKAVAKGPNSDRNTTPKAELFRKLYNPRIVVGTVASVLESFKTPDWTW LRENVSAIQVDEASQLPLYALAALALMFQRARLALVGDIHQLPPFEDSDLPKDIAAFAISRVLQEAIKRR TLPIIDLTVGRRCPPQVTRMYNELFYNQRLTSLWSPEKEAELRAFTAALKFGNDFPIQILDLQSSHTQSG TSLTNIEEAKAAVRIARTIQTRVGTNDIGILCFYKAQAGEVAALLGDAPFYVGTIDGSQGHEFQAVIILT TRTSSFRDSEFIEDCRRINVAISRTKRICCIIVDRPKVTTNGTWSRLIRRIPHEAKSNFSVMTARWL
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Derived: [1] (Consensus) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References: |
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