Repbase Reports

2004, Volume 4, Issue 12
December 31, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 317

Gypsy12-I_DR

An internal portions of the Gypsy12_DR LTR retrotransposon - a fossilized copy.

Submitted:
00-Dec-2004
Accepted:
31-Dec-2004
Key Words:
LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; reverse transcriptase; integrase; Gypsy12_DR; Gypsy12-LTR_DR; Gypsy12-I_DR
Source:
Danio rerio
Organism:
Danio rerio
Taxonomy:
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy12_DR, an LTR retrotransposon from zebrafish
Journal:
Repbase Reports 4:(12) p.317 (2004)
Abstract:
Gypsy12-I_DR is an internal portion of the Gypsy12_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy12-LTR_DR. Gypsy12_DR is characterized by 4-bp target site duplications. The internal portion encodes two proteins: the 469-aa gag Gypsy12_DR1p (pos. 153-1559) and 1543-aa polyprotein (pos. 1475-6105, conceptual translation) composed of the protease, reverse transcriptase, and integrase domains. PBS is identical to that in Gypsy9_DR. The internal portion is flanked by 99% LTRs. Gypsy12-I_DR1p: MDISQTAQWSTEENINSSRAIVLSNVPLNTSDETIEKVLNTVKVFGRTQIHGRRGDVTGKHLFV LVETRADLDPSTIPPEIGIESEAGPWPVHFVGRLQVQNPAPENDTFQSKLLTLMQQEGKSMDEV KAILMGEHSPKSDINVDLVDAIGKLVDRCNQASNDGPSYRKLRLFSGLKPVPPGEEEYEIWMEQ AAQMISEWQCTEASKKQRIVESLRGPAADIVRFLKVSQPSATATEYLAALETAYGTTECGPDLM AKFRHTYQDNGEKLSAFLYRLDKLLHRALLKGGIDVAGINKARMEQLIKGALTNDMVALRIRMT HTLQNPPSFTQLMKEIREEEHWVAARENVKASVATVISPQSDGPSELQSLKKEVKELSSQMSHL LNVATATCASECAPQKTSSKNSESVKRDKSQPTKLTQQPVPGIFCYKCGEDGHKKWECKGQEDL RKVNQKLIKMHRLQGNWAGVQ Gypsy12-I_DR2p: MQGTRGPQESKSKADQNASFAGKLGRSSVKERHGAPGTTRSNCDSFLLDASKPRLPEGLIGPVS EVPVQIEGVYAKALLDSGSQVTLLYRSFYDTYLKHLELQPVENLEIWGLSSHKYPYDGYLPLRL EFTESVAGVHQIIDTLAIVCPDPVKREGIAILLGTNTSLVKKLLESCRKQAGEEFLNVLTIHPV IREAFETIQLTDFSQDDSDTHGTVWFIKHNPVVLKPNQVRQLPGLLKFPGQSTESLVLVDRVAD SDTSSEHLDVRPELHAASVVSSRQVTVTVRNMSNREIWVKRGTPLAHVLPVSLVPQLTAKQPPV QNPLSPASFDFGDSPMPEEAKQSLREKMMQRKDVFSLHEWDVGCSKSTTHEIRLNDSRPFRERS RRLAPADLEDVRLHLQELQSSGIISESRSPYASPIVVVRKKSGKVRMCVDYRTLNQRTTPDQYT VPRIEDALHSLSGSKWFSVLDLRSGYYQIPMSDADKEKTAFICPLGFYQFERMPQGICGAPATF QRVMERTVGDMNFLEVLVYLDDLIVFGRTIDEHEERLLKVLDRLSDEGLKISLDKCQFGRTSVN YVGHIVSQDGISTDPSKIEAVVSWPKPQTVTELRSFLGFCGYYRRFVKDFSKFCRPLNELLKGY PSTRKNRDSLVCNTKPCYKSSEPFGSRWSAQCDTAFETLKKCLTQAPVLAFADVQKPYVLHVDA SMDGLGGVLYQEHESGLRPVAFISRSLSPSERNYPAHKLEFLALKWAVVDRLHDYLYGVPFEVR TDNNPLTYITKSAKLDAAGHRWLSALTTYNFSLKYRPGRRNVDADALSRRPHTYRSEDDEWQEI PAVGVRTFCQAVSLEKRAENGFYTCVVKQAGAHMSAVPKAYSHVMEVAADHLPLFSSSDLQTAQ RNDSLLGEVWKAVCDKKPASSIRSSHPSMKILKREWEKLVVNNGMLYRIVRQSNHKVKQQLVLP KQFHSSVLKSLHDDIGHLGFEKSYGLVRDRFYWPHMKPDVESYCKTCERCIKRKTLPQRAAPLS HMQSSGPLDLVCIDFLSIEADSRNVCNVLVVTDHYTRYAQAFPTRDQKASTVAKTLWEKYFIHY GLPTRIHSDQGRDFESQLVSEMLTMLGIKKSRTSPYHPQGDPHLRDLTELXNMLGTLQPSQKSK WSQHIARLVHAYNCTVNEATGFSPYFLMFGREARLPVDVCFGVSADSSSSGSYSKYVSKMKQEL QAAYQLAQVSSEKMNQSNKARYDQKVRYHSLSVGDRVLIRNLGLKGKQKLADRWSENPYVVESQ LSGIPVYRLKPVDGNGPIKVMHRNHLLPLGQEVRLKPKVDLGPTSLPKNLRHRSVKDKRKTAQS ENPPIAVDVFSREHDSSDSDSEYGCYVEDMAPISSESAQEIQGETPEQAVECLDYSNAHRVSEI PVIPCQSETSEFQLTDADRNTDVVDDVMTEVSESTSQTTVQTTDNETQPEIVPFEVRRSNRERK PSTRFTYDKLGVPYLHSVSSKCCGINALTTDVLNVYGSLNKSHAWWCNPNALCKTCKNRPVLVP CKQMVAM
Derived:
Positions 22688544 22682376 Accession No chr8 Zebrafish.v4
Download Sequence - Format:
IG, EMBL, FASTA
References:

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