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L1 Mobile Element

The sequence of a typical L1 Retrotransposon downloaded from NCBI.

LOCUS       HSU09116                6539 bp    DNA     linear   PRI 26-OCT-2005
DEFINITION  Human retrotransposable L1 element LRE2 from chromosome 1q.
ACCESSION   U09116
VERSION     U09116.1  GI:483914
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 6539)
  AUTHORS   Holmes,S.E., Dombroski,B.A., Krebs,C.M., Boehm,C.D. and
            Kazazian,H.H. Jr.
  TITLE     A new retrotransposable human L1 element from the LRE2 locus on
            chromosome 1q produces a chimaeric insertion
  JOURNAL   Nat. Genet. 7 (2), 143-148 (1994)
   PUBMED   7920631
REFERENCE   2  (bases 1 to 6539)
  AUTHORS   Holmes,S.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-APR-1994) Susan E. Holmes, Pediatrics, The Johns
            Hopkins University School of Medicine, 600 N. Wolfe Street,
            Baltimore, MD 21218, USA
FEATURES             Location/Qualifiers
     source          1..6539
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q"
     mobile_element  1..6539
                     /mobile_element_type="transposon:LRE2"
     5'UTR           1..884
     CDS             885..1901
                     /note="encodes a 40 kDa product"
                     /codon_start=1
                     /product="ORF1"
                     /protein_id="AAB60344.1"
                     /db_xref="GI:483915"
                     /translation="MGKKQNRKTGNSKTQSASPPPKERSSSPATEQSWMENDFDELRE
                     EGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELKTKARELRE
                     ECRSLRSRCDQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRL
                     IGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHII
                     VRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNF
                     QPRISFPAKLSFISEGERKYFTDKQMLRDFVTTRPTLKELLKEALNMERNNRYQPLQN
                     HAKM"
     CDS             1965..5792
                     /note="encodes a reverse transcriptase homolog"
                     /codon_start=1
                     /product="ORF2"
                     /protein_id="AAB60345.1"
                     /db_xref="GI:483916"
                     /translation="MTGSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQET
                     HLMCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG
                     SIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQK
                     VNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCK
                     RTEIITNYLSDHSAIKLELRIKNLTQSRSTTWKLNNLLLNDYWVHNEMKAEIKMFFET
                     NENKDTTYQNLWDAFKAVCRGKFIALNAYKRKQERSKIDTLTSQLKELEKQEQTHSKA
                     SRRQEITKIRAELKEIETQKTLQKINESRSWFFERINKIDRPLARLIKKKREKNQIDT
                     IKNDKGDITTDPTEIQTTIREYYKHLYANKLENLEEMDTFLDTYTLPRLKQEEVESLN
                     GPITGSEIVAIINSLPTKKSPGPDGFTAEFYQRYKEELVPFLLKLFQSIEKEGILPNS
                     FYEASIILIPKPGRDTTKKENFRPISLMNIDAKILNKILANRIQQHIKKLIHHDQVGF
                     IPGMQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDG
                     TYFKIIRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNIVLEVLARAIRQE
                     KEIKGIQLGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQA
                     FLYTNNRQTESQIMGELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNK
                     WKNIPCSWVGRINIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFIWNQKRARI
                     AKSILSQKNKAGGITLPYFKLYYKATVTKTAWYWYQNRDIDQWNRTEPSEIMPHIYNY
                     LIFDKPEKNKQWGKDSLFNKWCWENWLAICRKLKLDLFLTPYTKINSRWIKDLNVKPK
                     TIKTLEENLGITIQDIGVGKDFMSKTPKAMATKDKIDKWDLIKLKSFCTAKETTIRVN
                     RQPTTWEKIFATYSSDKGLISRIYNELKQIYKKKTNNPIKKWAKDMNRHFSKEDIYAA
                     KKHMKKCSSSLAIREMQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWD
                     CKLVQPLWKSVWRFLRDLELEIPFDPAIPLLGIYPEDYKSCCYKDTCTRMFIAALFTI
                     AKTWNQPKCPTMIDWIKKMWHIYTMEYYAAIKNDEFISFVGTWMKLETIILSKLSQEQ
                     KTKHRIFSLIGGN"
     variation       2576
                     /note="LRE2*1 allele"
                     /replace="t"
     variation       5508
                     /note="LRE2*1 allele"
                     /replace="a"
     variation       5546
                     /note="LRE2*3 allele"
                     /replace="a"
     3'UTR           5793..6035
     polyA_signal    5995..6001
                     /note="variant signal found within LRE2 3'UTR"
     variation       5999..6010
                     /note="LRE2*1 allele"
                     /replace=""
     misc_feature    6036..6539
                     /note="most of 3' flank was transcribed along with LRE2"
     misc_feature    6036..6524
                     /note="Unique Sequence Component (USC) was included in
                     readthrough transcript and forms part of chimeric
                     dystrophin insertion, GenBank Accession Number U09115"
     polyA_signal    6502..6507
                     /note="variant signal found within 3' flank (USC)"
ORIGIN      
        1 gaataggaac agctccggtc tacagctccc agcgtgagcg acgcagaaga cggtgatttc
       61 tgcatttcca tctgaggtac cgggttcatc tcactaggga gtgccagaca gtgggcgcag
      121 gccagtgtgt gtgcgcaccg tgcgcgagcc gaagcagggc gaggcattgc ctcacctggg
      181 aagcgcaagg ggtcagggag ttccctttcc gagtcaaaga aaggggtgat ggacgcacct
      241 ggaaaatcgg gtcactccca cccgaatatt gcgcttttca gaccggctta agaaacggcg
      301 caccacgaga ctatatccca cacctggctc agagggtcct acgcccacgg aatctcgctg
      361 attgctagca cagcagtctg agatcaaact gcaaggcggc aacgaggctg ggggaggggc
      421 gcccgccatt gcccaggctt gcttaggtaa acaaagcagc cgggaagctc gaactgggtg
      481 gagcccacca cagctcaagg aggcctgcct gcctctgtag gctccacctc tgggggcagg
      541 gcacagacaa acaaaaaggc agcagtaacc tctgcagact taagtgtccc tgtctgacag
      601 ctttgaagag agcagtggtt ctcccagcac gcagctggag atctgagaac gggcagactg
      661 cctcctcaag tgggtccctg acccctgacc cccgagcagc ctaactggga ggcacccccc
      721 agcaggggca cactgacacc tcacacggca gggtattcca acagacctgc agctgagggt
      781 cctgtctgtt agaaggaaaa ctaacaacca gaaaggacat ctacaccgaa aacccatctg
      841 tacatcacca tcatcaaaga ccaaaagtag ataaaaccac aaagatgggg aaaaaacaga
      901 acagaaaaac tggaaactct aaaacgcaga gcgcctctcc tcctccaaag gaacgcagtt
      961 cctcaccagc aacagaacaa agctggatgg agaatgattt tgacgagctg agagaagaag
     1021 gcttcagacg atcaaattac tctgagctac gggaggacat tcaaaccaaa ggcaaagaag
     1081 ttgaaaactt tgaaaaaaat ttagaagaat gtataactag aataaccaat acagagaagt
     1141 gcttaaagga gctgatggag ctgaaaacca aggctcgaga actacgtgaa gaatgcagaa
     1201 gcctcaggag ccgatgcgat caactggaag aaagggtatc agcaatggaa gatgaaatga
     1261 atgaaatgaa gcgagaaggg aagtttagag aaaaaagaat aaaaagaaat gagcaaagcc
     1321 tccaagaaat atgggactat gtgaaaagac caaatctacg tctgattggt gtacctgaaa
     1381 gtgatgtgga gaatggaacc aagttggaaa acactctgca ggatattatc caggagaact
     1441 tccccaatct agcaaggcag gccaacgttc agattcagga aatacagaga acgccacaaa
     1501 gatactcctc gagaagagca actccaagac acataattgt cagattcacc aaagttgaaa
     1561 tgaaggaaaa aatgttaagg gcagccagag agaaaggtcg ggttaccctc aaagggaagc
     1621 ctatcagact aacagcagat ctctcggcag aaaccctaca agccagaaga gagtgggggc
     1681 caatattcaa cattcttaaa gaaaagaatt ttcaacccag aatttcattt ccagccaaac
     1741 taagcttcat aagtgaagga gaaagaaaat actttacaga caagcaaatg ctgagagatt
     1801 ttgtcaccac caggcctacc ctaaaagagc tcctgaagga agcactaaac atggaaagga
     1861 acaaccggta ccagccgctg caaaatcatg ccaaaatgta aagaccatcg agactaggaa
     1921 gaaactgcat caactaatga gcaaaatcac cagctaacat cataatgaca ggatcaaatt
     1981 cacacataac aatattaact ttaaatataa atggactaaa ttctgcaatt aaaagacaca
     2041 gactggcaag ttggataaag agtcaagacc catcagtgtg ctgtattcag gaaacccatc
     2101 tcatgtgcag agacacacat aggctcaaaa taaaaggatg gaggaagatc taccaagcaa
     2161 atggaaaaca aaaaaaggca ggggttgcaa tcctagtctc tgataaaaca gactttaaac
     2221 caacaaagat caaaagagac aaagaaggcc attacataat ggtaaaggga tcaattcaac
     2281 aagaggagct aactatccta aatatttatg cacccaatac aggagcaccc agattcataa
     2341 agcaagtcct gagtgaccta caaagagact tagactccca cacattaata atgggagact
     2401 ttaacacccc actgtcaata ttagacagat caacgagaca gaaagtcaac aaggataccc
     2461 aggaattgaa ctcagctctg caccaagcag acctaataga catctacaga actctccacc
     2521 ccaaatcaac agaatataca tttttttcag caccacacca cacctattcc aaaatcgacc
     2581 acatagttgg aagtaaagct ctcctcagca aatgtaaaag aacagaaatt ataacaaact
     2641 atctctcaga ccacagtgca atcaaactag aactcaggat taagaatctc actcaaagcc
     2701 gctcaactac atggaaactg aacaacctgc tcctgaatga ctactgggta cataacgaaa
     2761 tgaaggcaga aataaagatg ttctttgaaa ccaacgagaa caaagacacc acataccaga
     2821 atctctggga cgcattcaaa gcagtgtgta gagggaaatt tatagcacta aatgcctaca
     2881 agagaaagca ggaaagatcc aaaattgaca ccctaacatc acaattaaaa gaactagaaa
     2941 agcaagagca aacacattca aaagctagca gaaggcaaga aataactaaa atcagagcag
     3001 aactgaagga aatagagaca caaaaaaccc ttcaaaaaat caatgaatcc aggagctggt
     3061 tttttgaaag gatcaacaaa attgatagac cgctagcaag actaataaag aaaaaaagag
     3121 agaagaatca aatagacaca ataaaaaatg ataaagggga tatcaccacc gatcccacag
     3181 aaatacaaac taccatcaga gaatactaca aacacctcta cgcaaataaa ctagaaaatc
     3241 tagaagaaat ggatacattc ctcgacacat acactctccc aagactaaaa caggaagaag
     3301 ttgaatctct gaatggacca ataacaggct ctgaaattgt ggcaataatc aatagtttac
     3361 caaccaaaaa gagtccagga ccagatggat tcacagccga attctaccag aggtacaagg
     3421 aggaactggt accattcctt ctgaaactat tccaatcaat agaaaaagag ggaatcctcc
     3481 ctaactcatt ttatgaggcc agcatcattc tgataccaaa gccgggcaga gacacaacca
     3541 aaaaagagaa ttttagacca atatccttga tgaacattga tgcaaaaatc ctcaataaaa
     3601 tactggcaaa ccgaatccag cagcacatca aaaagcttat ccaccatgat caagtgggct
     3661 tcatccctgg gatgcaaggc tggttcaata tacgcaaatc aataaatgta atccagcata
     3721 taaacagagc caaagacaaa aaccacatga ttatctcaat agatgcagaa aaagcctttg
     3781 acaaaattca acaacccttc atgctaaaaa ctctcaataa attaggtatt gatgggacgt
     3841 atttcaaaat aataagagct atctatgaca aacccacagc caatatcata ctgaatgggc
     3901 aaaaactgga agcattccct ttgaaaactg gcacaagaca gggatgccct ctctcaccgc
     3961 tcctattcaa catagtgttg gaagttctgg ccagggcaat caggcaggag aaggaaataa
     4021 agggtattca attaggaaaa gaggaagtca aattgtccct gtttgcagac gacatgattg
     4081 tttatctaga aaaccccatt gtctcagccc aaaatctcct taagctgata agcaacttca
     4141 gcaaagtctc aggatacaaa atcaatgtac aaaaatcaca agcattctta tacaccaaca
     4201 acagacaaac agagagccaa atcatgggtg aactcccatt cacaattgct tcaaagagga
     4261 taaaatacct aggaatccaa cttacaaggg atgtgaagga cctcttcaag gagaactaca
     4321 aaccactgct caaggaaata aaagaggaca caaacaaatg gaagaacatt ccatgctcat
     4381 gggtaggaag aatcaatatc gtgaaaatgg ccatactgcc caaggtaatt tacagattca
     4441 atgccatccc catcaagcta ccaatgactt tcttcacaga attggaaaaa actactttaa
     4501 agttcatatg gaaccaaaaa agagcccgca ttgccaagtc aatcctaagc caaaagaaca
     4561 aagctggagg catcacacta ccttacttca aactatacta caaggctaca gtaaccaaaa
     4621 cagcatggta ctggtaccaa aacagagata tagatcaatg gaacagaaca gagccctcag
     4681 aaataatgcc acatatctac aactatctga tctttgacaa acctgagaaa aacaagcaat
     4741 ggggaaagga ttccctattt aataaatggt gctgggaaaa ctggctagcc atatgtagaa
     4801 agctgaaact ggatctcttc cttacacctt atacaaaaat caattcaaga tggattaaag
     4861 atttaaacgt taaacctaaa accataaaaa ccctagaaga aaacctaggc attaccattc
     4921 aggacatagg cgtgggcaag gacttcatgt ccaaaacacc aaaagcaatg gcaacaaaag
     4981 acaaaattga caaatgggat ctaattaaac taaagagctt ctgcacagca aaagaaacta
     5041 ccatcagagt gaacaggcaa cctacaacat gggagaaaat tttcgcaacc tactcatctg
     5101 acaaagggct aatatccaga atctacaatg aactcaaaca aatttacaag aaaaaaacaa
     5161 acaaccccat caaaaagtgg gcgaaggaca tgaacagaca cttctcaaaa gaagacattt
     5221 atgcagccaa aaaacacatg aagaaatgct catcatcact ggccatcaga gaaatgcaaa
     5281 tcaaaaccac tatgagatat catctcacac cagttagaat ggcaatcatt aaaaagtcag
     5341 gaaacaacag gtgctggaga ggatgcggag aaataggaac acttttacac tgttggtggg
     5401 actgtaaact agttcaacca ttgtggaagt cagtgtggcg attcctcagg gatctagaac
     5461 tagaaatacc atttgaccca gccatcccat tactgggtat atacccagag gactataaat
     5521 catgctgcta taaagacaca tgcactcgta tgtttattgc ggcactattc acaatagcaa
     5581 aaacttggaa ccaacccaaa tgtccaacaa tgatagactg gattaagaaa atgtggcaca
     5641 tatacaccat ggaatattat gcagccataa aaaatgatga gttcatatcc tttgtaggga
     5701 catggatgaa attggaaacc atcattctca gtaaactatc gcaagaacaa aaaaccaaac
     5761 accgcatatt ctcactcata ggtgggaatt gaacaatgag atcacatgga cacaggaagg
     5821 ggaatatcac actctgggga ctgtggtggg gtcgggggag gggggagggg tagcattggg
     5881 agatatacct aatgctagat gacacattag tgggtgcagc gcaccagcat ggcacatgta
     5941 tacatatgta actaacctgc acaatgtgca catgtaccct aaaacttaga gtataattaa
     6001 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaagatca caccactgca ctccagcctg
     6061 ggtgtcaaag cgagaccctg tctcaggaaa aaaaaaaaaa aaaaaaaaaa aggcttaatt
     6121 gattgaacca gattcgagaa aacagtgcta aattataatt ttctcaatac tgtaaatatt
     6181 tttcaatctt cagcttcatt aacttctata attgaaatta tcccaattat tacctgacat
     6241 gtactaaaat tccctaaaat ggatcttgag taacattttc acagtacgat aatttttctc
     6301 tctgtatata tttatatagt cacatatatg cacatacatt atacaagcat tacttttcta
     6361 taactgtaag gtcagaattt gaagttgtgt tttctttatc tttttatttc caatacttgg
     6421 catcaagttg atattcatta gaagtaaagg aggaaggaaa tgaataatct tcagatacta
     6481 agaacattac acttaaatta ttattaaatc taatttgcat tctcatatat ggcttagct
//

Tags: Cell DNA Genetics

Comparing Markdown and Creole as Markup Languages

At the moment I opted for Creole but I'm not sure whether this was decision has a future as Creole development stoped a few year ago (The Creole is live press release is from 2007!) and Markdown is still active (The most recent news is from 2009 :-( ! not so recent any more, actually). Moreover markdown is integrated into Django. Some more differences important to my application are listed in the table below.

featureCreoleMarkdown
Linkhttp://wikicreole.org/wiki/Homehttp://www.freewisdom.org/projects/python-markdown/
Tablescolspan and rowspan not allowedcolspan and rowspan not allowed
Macros/ExtensionsMacros can be easily handled
from Creole text
Extensions are probably a more powerful tool,
but more complex to handle
TOCI already implemented table of content as a macroTable of content is an extension
that I didn't test so far
ReferencesI Already have an idea
how to implement references
A new extension is necessary, probably

More Markdown feature not so important at the moment are listed here. Definitely I have to learn how to write extensions, so I can improve my pythoknowledge and evaluate the efforts necessary to write or change an extension.


Tags: Software

 
   

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