PMC:3396637 / 2802-4238 JSONTXT

{"project":"2_test","denotations":[{"id":"22807622-10899146-29768477","span":{"begin":353,"end":354},"obj":"10899146"},{"id":"22807622-12188048-29768478","span":{"begin":355,"end":356},"obj":"12188048"},{"id":"22807622-21414203-29768479","span":{"begin":516,"end":517},"obj":"21414203"},{"id":"22807622-17363976-29768480","span":{"begin":518,"end":519},"obj":"17363976"},{"id":"22807622-16365385-29768481","span":{"begin":718,"end":719},"obj":"16365385"},{"id":"22807622-18093339-29768482","span":{"begin":720,"end":721},"obj":"18093339"},{"id":"22807622-21573203-29768483","span":{"begin":815,"end":816},"obj":"21573203"},{"id":"22807622-17331616-29768484","span":{"begin":910,"end":911},"obj":"17331616"},{"id":"22807622-21414203-29768485","span":{"begin":1085,"end":1086},"obj":"21414203"},{"id":"22807622-20532223-29768486","span":{"begin":1260,"end":1261},"obj":"20532223"},{"id":"22807622-17594509-29768486","span":{"begin":1260,"end":1261},"obj":"17594509"},{"id":"22807622-20525173-29768486","span":{"begin":1260,"end":1261},"obj":"20525173"},{"id":"22807622-19166620-29768487","span":{"begin":1434,"end":1436},"obj":"19166620"}],"text":"Repetitive sequence (RS) elements are characterized as multi-copied sequences in two broadly defined classes: satellite sequences (SSs), including both micro-satellites and mini-satellites, and transposable elements (TEs) that are characterized based on sequence identity and structure, biogenesis, insertion site preference, and degree of redundancies.1,2 The RSs are evolutionarily active and show significant influences on the structures of genes and genomes, and are thus highly relevant to biological functions.3,4 It has been reported that TE-free regions are negatively selected for certain regulatory elements throughout vertebrate genomes, although the conservation of the sequence contents is often variable.5,6 Furthermore, TEs have different distributions among exonic, intronic, and intergenic regions.7 Indeed, a small number of TE classes are still active, generating population differentiation,8 and the compositional dynamics of genomic sequences exhibits step-by-step evolutionary changes as a consequence of competitions between host genomes and parasitic sequences.3 In addition, TE transposition often serves as a driving force for the conversion of introns into exons or gaining novel introns as well as alternatively spliced transcripts.9–11 Therefore, new sequence integration and the balance of exons and introns in number, length, and ordinal position of a gene provide basic materials for species evolution.12"}

{"project":"MyTest","denotations":[{"id":"22807622-10899146-29768477","span":{"begin":353,"end":354},"obj":"10899146"},{"id":"22807622-12188048-29768478","span":{"begin":355,"end":357},"obj":"12188048"},{"id":"22807622-21414203-29768479","span":{"begin":516,"end":517},"obj":"21414203"},{"id":"22807622-17363976-29768480","span":{"begin":518,"end":520},"obj":"17363976"},{"id":"22807622-16365385-29768481","span":{"begin":718,"end":719},"obj":"16365385"},{"id":"22807622-18093339-29768482","span":{"begin":720,"end":722},"obj":"18093339"},{"id":"22807622-21573203-29768483","span":{"begin":815,"end":817},"obj":"21573203"},{"id":"22807622-17331616-29768484","span":{"begin":910,"end":912},"obj":"17331616"},{"id":"22807622-21414203-29768485","span":{"begin":1085,"end":1087},"obj":"21414203"},{"id":"22807622-20532223-29768486","span":{"begin":1260,"end":1261},"obj":"20532223"},{"id":"22807622-17594509-29768486","span":{"begin":1260,"end":1261},"obj":"17594509"},{"id":"22807622-20525173-29768486","span":{"begin":1260,"end":1261},"obj":"20525173"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Repetitive sequence (RS) elements are characterized as multi-copied sequences in two broadly defined classes: satellite sequences (SSs), including both micro-satellites and mini-satellites, and transposable elements (TEs) that are characterized based on sequence identity and structure, biogenesis, insertion site preference, and degree of redundancies.1,2 The RSs are evolutionarily active and show significant influences on the structures of genes and genomes, and are thus highly relevant to biological functions.3,4 It has been reported that TE-free regions are negatively selected for certain regulatory elements throughout vertebrate genomes, although the conservation of the sequence contents is often variable.5,6 Furthermore, TEs have different distributions among exonic, intronic, and intergenic regions.7 Indeed, a small number of TE classes are still active, generating population differentiation,8 and the compositional dynamics of genomic sequences exhibits step-by-step evolutionary changes as a consequence of competitions between host genomes and parasitic sequences.3 In addition, TE transposition often serves as a driving force for the conversion of introns into exons or gaining novel introns as well as alternatively spliced transcripts.9–11 Therefore, new sequence integration and the balance of exons and introns in number, length, and ordinal position of a gene provide basic materials for species evolution.12"}