The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Repetitive Sequences in Complex Genomes: Structure and Evolution
Abstract
Eukaryotic genomes contain vast amounts of repetitive DNA derived from transposable elements (TEs). Large-scale sequencing of these genomes has produced an unprecedented wealth of information about the origin, diversity, and genomic impact of what was once thought to be “junk DNA.” This has also led to the identification of two new classes of DNA transposons, Helitrons and Polintons, as well as several new superfamilies and thousands of new families. TEs are evolutionary precursors of many genes, including RAG1, which plays a role in the vertebrate immune system. They are also the driving force in the evolution of epigenetic regulation and have a long-term impact on genomic stability and evolution. Remnants of TEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Most eukaryotic genomes contain a large number of interspersed repeats that by and large represent copies of transposable elements (TEs) at varying stages of evolutionary decay (Smit 1999;Consortium and International Human Genome Sequencing Consortium 2001;Jurka et al. 2007;Huang et al. 2012;Bourque et al. 2018).”
From RepeatModeler2 for automated genomic discovery of transposable element families (2020) · cites this paper as Jurka et al. 2007
Citations
Cites
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 2×
“represent densities in conserved human sequences (106) and cis-regulatory modules (CRMs) (9).”
BackgroundGenome sequence, comparative analysis and haplotype structure of the domestic dog
members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568
Molecular paleontology of transposable elements in the Drosophila melanogaster genome
Kapitonov, V. V., & Jurka, J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0732024100 · Cited by 288
Self-citationA family of conserved noncoding elements derived from an ancient transposable element
Xie, X., Kamal, M., & Lander, E. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604768103 · Cited by 66
Research works printed but not linked: 123
- 10.1093/nar/25.17.3389 · DOI · Paper page
- 10.1038/ng1074 · DOI
- 10.1098/rspb.2004.3045 · DOI
- 10.1086/344397 · DOI
- 10.1038/nature04696 · DOI
- 10.1126/science.1098119 · DOI · Paper page
- 10.1101/gad.1324305 · DOI
- 10.1038/443521a · DOI
- 10.1101/gr.4866006 · DOI
- 10.1074/jbc.271.15.8509 · DOI
- 10.1038/nsmb1167 · DOI
- 10.1159/000084963 · DOI
- 10.1126/science.165.3891.349 · DOI
- 10.1126/science.161.3841.529 · DOI
- 10.1016/j.tig.2006.03.003 · DOI
- 10.1126/science.1990437 · DOI
- 10.1038/sj.hdy.6800789 · DOI
- 10.1016/j.tig.2006.09.006 · DOI
- 10.1016/0092-8674(85)90016-9 · DOI
- 10.1023/A:1018300721953 · DOI
- 10.1126/science.1085242 · DOI
- 10.1038/nrg1601 · DOI
- 10.1126/science.270.5234.253 · DOI
- 10.1006/jmbi.1998.1805 · DOI
- 10.1093/jhered/esj022 · DOI
- 10.1353/hub.2003.0075 · DOI
- 10.1073/pnas.91.3.942 · DOI
- Duncan L, 2002, Genetics, 162, 1617, 10.1093/genetics/162.4.1617 · DOI
- 10.1128/9781555817954.ch49 · DOI
- 10.1159/000084984 · DOI
- 10.1093/molbev/msh188 · DOI
- Fowler KJ, 2000, Genome Res., 10, 30
- 10.1038/nature04341 · DOI
- 10.1007/BF00294683 · DOI
- 10.1038/nature01097 · DOI · Paper page
- 10.1093/molbev/msi188 · DOI
- Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, et al. 2007. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. In press. doi:10.1101/gr.6070707 · DOI · Paper page
- 10.1099/mic.0.26529-0 · DOI
- 10.1093/oxfordjournals.molbev.a003748 · DOI
- 10.1093/molbev/msh072 · DOI
- 10.1101/SQB.1979.043.01.142 · DOI
- 10.1007/s00239-004-0197-2 · DOI
- 10.1016/0092-8674(83)90184-8 · DOI
- 10.1128/MCB.13.8.4523 · DOI
- Howlett SK, 1991, Development, 113, 119, 10.1242/dev.113.1.119 · DOI
- Irelan JT, 2001, Genetics, 157, 1191, 10.1093/genetics/157.3.1191 · DOI
- 10.1128/EC.2.1.103-114.2003 · DOI
- 10.1073/pnas.96.22.12621 · DOI
- 10.1016/j.cub.2006.05.045 · DOI
- 10.1016/j.gde.2004.08.008 · DOI
- 10.1023/A:1003989620068 · DOI
- 10.1159/000084979 · DOI
- 10.1073/pnas.0308084100 · DOI
- 10.1159/000084943 · DOI
- 10.1006/tpbi.2002.1602 · DOI
- 10.1093/nar/gki323 · DOI
- 10.1073/pnas.0511238103 · DOI
- 10.1023/A:1004030922447 · DOI
- 10.1073/pnas.151269298 · DOI
- 10.1089/104454904323090949 · DOI · Paper page
- Kapitonov VV, 2005, Repbase Rep., 5, 393
- 10.1371/journal.pbio.0030181 · DOI · Paper page
- 10.1073/pnas.0600833103 · DOI
- Kapitonov VV, 2004, Encyclopedia of Molecular Cell Biology and Molecular Medicine, 251
- Kidwell MG, 1977, Genetics, 86, 813, 10.1093/genetics/86.4.813 · DOI
- 10.1111/j.0014-3820.2001.tb01268.x · DOI
- 10.1126/science.1090005 · DOI · Paper page
- 10.1093/molbev/msg235 · DOI
- 10.1111/j.1432-1033.1997.00772.x · DOI
- 10.1038/nsmb1107 · DOI
- Kunze R, Weil CF. 2002. The hAT and CACTA superfamilies of plant transposons. InMobile DNA II, ed.NL Craig, R Craigie, M Gellert, AM Lambowitz, pp.565–610. Washington, DC: ASM Press · DOI
- 10.1093/oxfordjournals.molbev.a026182 · DOI
- 10.1073/pnas.0502923102 · DOI
- 10.1038/35057062 · DOI · Paper page
- 10.1128/MCB.23.12.4083-4093.2003 · DOI
- 10.1093/oxfordjournals.molbev.a003947 · DOI
- 10.1146/annurev.genet.36.040202.092802 · DOI
- 10.1016/j.molbiopara.2005.10.002 · DOI
- 10.1074/jbc.M409197200 · DOI
- 10.1159/000014969 · DOI
- 10.1007/s002390010174 · DOI
- 10.1089/104303403321070838 · DOI
- 10.1101/gr.1971104 · DOI
- 10.1126/science.15739260 · DOI
- 10.1073/pnas.89.20.9579 · DOI
- 10.1146/annurev.genom.5.061903.180057 · DOI
- 10.1038/ng1615 · DOI
- 10.1038/nature05560 · DOI
- 10.1101/gr.5255506 · DOI
- 10.1038/29985 · DOI
- 10.1006/geno.2001.6494 · DOI
- 10.1038/ng1699 · DOI
- 10.1016/j.devcel.2004.09.004 · DOI · Paper page
- 10.1128/9781555817954.ch22 · DOI
- 10.1159/000084991 · DOI
- 10.1016/S0378-1119(03)00679-6 · DOI
- 10.1038/nature05198 · DOI
- 10.1038/nrg1834 · DOI
- 10.1126/science.220.4593.157 · DOI
- 10.1016/0092-8674(89)90760-5 · DOI
- 10.1038/ng1171 · DOI
- 10.1146/annurev.genom.7.080505.115618 · DOI
- 10.1101/gr.4624306 · DOI
- 10.1016/j.tig.2005.04.008 · DOI · Paper page
- 10.1016/j.tig.2006.08.007 · DOI
- 10.1073/pnas.93.4.1443 · DOI · Paper page
- 10.1016/j.tig.2006.11.005 · DOI
- 10.1016/S1383-5718(01)00315-1 · DOI
- 10.1038/302575a0 · DOI · Paper page
- 10.1038/ng0995-71 · DOI
- 10.1006/jmbi.1998.2477 · DOI
- 10.1007/BF00299145 · DOI
- 10.1016/j.cub.2006.09.020 · DOI
- 10.1126/science.1117805 · DOI
- 10.1093/oxfordjournals.molbev.a003801 · DOI
- 10.1002/bies.20452 · DOI
- 10.1007/s004380100468 · DOI
- 10.1128/9781555817954.ch23 · DOI
- 10.1159/000090821 · DOI
- 10.1146/annurev.bi.55.070186.003215 · DOI
- 10.1073/pnas.71.8.3028 · DOI
- Wray GA, 2003, Int. J. Dev. Biol., 47, 675
- 10.1016/j.gde.2005.07.002 · DOI
Cited by
Sorted by citations
RepeatModeler2 for automated genomic discovery of transposable element families
Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921046117 · Cited by 3,848
Ten things you should know about transposable elements
Bourque, G., Burns, K. H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H. L., Macfarlan, T. S., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1577-z · Cited by 1,430
Resurrection of endogenous retroviruses during aging reinforces senescence
Liu, X., Liu, Z., Wu, Z., Ren, J., Fan, Y., Sun, L., Cao, G., Niu, Y., Zhang, B., Ji, Q., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.017 · Cited by 390
Inevitability of Genetic Parasites
Iranzo, J., Puigbò, P., Lobkovsky, A. E., Wolf, Y. I., & Koonin, E. V. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw193 · Cited by 90
Metadata
- Authors
- Jurka, J., Kapitonov, V. V., Kohany, O., & Jurka, M. V.
- Affiliations
- Genetic Information Research Institute, Mountain View, California 94043;, , ,
- Venue
- Annual Review of Genomics and Human Genetics
- Publisher
- Annual Reviews
- Published
- 2007-09-01
- Volume
- 8
- Issue
- 1
- Pages
- 241-259
- ISSN
- 1527-8204
- 1545-293X
- Cited by
- 331
- References
- 4
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Repetitive Sequences in Complex Genomes: Structure and Evolution. https://app.cochat.ai/papers/10.1146/annurev.genom.8.080706.092416
- The paper
- Jurka, J., Kapitonov, V. V., Kohany, O., & Jurka, M. V. (2007). Repetitive Sequences in Complex Genomes: Structure and Evolution. Annual Review of Genomics and Human Genetics. https://doi.org/10.1146/annurev.genom.8.080706.092416
