The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The Transcriptional Landscape of the Mammalian Genome
Abstract
This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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Citations
Cites
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095
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Items 101–107 of 107
Oscillatory Behaviors of microRNA Networks: Emerging Roles in Retinal Development
Fishman, E. S., Han, J. S., & La Torre, A. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.831750 · Cited by 16
A resource for transcriptomic analysis in the mouse brain
Plessy, C., Fagiolini, M., Wagatsuma, A., Harasawa, N., Kuji, T., Asaka-Oba, A., Kanzaki, Y., Fujishima, S., Waki, K., Nakahara, H., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003012 · Cited by 12
Self-citationMaking Biological Sense of Genetic Studies of Age-Related Macular Degeneration
Singh, N., Swaroop, A., & Ratnapriya, R. (2021) · Advances in Experimental Medicine and Biology · doi:10.1007/978-3-030-66014-7_8 · Cited by 11
Structural basis for the synergistic assembly of the snRNA export complex
Dubiez, E., Garland, W., Finderup Brask, M., Boeri Erba, E., Heick Jensen, T., Kadlec, J., & Cusack, S. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01595-5 · Cited by 9
Pre-piRNA trimming safeguards piRNAs against erroneous targeting by RNA-dependent RNA polymerase
(2024) · doi:10.1016/j.celrep.2024.113692 · Cited by 7
Post-transcriptional control of antifungal resistance in human fungal pathogens
Sharma, C., & Kadosh, D. (2023) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2022.2080527 · Cited by 6
Epigenetic and experimental approaches influencing non-coding RNAs
(2025) · Progress in Molecular Biology and Translational Science · doi:10.1016/bs.pmbts.2025.05.001 · Cited by 3
Metadata
- Authors
- Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., Gatta, G. D., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Babu, M. M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schönbach, C., Sekiguchi, K., Semple, C. A. M., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., & Hayashizaki, Y.
- Venue
- Science
- Published
- 2005-09-02
- Volume
- 309
- Issue
- 5740
- Pages
- 1559-1563
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2099468911
- Cited by
- 3,499
- References
- 2
- FWCI
- 66.38
- Type
- journal article
- Language
- en
- Open access
- closed
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