Riken CAGE Track Settings
 
Riken CAGE - Predicted Gene Start Sites   (All Pilot ENCODE Transcription tracks)

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Source data version: ENCODE June 2005 Freeze
Data coordinates converted via liftOver from: July 2003 (NCBI34/hg16)

Description

This track shows the number of 5' cap analysis gene expression (CAGE) tags that map to the genome on the "plus" and "minus" strands at a specific location. For clarity, only the first 5' nucleotide in the tag (relative to the transcript direction) is considered. Areas in which many tags map to the same region may indicate a significant transcription start site.

Display Conventions and Configuration

The position of the first 5' nucleotide in the tag is represented by a solid block. The height of the block indicates the number of 5' cDNA starts that map at that location.

This composite annotation track contains multiple subtracks that may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. For more information about the graphical configuration options, click the Graph configuration help link. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

Methods

The CAGE tags are sequenced from the 5' ends of full-length cDNAs produced using RIKEN full-length cDNA technology. To create the tag, a linker was attached to the 5' end of full-length cDNAs which were selected by cap trapping. The first 20 bp of the cDNA were cleaved using class II restriction enzymes, followed by PCR amplification and then concatamers of the resulting 32 bp tags were formed for more efficient sequencing. For more information on CAGE analysis, see Shiraki et al. (2003) below. Refer to the RIKEN website for information about RIKEN full-length cDNA technologies. The mapping methodology employed in this annotation will be described in upcoming publications.

Verification

The techniques used to verify these data will be described in upcoming publications.

Credits

These data were contributed by the Functional Annotation of Mouse (FANTOM) Consortium, RIKEN Genome Science Laboratory and RIKEN Genome Exploration Research Group (Genome Network Project Core Group).

FANTOM Consortium: P. Carninci, T. Kasukawa, S. Katayama, Gough, M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, V. Harokopos, Y. Hayashi, S. Henning, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A.F. Kruger, K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, W. Qu, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. Salzberg, A. Sandelin, C. Schneider, C. Schoenbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegene, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. Mattick, D. Hume.

RIKEN Genome Exploration Research Group: C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai.

General Organizer: Y. Hayashizaki

References

Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A. 100(26), 15776-81 (2003).