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Journal Articles

The H-Invitational Database (H-InvDB); A Comprehensive annotation resource for human genes and transcripts

Yamasaki, Chisato*; Murakami, Katsuhiko*; Fujii, Yasuyuki*; Sato, Yoshiharu*; Harada, Erimi*; Takeda, Junichi*; Taniya, Takayuki*; Sakate, Ryuichi*; Kikugawa, Shingo*; Shimada, Makoto*; et al.

Nucleic Acids Research, 36(Database), p.D793 - D799, 2008/01

 Times Cited Count:51 Percentile:71.37(Biochemistry & Molecular Biology)

Here we report the new features and improvements in our latest release of the H-Invitational Database, a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of fulllength cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 protein-coding and 642 non-protein-coding loci; 858 transcribed loci overlapped with predicted pseudogenes.

Journal Articles

Alternative splicing in human transcriptome; Functional and structural influence on proteins

Yura, Kei; Shionyu, Masafumi*; Hagino, Kei*; Hijikata, Atsushi*; Hirashima, Yoshinori*; Nakahara, Taku*; Eguchi, Tatsuya*; Shinoda, Kazuki*; Yamaguchi, Akihiro*; Takahashi, Kenichi*; et al.

Gene, 380(2), p.63 - 71, 2006/10

 Times Cited Count:55 Percentile:72.39(Genetics & Heredity)

Alternative splicing is a molecular mechanism that produces multiple proteins from a single gene, and is thought to produce variety in proteins translated from a limited number of genes. Here we analyzed how alternative splicing produced variety in protein structure and function, by using human full-length cDNAs, on the assumption that all of the alternatively spliced mRNAs were translated to proteins. We found that the length of alternatively spliced amino acid sequences, in most cases, fell into a size shorter than that of average protein domain. We evaluated comprehensively the presumptive three-dimensional structures of the alternatively spliced products to assess the impact of alternative splicing on gene function. We found that more than half of the products encoded proteins which were involved in signal transduction, transcription and translation, and more than half of alternatively spliced regions comprised interaction sites between proteins and their binding partners, including substrates, DNA/RNA, and other proteins. Intriguingly, 67% of the alternatively spliced isoforms showed significant alterations to regions of the protein structural core, which likely resulted in large conformational change. Based on those findings, we speculate that there are a large number of cases that alternative splicing modulates protein networks through significant alteration in protein conformation.

Journal Articles

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

Takeda, Junichi*; Suzuki, Yutaka*; Nakao, Mitsuteru*; Barrero, R. A.*; Koyanagi, Kanako*; Jin, L.*; Motono, Chie*; Hata, Hiroko*; Isogai, Takao*; Nagai, Keiichi*; et al.

Nucleic Acids Research, 34(14), p.3917 - 3928, 2006/00

 Times Cited Count:34 Percentile:54.48(Biochemistry & Molecular Biology)

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function which is mediated by the alternative splicing variants.

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