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7 results on '"Hackel C"'

1. Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer.

Author

Reis EM, Ojopi EP, Alberto FL, Rahal P, Tsukumo F, Mancini UM, Guimarães GS, Thompson GM, Camacho C, Miracca E, Carvalho AL, Machado AA, Paquola AC, Cerutti JM, da Silva AM, Pereira GG, Valentini SR, Nagai MA, Kowalski LP, Verjovski-Almeida S, Tajara EH, Dias-Neto E, Bengtson MH, Canevari RA, Carazzolle MF, Colin C, Costa FF, Costa MC, Estécio MR, Esteves LI, Federico MH, Guimarães PE, Hackel C, Kimura ET, Leoni SG, Maciel RM, Maistro S, Mangone FR, Massirer KB, Matsuo SE, Nobrega FG, Nóbrega MP, Nunes DN, Nunes F, Pandolfi JR, Pardini MI, Pasini FS, Peres T, Rainho CA, dos Reis PP, Rodrigus-Lisoni FC, Rogatto SR, dos Santos A, dos Santos PC, Sogayar MC, and Zanelli CF

Subjects
Alternative Splicing, Expressed Sequence Tags, Head and Neck Neoplasms metabolism, Humans, Larynx metabolism, Mouth metabolism, Pharynx metabolism, Polymerase Chain Reaction, Protein Isoforms, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Thyroid Gland metabolism, Thyroid Neoplasms metabolism, Gene Expression Profiling, Genetic Markers, Head and Neck Neoplasms genetics, RNA, Messenger genetics, Thyroid Neoplasms genetics, Transcription, Genetic
Abstract

A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. In addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.

Published
2005
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2. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences.

Author

Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG, Andrade LE, Cruz LO, Degaki TL, Faria M Jr, Festa F, Giannella-Neto D, Giorgi RR, Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CV, Marie SK, Martinez-Rossi NM, Oba-Shinjo SM, Pardini MI, Rahal P, Rainho CA, Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva ID, da Silva NP, de Souza SJ, Tajara EH, Silva WA Jr, Simpson AJ, Sogayar MC, Camargo AA, and Carraro DM

Subjects
Amino Acid Sequence, Animals, Chromosome Mapping, Gene Library, Humans, Male, Mice, Molecular Sequence Data, DNA, Complementary genetics, Genome, Human, Sequence Analysis, DNA methods, Testis chemistry, Transcription, Genetic genetics
Abstract

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

Published
2004

3. A transcript finishing initiative for closing gaps in the human transcriptome.

Author

Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJ, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MA, De Souza SJ, Faria M Jr, Giuliatti S, Kopp L, de Oliveira PS, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LE, Baia GS, Briones MR, Cavaleiro-Luna AM, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MA, Furchi JR, Giannella-Neto D, Goldman GH, Goldman MH, Gruber A, Guimarães GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SK, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paço-Larson ML, Paixão BM, Pandolfi JR, Pardini MI, Passos Bueno MR, Passos GA, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sá RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA Jr, Silva ID, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, and Zanette DL

Subjects
Alternative Splicing genetics, Cell Line, Cell Line, Tumor, Computational Biology methods, Computational Biology statistics & numerical data, Consensus Sequence genetics, DNA, Neoplasm, Databases, Genetic classification, Expressed Sequence Tags, Genes genetics, Genome, Human, HeLa Cells pathology, Humans, Molecular Sequence Data, Open Reading Frames genetics, Software Design, Software Validation, U937 Cells pathology, Software, Transcription, Genetic genetics
Abstract

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms., (Copyright 2004 Cold Spring Harbor Laboratory Press ISSN)

Published
2004
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4. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome.

Author

Camargo AA, Samaia HP, Dias-Neto E, Simão DF, Migotto IA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, Sonati MF, Tajara EH, Valentini SR, Alberto FL, Amaral ME, Aneas I, Arnaldi LA, de Assis AM, Bengtson MH, Bergamo NA, Bombonato V, de Camargo ME, Canevari RA, Carraro DM, Cerutti JM, Correa ML, Correa RF, Costa MC, Curcio C, Hokama PO, Ferreira AJ, Furuzawa GK, Gushiken T, Ho PL, Kimura E, Krieger JE, Leite LC, Majumder P, Marins M, Marques ER, Melo AS, Melo MB, Mestriner CA, Miracca EC, Miranda DC, Nascimento AL, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Prevedel AC, Rahal P, Rainho CA, Reis EM, Ribeiro ML, da Ros N, de Sa RG, Sales MM, Sant'anna SC, dos Santos ML, da Silva AM, da Silva NP, Silva WA Jr, da Silveira RA, Sousa JF, Stecconi D, Tsukumo F, Valente V, Soares F, Moreira ES, Nunes DN, Correa RG, Zalcberg H, Carvalho AF, Reis LF, Brentani RR, Simpson AJ, and de Souza SJ

Subjects
Humans, Expressed Sequence Tags, Genome, Human, Open Reading Frames, Transcription, Genetic
Abstract

Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

Published
2001
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5. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags.

Author

de Souza SJ, Camargo AA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, de Fátima Sonati M, Tajara EH, Valentini SR, Acencio M, Alberto FL, Amaral ME, Aneas I, Bengtson MH, Carraro DM, Carvalho AF, Carvalho LH, Cerutti JM, Corrêa ML, Costa MC, Curcio C, Gushiken T, Ho PL, Kimura E, Leite LC, Maia G, Majumder P, Marins M, Matsukuma A, Melo AS, Mestriner CA, Miracca EC, Miranda DC, Nascimento AN, Nóbrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Rahal P, Rainho CA, da Rós N, de Sá RG, Sales MM, da Silva NP, Silva TC, da Silva W Jr, Simão DF, Sousa JF, Stecconi D, Tsukumo F, Valente V, Zalcbeg H, Brentani RR, Reis FL, Dias-Neto E, and Simpson AJ

Subjects
Expressed Sequence Tags, Gene Expression Profiling, Humans, Open Reading Frames, Chromosomes, Human, Pair 22, Transcription, Genetic
Abstract

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1, 181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html).

Published
2000
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6. A transcript finishing initiative for closing gaps in the human transcriptome

Author

Sogayar, M. C., Camargo, A. A., Bettoni, F., Carraro, D. M., Pires, L. C., Parmigiani, M. B., Ferreira, E. N., Moreira, E. S., Latorre, MRDO, Simpson, AJG, Cruz, L. O., Degaki, T. L., Festa, F., Massirer, K. B., Camargo, F., Camargo, L. P., Cunha, MAV, De Souza, S. J., Faria, M., Giuliatti, S., Kopp, Oliviera, PSL, Paiva, P. B., Pereira, A. A., Pinheiro, D. G., Puga, R. D., Souza, JES, Albuquerque, D. M., Andrade, LEC, Baia, G. S., Briones, MRS, Cavaleiro-Luna, AMS, Cerutti, J. M., Costa, F. F., Constanzi-Strauss, E., Espreafico, E. M., Ferrasi, A. C., Ferro, E. S., Fortes, MAHZ, Furchi, JRF, Gianella-Neto, D., Goldman, G. H., Goldman, MHS, Gruber, A., Guimaraes, G. S., Hackel, C., Henrique-Silva, F., Kimura, E. T., Leoni, S. G., Macedo, C., Malnic, B., Manzini, C. V., Marie, SKN, Martinez-Rossi, N. M., Menossi, M., Miracca, E. C., Nagai, M. A., Nobrega, F. G., Nobrega, M. P., Oba-Shinjo, S. M., Oliviera, M. K., Orabona, G. M., Otsuke, A. Y., Paco-Larson, M. L., Paixao, BMC, Pandolfi, JRC, Pardini, MIMC, Passos-Bueno, M. R., Passos, GAS, Pesquero, J. B., Pessoa, J. G., Rahal, Paula [UNESP], Rainho, C. A., Reis, C. P., Ricca, T. I., Rodriguez, V, Rogatto, Silvia Regina [UNESP], Romano, C. M., Romeiro, J. G., Rossi, A., Sa, R. G., Sales, M. M., SantAnna, S. C., Santarosa, P. L., Segato, F., Silva, W. A., Silva, IDCG, Silva, N. P., Soares-Costa, A., Sonati, M. F., Strauss, B. E., Tajara, E. H., Valentini, Sandro Roberto [UNESP], Villanova, F. E., Ward, L. S., Zanette, D. L., Universidade de São Paulo (USP), Ludwig Inst Canc Res, Univ Ribeirao Preto, Inst Ludwig, Universidade Federal de São Paulo (UNIFESP), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual Paulista (Unesp), Universidade Federal de São Carlos (UFSCar), and Univ Vale Paraiba

Subjects
Transcription, Genetic, Software Validation, Molecular Sequence Data, Biology, Cell Line, Open Reading Frames, Exon, Software Design, Cell Line, Tumor, Complementary DNA, Consensus Sequence, Databases, Genetic, Methods, Genetics, Consensus sequence, Humans, Gene, Genetics (clinical), Expressed Sequence Tags, Expressed sequence tag, Genome, Human, Alternative splicing, Computational Biology, DNA, Neoplasm, U937 Cells, HISTOLOGIA, Alternative Splicing, Open reading frame, Genes, Human genome, Software, HeLa Cells
Abstract

Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2014-02-26T17:19:33Z No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Made available in DSpace on 2014-02-26T17:19:33Z (GMT). No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Previous issue date: 2004-07-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T13:50:12Z No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Made available in DSpace on 2014-05-20T13:50:12Z (GMT). No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Previous issue date: 2004-07-01 We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST Clusters, mapped against the genomic sequence. Each pair of EST Clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted Set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms. Univ São Paulo, Inst Quim, BR-05513970 São Paulo, Brazil Ludwig Inst Canc Res, BR-01509010 São Paulo, Brazil Univ São Paulo, Dept Epidemiol, Sch Publ Hlth, BR-01246904 São Paulo, SP, Brazil Univ Ribeirao Preto, Dept Quim Informat Bioinformat, BR-14096380 Ribeirao Preto, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Centro Terapia Celular, Hemocentro, BR-14051140 Ribeirao Preto, SP, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Clin Med, BR-14051140 Ribeirao Preto, SP, Brazil Inst Ludwig, Lab Biol Computacional, BR-01509010 São Paulo, SP, Brazil Univ São Paulo, Lab Genet Cardiol Mol, Inst Coracao, BR-05403000 São Paulo, SP, Brazil Univ Fed São Paulo, Bioinform Lab, Hlth Informatics Dept, BR-04039032 São Paulo, Brazil Univ Estad Campinas, Dept Clin Med, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ Fed São Paulo, Rheumatol Div, BR-04113001 São Paulo, Brazil Univ São Paulo, Dept Histol Embriol, Inst Ciências Biomed, BR-05508900 São Paulo, Brazil Univ Fed São Paulo, Dept Microbiol Immunol Parasitol, BR-04023062 São Paulo, Brazil Univ São Paulo, Lab Cellular Mol Endocrinol, Sch Med, BR-01246903 São Paulo, Brazil Univ Fed São Paulo, Dept Med, Disciplina Endocrinol, Lab Endocrinol Mol, BR-04039002 São Paulo, Brazil Univ São Paulo, Inst Ciências Biomed, Lab Transferencia Genica, BR-05508900 São Paulo, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Biol Celular Mol Bioagentes Patogenicas, BR-14049900 Ribeirao Preto, SP, Brazil Univ Estadual Paulista, Lab Biol Mol, Hemocentro, Fac Med, BR-18618970 Botucatu, SP, Brazil Univ Fed Sao Carlos, Dept Genet Evol, BR-13565905 Sao Carlos, SP, Brazil Univ São Paulo, Fac Ciências Farmaceuticas Ribeirao Preto, BR-14040903 Ribeirao Preto, SP, Brazil Univ São Paulo, Fac Filosofia Ciências Letras Ribeirao Preto, Ribeirao Preto, SP, Brazil Univ São Paulo, Dept Patol, Fac Med Vet Zootecnia, BR-05508000 São Paulo, Brazil Univ Estadual Campinas, Dept Genet Med, Fac Ciências Med, BR-13081970 Campinas, SP, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Genet, BR-14040900 Ribeirao Preto, SP, Brazil Univ São Paulo, Dept Bioquim, Inst Quim, BR-05599970 São Paulo, Brazil Univ São Paulo, Dept Neurol, Fac Med, BR-01246903 São Paulo, Brazil Univ Estadual Campinas, Lab Genoma Funcional, Centro Biol Mol Engenharia Genet, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Dept Genet Evol, Inst Biol, Campinas, SP, Brazil Univ São Paulo, Dept Radiol, Disciplina Oncol, Fac Med, BR-01246903 São Paulo, Brazil Univ Vale Paraiba, Inst Pesquisa Desenvolvimento, BR-12244000 Sao Jose Dos Campos, SP, Brazil Univ São Paulo, Inst Biociencias, Centro Estudios Genoma Humano, Dept Biol, BR-055508900 São Paulo, Brazil Univ Fed São Paulo, Lab Mol Gynecol, Dept Gynecol, BR-04039001 São Paulo, Brazil São Paulo State Univ, Sch Pharmacol, Dept Biol Sci, BR-14801902 Araraquara, SP, Brazil Univ São Paulo, Discipl Genet, Fac Odontol, BR-14040900 Ribeirao Preto, SP, Brazil Univ Fed São Paulo, Dept Biofisica, BR-04023062 São Paulo, Brazil Univ Estadual Paulista, Dept Biol, Inst Biociencias Letras Ciências Exatas, BR-15054000 Sao Jose do Rio Preto, SP, Brazil Univ Estadual Paulista, Dept Genet, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil Univ São Paulo, Dept Bioquim Imunol, Fac Med Ribeirao Preto, BR-14049900 Ribeirao Preto, SP, Brazil Univ Estadual Campinas, Lab Genet Mol Cancer, Dept Clin Med, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Dept Patol Clin, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ São Paulo, Setor Vetores Virals, Lab Cardiol Mol, Inst Coracao, BR-15403000 São Paulo, Brazil Univ Estadual Paulista, Lab Biol Mol, Hemocentro, Fac Med, BR-18618970 Botucatu, SP, Brazil São Paulo State Univ, Sch Pharmacol, Dept Biol Sci, BR-14801902 Araraquara, SP, Brazil Univ Estadual Paulista, Dept Biol, Inst Biociencias Letras Ciências Exatas, BR-15054000 Sao Jose do Rio Preto, SP, Brazil Univ Estadual Paulista, Dept Genet, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil

Published
2004

7. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

Author

Ferreira, E. N., Pires, L. C., Parmigiani, R. B., Bettoni, F., Puga, R. D., Pinheiro, D. G., Andrade, L. E. C., Cruz, L. O., Degaki, T. L., Faria Jr, M., Festa, F., Giannella-Neto, D., Giorgi, R. R., Goldman, G. H., Granja, F., Gruber, A., Hackel, C., Henrique-Silva, F., Malnic, B., Manzini, C. V. B., Marie, S. K. N., Martinez-Rossi, N. M., Oba-Shinjo, S. M., Pardini, M. I. M. C., Rahal, P., Rainho, C. A., Rogatto, S. R., Romano, C. M., Rodrigues, V., Sales, M. M., Savoldi, M., Da Silva, I. D. C. G., Da Silva, N. P., Souza, S. J., Tajara, E. H., Wilson Araujo Silva Jr, Simpson, A. J. G., Sogayar, M. C., Camargo, A. A., and Carraro, D. M.

Subjects
Male, Mice, DNA, Complementary, Transcription, Genetic, Genome, Human, Molecular Sequence Data, Testis, Animals, Chromosome Mapping, Humans, Amino Acid Sequence, Sequence Analysis, DNA, Gene Library
Abstract

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

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