A transcript finishing initiative for closing gaps in the human transcriptome

Mari Cleide Sogayar; Anamaria A. Camargo; Fabiana Bettoni; Dirce Maria Carraro; Lilian C. Pires; Raphael B. Parmigiani; Elisa N. Ferreira; E. de Sá Moreira; D. Do Rosário; O. Latorre; J. G. Simpson; Luciana Oliveira Cruz; Theri Leica Degaki; Fernanda Festa; Katlin B. Massirer; Fernando Camargo Filho; Luiz Paulo Camargo; Marco A.V. Cunha; Sandro J. De Souza; Maria Faria Junior; Silvana Giuliatti; Leonardo Kopp; Paulo S.L. de Oliveira; Paulo B. Paiva; Anderson A. Pereira; Daniel G. Pinheiro; Renato D. Puga; Jorge Estefano S. de Souza; Dulcineia M. Albuquerque; Luís E.C. Andrade; Gilson S. Baia; Marcelo R.S. Briones; Ana M.S. Cavaleiro-Luna; Janete M. Cerutti; Fernando F. Costa; Eugenia Costanzi-Strauss; Enilza M. Espreafico; Adriana C. Ferrasi; Emer S. Ferro; Joelma R.F. Furchi; Daniel Giannella-Neto; Gustavo H. Goldman; Maria H.S. Goldman; Arthur Gruber; Gustavo S. Guimarães; Christine Hackel; Flavio Henrique-Silva; Edna T. Kimura; Suzana G. Leoni; Cláudia Macedo; Bettina Malnic; Carina V. Manzini B.; Suely K.N. Marie; Nilce M. Martinez-Rossi; Marcelo Menossi; Elisabete C. Miracca; Maria A. Nagai; Francisco G. Nobrega; Marina P. Nobrega; Sueli M. Oba-Shinjo; Márika K. Oliveira; Guilherme M. Orbana; Audrey Y. Otsuka; Maria L. Paço-Larson; Beatriz M.C. Paixão; Jose R.C. Pandolfi; Maria I.M.C. Pardini; Maria R. Passos Bueno; Geraldo A.S. Passos A.S.; Joao B. Pesquero; Juliana G. Pessoa; Paula Rahal; Cláudia A. Rainho; Caroline P. Reis; Tatiana I. Ricca; Vanderlei Rodrigues; Silvia R. Rogatto; Camila M. Romano; Janaína G. Romeiro; Antonio Rossi; Renata G. Sá; Magaly M. Sales; Simone C. Sant'Anna; Patría L. Santarosa; Fernando Segato; Wilson A. Silva; Ismael D.C.G. Silva; Neusa P. Silva; Andrea Soares-Costa; Maria F. Sonati; Bryan E. Strauss; Eloiza H. Tajara; Sandro R. Valentini; Fabiola E. Villanova; Laura S. Ward; Dalila L. Zanette

doi:10.1101/gr.2111304

A transcript finishing initiative for closing gaps in the human transcriptome

Mari Cleide Sogayar, Anamaria A. Camargo, Fabiana Bettoni, Dirce Maria Carraro, Lilian C. Pires, Raphael B. Parmigiani, Elisa N. Ferreira, E. de Sá Moreira, D. Do Rosário, O. Latorre, J. G. Simpson, Luciana Oliveira Cruz, Theri Leica Degaki, Fernanda Festa, Katlin B. Massirer, Fernando Camargo Filho, Luiz Paulo Camargo, Marco A.V. Cunha, Sandro J. De Souza, Maria Faria JuniorSilvana Giuliatti, Leonardo Kopp, Paulo S.L. de Oliveira, Paulo B. Paiva, Anderson A. Pereira, Daniel G. Pinheiro, Renato D. Puga, Jorge Estefano S. de Souza, Dulcineia M. Albuquerque, Luís E.C. Andrade, Gilson S. Baia, Marcelo R.S. Briones, Ana M.S. Cavaleiro-Luna, Janete M. Cerutti, Fernando F. Costa, Eugenia Costanzi-Strauss, Enilza M. Espreafico, Adriana C. Ferrasi, Emer S. Ferro, Joelma R.F. Furchi, Daniel Giannella-Neto, Gustavo H. Goldman, Maria H.S. Goldman, Arthur Gruber, Gustavo S. Guimarães, Christine Hackel, Flavio Henrique-Silva, Edna T. Kimura, Suzana G. Leoni, Cláudia Macedo, Bettina Malnic, Carina V. Manzini B., Suely K.N. Marie, Nilce M. Martinez-Rossi, Marcelo Menossi, Elisabete C. Miracca, Maria A. Nagai, Francisco G. Nobrega, Marina P. Nobrega, Sueli M. Oba-Shinjo, Márika K. Oliveira, Guilherme M. Orbana, Audrey Y. Otsuka, Maria L. Paço-Larson, Beatriz M.C. Paixão, Jose R.C. Pandolfi, Maria I.M.C. Pardini, Maria R. Passos Bueno, Geraldo A.S. Passos A.S., Joao B. Pesquero, Juliana G. Pessoa, Paula Rahal, Cláudia A. Rainho, Caroline P. Reis, Tatiana I. Ricca, Vanderlei Rodrigues, Silvia R. Rogatto, Camila M. Romano, Janaína G. Romeiro, Antonio Rossi, Renata G. Sá, Magaly M. Sales, Simone C. Sant'Anna, Patría L. Santarosa, Fernando Segato, Wilson A. Silva, Ismael D.C.G. Silva, Neusa P. Silva, Andrea Soares-Costa, Maria F. Sonati, Bryan E. Strauss, Eloiza H. Tajara, Sandro R. Valentini, Fabiola E. Villanova, Laura S. Ward, Dalila L. Zanette

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1413-1423
Number of pages	11
Journal	Genome research
Volume	14
Issue number	7
DOIs	https://doi.org/10.1101/gr.2111304
State	Published - Jul 1 2004
Externally published	Yes

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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10.1101/gr.2111304

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Sogayar, M. C., Camargo, A. A., Bettoni, F., Carraro, D. M., Pires, L. C., Parmigiani, R. B., Ferreira, E. N., de Sá Moreira, E., Do Rosário, D., Latorre, O., Simpson, J. G., Cruz, L. O., Degaki, T. L., Festa, F., Massirer, K. B., Filho, F. C., Camargo, L. P., Cunha, M. A. V., De Souza, S. J., ... Zanette, D. L. (2004). A transcript finishing initiative for closing gaps in the human transcriptome. Genome research, 14(7), 1413-1423. https://doi.org/10.1101/gr.2111304

Sogayar, MC, Camargo, AA, Bettoni, F, Carraro, DM, Pires, LC, Parmigiani, RB, Ferreira, EN, de Sá Moreira, E, Do Rosário, D, Latorre, O, Simpson, JG, Cruz, LO, Degaki, TL, Festa, F, Massirer, KB, Filho, FC, Camargo, LP, Cunha, MAV, De Souza, SJ, Junior, MF, Giuliatti, S, Kopp, L, de Oliveira, PSL, Paiva, PB, Pereira, AA, Pinheiro, DG, Puga, RD, de Souza, JES, Albuquerque, DM, Andrade, LEC, Baia, GS, Briones, MRS, Cavaleiro-Luna, AMS, Cerutti, JM, Costa, FF, Costanzi-Strauss, E, Espreafico, EM, Ferrasi, AC, Ferro, ES, Furchi, JRF, Giannella-Neto, D, Goldman, GH, Goldman, MHS, Gruber, A, Guimarães, GS, Hackel, C, Henrique-Silva, F, Kimura, ET, Leoni, SG, Macedo, C, Malnic, B, Manzini B., CV, Marie, SKN, Martinez-Rossi, NM, Menossi, M, Miracca, EC, Nagai, MA, Nobrega, FG, Nobrega, MP, Oba-Shinjo, SM, Oliveira, MK, Orbana, GM, Otsuka, AY, Paço-Larson, ML, Paixão, BMC, Pandolfi, JRC, Pardini, MIMC, Passos Bueno, MR, Passos A.S., GAS, 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, Silva, IDCG, Silva, NP, Soares-Costa, A, Sonati, MF, Strauss, BE, Tajara, EH, Valentini, SR, Villanova, FE, Ward, LS & Zanette, DL 2004, 'A transcript finishing initiative for closing gaps in the human transcriptome', Genome research, vol. 14, no. 7, pp. 1413-1423. https://doi.org/10.1101/gr.2111304

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title = "A transcript finishing initiative for closing gaps in the human transcriptome",

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.",

author = "Sogayar, {Mari Cleide} and Camargo, {Anamaria A.} and Fabiana Bettoni and Carraro, {Dirce Maria} and Pires, {Lilian C.} and Parmigiani, {Raphael B.} and Ferreira, {Elisa N.} and {de S{\'a} Moreira}, E. and {Do Ros{\'a}rio}, D. and O. Latorre and Simpson, {J. G.} and Cruz, {Luciana Oliveira} and Degaki, {Theri Leica} and Fernanda Festa and Massirer, {Katlin B.} and Filho, {Fernando Camargo} and Camargo, {Luiz Paulo} and Cunha, {Marco A.V.} and {De Souza}, {Sandro J.} and Junior, {Maria Faria} and Silvana Giuliatti and Leonardo Kopp and {de Oliveira}, {Paulo S.L.} and Paiva, {Paulo B.} and Pereira, {Anderson A.} and Pinheiro, {Daniel G.} and Puga, {Renato D.} and {de Souza}, {Jorge Estefano S.} and Albuquerque, {Dulcineia M.} and Andrade, {Lu{\'i}s E.C.} and Baia, {Gilson S.} and Briones, {Marcelo R.S.} and Cavaleiro-Luna, {Ana M.S.} and Cerutti, {Janete M.} and Costa, {Fernando F.} and Eugenia Costanzi-Strauss and Espreafico, {Enilza M.} and Ferrasi, {Adriana C.} and Ferro, {Emer S.} and Furchi, {Joelma R.F.} and Daniel Giannella-Neto and Goldman, {Gustavo H.} and Goldman, {Maria H.S.} and Arthur Gruber and Guimar{\~a}es, {Gustavo S.} and Christine Hackel and Flavio Henrique-Silva and Kimura, {Edna T.} and Leoni, {Suzana G.} and Cl{\'a}udia Macedo and Bettina Malnic and {Manzini B.}, {Carina V.} and Marie, {Suely K.N.} and Martinez-Rossi, {Nilce M.} and Marcelo Menossi and Miracca, {Elisabete C.} and Nagai, {Maria A.} and Nobrega, {Francisco G.} and Nobrega, {Marina P.} and Oba-Shinjo, {Sueli M.} and Oliveira, {M{\'a}rika K.} and Orbana, {Guilherme M.} and Otsuka, {Audrey Y.} and Pa{\c c}o-Larson, {Maria L.} and Paix{\~a}o, {Beatriz M.C.} and Pandolfi, {Jose R.C.} and Pardini, {Maria I.M.C.} and {Passos Bueno}, {Maria R.} and {Passos A.S.}, {Geraldo A.S.} and Pesquero, {Joao B.} and Pessoa, {Juliana G.} and Paula Rahal and Rainho, {Cl{\'a}udia A.} and Reis, {Caroline P.} and Ricca, {Tatiana I.} and Vanderlei Rodrigues and Rogatto, {Silvia R.} and Romano, {Camila M.} and Romeiro, {Jana{\'i}na G.} and Antonio Rossi and S{\'a}, {Renata G.} and Sales, {Magaly M.} and Sant'Anna, {Simone C.} and Santarosa, {Patr{\'i}a L.} and Fernando Segato and Silva, {Wilson A.} and Silva, {Ismael D.C.G.} and Silva, {Neusa P.} and Andrea Soares-Costa and Sonati, {Maria F.} and Strauss, {Bryan E.} and Tajara, {Eloiza H.} and Valentini, {Sandro R.} and Villanova, {Fabiola E.} and Ward, {Laura S.} and Zanette, {Dalila L.}",

year = "2004",

month = jul,

day = "1",

doi = "10.1101/gr.2111304",

language = "English (US)",

volume = "14",

pages = "1413--1423",

journal = "Genome research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

number = "7",

}

TY - JOUR

T1 - A transcript finishing initiative for closing gaps in the human transcriptome

AU - Sogayar, Mari Cleide

AU - Camargo, Anamaria A.

AU - Bettoni, Fabiana

AU - Carraro, Dirce Maria

AU - Pires, Lilian C.

AU - Parmigiani, Raphael B.

AU - Ferreira, Elisa N.

AU - de Sá Moreira, E.

AU - Do Rosário, D.

AU - Latorre, O.

AU - Simpson, J. G.

AU - Cruz, Luciana Oliveira

AU - Degaki, Theri Leica

AU - Festa, Fernanda

AU - Massirer, Katlin B.

AU - Filho, Fernando Camargo

AU - Camargo, Luiz Paulo

AU - Cunha, Marco A.V.

AU - De Souza, Sandro J.

AU - Junior, Maria Faria

AU - Giuliatti, Silvana

AU - Kopp, Leonardo

AU - de Oliveira, Paulo S.L.

AU - Paiva, Paulo B.

AU - Pereira, Anderson A.

AU - Pinheiro, Daniel G.

AU - Puga, Renato D.

AU - de Souza, Jorge Estefano S.

AU - Albuquerque, Dulcineia M.

AU - Andrade, Luís E.C.

AU - Baia, Gilson S.

AU - Briones, Marcelo R.S.

AU - Cavaleiro-Luna, Ana M.S.

AU - Cerutti, Janete M.

AU - Costa, Fernando F.

AU - Costanzi-Strauss, Eugenia

AU - Espreafico, Enilza M.

AU - Ferrasi, Adriana C.

AU - Ferro, Emer S.

AU - Furchi, Joelma R.F.

AU - Giannella-Neto, Daniel

AU - Goldman, Gustavo H.

AU - Goldman, Maria H.S.

AU - Gruber, Arthur

AU - Guimarães, Gustavo S.

AU - Hackel, Christine

AU - Henrique-Silva, Flavio

AU - Kimura, Edna T.

AU - Leoni, Suzana G.

AU - Macedo, Cláudia

AU - Malnic, Bettina

AU - Manzini B., Carina V.

AU - Marie, Suely K.N.

AU - Martinez-Rossi, Nilce M.

AU - Menossi, Marcelo

AU - Miracca, Elisabete C.

AU - Nagai, Maria A.

AU - Nobrega, Francisco G.

AU - Nobrega, Marina P.

AU - Oba-Shinjo, Sueli M.

AU - Oliveira, Márika K.

AU - Orbana, Guilherme M.

AU - Otsuka, Audrey Y.

AU - Paço-Larson, Maria L.

AU - Paixão, Beatriz M.C.

AU - Pandolfi, Jose R.C.

AU - Pardini, Maria I.M.C.

AU - Passos Bueno, Maria R.

AU - Passos A.S., Geraldo A.S.

AU - Pesquero, Joao B.

AU - Pessoa, Juliana G.

AU - Rahal, Paula

AU - Rainho, Cláudia A.

AU - Reis, Caroline P.

AU - Ricca, Tatiana I.

AU - Rodrigues, Vanderlei

AU - Rogatto, Silvia R.

AU - Romano, Camila M.

AU - Romeiro, Janaína G.

AU - Rossi, Antonio

AU - Sá, Renata G.

AU - Sales, Magaly M.

AU - Sant'Anna, Simone C.

AU - Santarosa, Patría L.

AU - Segato, Fernando

AU - Silva, Wilson A.

AU - Silva, Ismael D.C.G.

AU - Silva, Neusa P.

AU - Soares-Costa, Andrea

AU - Sonati, Maria F.

AU - Strauss, Bryan E.

AU - Tajara, Eloiza H.

AU - Valentini, Sandro R.

AU - Villanova, Fabiola E.

AU - Ward, Laura S.

AU - Zanette, Dalila L.

PY - 2004/7/1

Y1 - 2004/7/1

N2 - 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.

AB - 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.

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UR - http://www.scopus.com/inward/citedby.url?scp=3543131342&partnerID=8YFLogxK

U2 - 10.1101/gr.2111304

DO - 10.1101/gr.2111304

M3 - Article

C2 - 15197164

AN - SCOPUS:3543131342

SN - 1088-9051

VL - 14

SP - 1413

EP - 1423

JO - Genome research

JF - Genome research

IS - 7

ER -

A transcript finishing initiative for closing gaps in the human transcriptome

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