A transcript finishing initiative for closing gaps in the human transcriptome.
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.
Sogayar
Mari Cleide
MC
Camargo
Anamaria A
AA
Bettoni
Fabiana
F
Carraro
Dirce Maria
DM
Pires
Lilian C
LC
Parmigiani
Raphael B
RB
Ferreira
Elisa N
EN
de Sá Moreira
Eloísa
E
do Rosário D de O Latorre
Maria
M
Simpson
Andrew J G
AJ
Cruz
Luciana Oliveira
LO
Degaki
Theri Leica
TL
Festa
Fernanda
F
Massirer
Katlin B
KB
Sogayar
Mari C
MC
Filho
Fernando Camargo
FC
Camargo
Luiz Paulo
LP
Cunha
Marco A V
MA
De Souza
Sandro J
SJ
Faria
Milton
M
Giuliatti
Silvana
S
Kopp
Leonardo
L
de Oliveira
Paulo S L
PS
Paiva
Paulo B
PB
Pereira
Anderson A
AA
Pinheiro
Daniel G
DG
Puga
Renato D
RD
S de Souza
Jorge Estefano
JE
Albuquerque
Dulcineia M
DM
Andrade
Luís E C
LE
Baia
Gilson S
GS
Briones
Marcelo R S
MR
Cavaleiro-Luna
Ana M S
AM
Cerutti
Janete M
JM
Costa
Fernando F
FF
Costanzi-Strauss
Eugenia
E
Espreafico
Enilza M
EM
Ferrasi
Adriana C
AC
Ferro
Emer S
ES
Fortes
Maria A H Z
MA
Furchi
Joelma R F
JR
Giannella-Neto
Daniel
D
Goldman
Gustavo H
GH
Goldman
Maria H S
MH
Gruber
Arthur
A
Guimarães
Gustavo S
GS
Hackel
Christine
C
Henrique-Silva
Flavio
F
Kimura
Edna T
ET
Leoni
Suzana G
SG
Macedo
Cláudia
C
Malnic
Bettina
B
Manzini B
Carina V
CV
Marie
Suely K N
SK
Martinez-Rossi
Nilce M
NM
Menossi
Marcelo
M
Miracca
Elisabete C
EC
Nagai
Maria A
MA
Nobrega
Francisco G
FG
Nobrega
Marina P
MP
Oba-Shinjo
Sueli M
SM
Oliveira
Márika K
MK
Orabona
Guilherme M
GM
Otsuka
Audrey Y
AY
Paço-Larson
Maria L
ML
Paixão
Beatriz M C
BM
Pandolfi
Jose R C
JR
Pardini
Maria I M C
MI
Passos Bueno
Maria R
MR
Passos
Geraldo A S
GA
Pesquero
Joao B
JB
Pessoa
Juliana G
JG
Rahal
Paula
P
Rainho
Cláudia A
CA
Reis
Caroline P
CP
Ricca
Tatiana I
TI
Rodrigues
Vanderlei
V
Rogatto
Silvia R
SR
Romano
Camila M
CM
Romeiro
Janaína G
JG
Rossi
Antonio
A
Sá
Renata G
RG
Sales
Magaly M
MM
Sant'Anna
Simone C
SC
Santarosa
Patrícia L
PL
Segato
Fernando
F
Silva
Wilson A
WA
Silva
Ismael D C G
ID
Silva
Neusa P
NP
Soares-Costa
Andrea
A
Sonati
Maria F
MF
Strauss
Bryan E
BE
Tajara
Eloiza H
EH
Valentini
Sandro R
SR
Villanova
Fabiola E
FE
Ward
Laura S
LS
Zanette
Dalila L
DL
D017398:Alternative Splicing / Q000235:genetics; D002460:Cell Line; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D016384:Consensus Sequence / Q000235:genetics; D004273:DNA, Neoplasm; D030541:Databases, Genetic / Q000145:classification; D020224:Expressed Sequence Tags; D005796:Genes / Q000235:genetics; D015894:Genome, Human; D006367:HeLa Cells / Q000473:pathology; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D012984:Software; D012985:Software Design; D012986:Software Validation; D014158:Transcription, Genetic / Q000235:genetics*; D020298:U937 Cells / Q000473:pathology
D004273:DNA, Neoplasm