PACdb:: PolyA cleavage site and 3′-UTR database

被引:47
作者
Brockman, JM
Singh, P
Liu, DL
Quinlan, S
Salisbury, J
Graber, JH
机构
[1] Jackson Lab, Bar Harbor, ME 04609 USA
[2] Boston Univ, Bioinformat Program, Boston, MA 02215 USA
[3] Univ Maine, Funct Genom Program, Orono, ME 04469 USA
关键词
D O I
10.1093/bioinformatics/bti589
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The PolyA Cleavage Site and 3'-UTR Database (PACdb) is a web-accessible database that catalogs putative 3'-processing sites and 3'-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3'-processing events.
引用
收藏
页码:3691 / 3693
页数:3
相关论文
共 18 条
[1]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[2]   Patterns of variant polyadenylation signal usage in human genes [J].
Beaudoing, E ;
Freier, S ;
Wyatt, JR ;
Claverie, JM ;
Gautheret, D .
GENOME RESEARCH, 2000, 10 (07) :1001-1010
[3]   Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays [J].
Brenner, S ;
Johnson, M ;
Bridgham, J ;
Golda, G ;
Lloyd, DH ;
Johnson, D ;
Luo, SJ ;
McCurdy, S ;
Foy, M ;
Ewan, M ;
Roth, R ;
George, D ;
Eletr, S ;
Albrecht, G ;
Vermaas, E ;
Williams, SR ;
Moon, K ;
Burcham, T ;
Pallas, M ;
DuBridge, RB ;
Kirchner, J ;
Fearon, K ;
Mao, J ;
Corcoran, K .
NATURE BIOTECHNOLOGY, 2000, 18 (06) :630-634
[4]   Saccharomyces genome database:: Underlying principles and organisation [J].
Dwight, SS ;
Balakrishnan, R ;
Christie, KR ;
Costanzo, MC ;
Dolinski, K ;
Engel, SR ;
Feierbach, B ;
Fisk, DG ;
Hirschman, J ;
Hong, EL ;
Issel-Tarver, L ;
Nash, RS ;
Sethuraman, A ;
Starr, B ;
Theesfeld, CL ;
Andrada, R ;
Binkley, G ;
Dong, Q ;
Lane, C ;
Schroeder, M ;
Weng, S ;
Botstein, D ;
Cherry, JM .
BRIEFINGS IN BIOINFORMATICS, 2004, 5 (01) :9-22
[5]   Alternative poly(A) site selection in complex transcription units: Means to an end? [J].
EdwaldsGilbert, G ;
Veraldi, KL ;
Milcarek, C .
NUCLEIC ACIDS RESEARCH, 1997, 25 (13) :2547-2561
[6]   Alternate polyadenylation in human mRNAs: A large-scale analysis by EST clustering [J].
Gautheret, D ;
Poirot, O ;
Lopez, F ;
Audic, S ;
Claverie, JM .
GENOME RESEARCH, 1998, 8 (05) :524-530
[7]   The Ensembl genome database project [J].
Hubbard, T ;
Barker, D ;
Birney, E ;
Cameron, G ;
Chen, Y ;
Clark, L ;
Cox, T ;
Cuff, J ;
Curwen, V ;
Down, T ;
Durbin, R ;
Eyras, E ;
Gilbert, J ;
Hammond, M ;
Huminiecki, L ;
Kasprzyk, A ;
Lehvaslaiho, H ;
Lijnzaad, P ;
Melsopp, C ;
Mongin, E ;
Pettett, R ;
Pocock, M ;
Potter, S ;
Rust, A ;
Schmidt, E ;
Searle, S ;
Slater, G ;
Smith, J ;
Spooner, W ;
Stabenau, A ;
Stalker, J ;
Stupka, E ;
Ureta-Vidal, A ;
Vastrik, I ;
Clamp, M .
NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :38-41
[8]   Gene structure prediction and alternative splicing analysis using genomically aligned ESTs [J].
Kan, ZY ;
Rouchka, EC ;
Gish, WR ;
States, DJ .
GENOME RESEARCH, 2001, 11 (05) :889-900
[9]   A comparison of mammalian and yeast pre-mRNA 3'-end processing [J].
Keller, W ;
MinvielleSebastia, L .
CURRENT OPINION IN CELL BIOLOGY, 1997, 9 (03) :329-336
[10]   Reexamining the polyadenylation signal: were we wrong about AAUAAA? [J].
MacDonald, CC ;
Redondo, JL .
MOLECULAR AND CELLULAR ENDOCRINOLOGY, 2002, 190 (1-2) :1-8