PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes

被引：114

作者：

Lee, Ju Youn ^{[1
]}

Yeh, Ijen ^{[1
]}

Park, Ji Yeon ^{[1
]}

Tian, Bin ^{[1
]}

机构：

[1] Univ Med & Dent New Jersey, Sch Med, Dept Biochem & Mol Biol, Newark, NJ 07101 USA

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

关键词：

D O I：

10.1093/nar/gkl870

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Polyadenylation of nascent transcripts is one of the key mRNA processing events in eukaryotic cells. A large number of human and mouse genes have alternative polyadenylation sites, or poly(A) sites, leading to mRNA variants with different protein products and/or 3'-untranslated regions (3'-UTRs). PolyA_DB 2 contains poly(A) sites identified for genes in several vertebrate species, including human, mouse, rat, chicken and zebrafish, using alignments between cDNA/ESTs and genome sequences. Several new features have been added to the database since its last release, including syntenic genome regions for human poly(A) sites in seven other vertebrates and cis-element information adjacent to poly(A) sites. Trace sequences are used to provide additional evidence for poly(A/T) tails in cDNA/ESTs. The updated database is intended to broaden poly(A) site coverage in vertebrate genomes, and provide means to assess the authenticity of poly(A) sites identified by bioinformatics.

引用

页码：D165 / D168

页数：4

共 26 条

[1] PACdb:: PolyA cleavage site and 3′-UTR database [J].

Brockman, JM ;

Singh, P ;

Liu, DL ;

Quinlan, S ;

Salisbury, J ;

Graber, JH .

BIOINFORMATICS, 2005, 21 (18) :3691-3693

[2] Prediction of mRNA polyadenylation sites by support vector machine [J].

Cheng, Yiming ;

Miura, Robert M. ;

Tian, Bin .

BIOINFORMATICS, 2006, 22 (19) :2320-2325

[3] Multiple sequence alignment with the Clustal series of programs [J].

Chenna, R ;

Sugawara, H ;

Koike, T ;

Lopez, R ;

Gibson, TJ ;

Higgins, DG ;

Thompson, JD .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3497-3500

[4] Mechanism and regulation of mRNA polyadenylation [J].

Colgan, DF ;

Manley, JL .

GENES & DEVELOPMENT, 1997, 11 (21) :2755-2766

[5] A history of poly A sequences: From formation to factors to function [J].

Edmonds, M .

PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY, VOL 71, 2002, 71 :285-389

[6]

EDWALDSGILBERG G, 1997, NUCLEIC ACIDS RES, V525, P2547

[7] 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

[8] RNA-quality control by the exosome [J].

Houseley, Jonathan ;

LaCava, John ;

Tollervey, David .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2006, 7 (07) :529-539

[9] Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation [J].

Hu, J ;

Lutz, CS ;

Wilusz, J ;

Tian, B .

RNA, 2005, 11 (10) :1485-1493

[10] Long-range heterogeneity at the 3′ ends of human mRNAs [J].

Iseli, C ;

Stevenson, BJ ;

de Souza, SJ ;

Samaia, HB ;

Camargo, AA ;

Buetow, KH ;

Strausberg, RL ;

Simpson, AJG ;

Bucher, P ;

Jongeneel, CV .

GENOME RESEARCH, 2002, 12 (07) :1068-1074

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