Article |
GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences
Bioinformatics Group, School of Theoretical and Applied Science, Ramapo College of New Jersey Mahwah, NJ 07430, USA
*To whom correspondence should be addressed. Tel: +1 201 684 7722; Fax: +1 201 684 7637; Email: pbagga{at}ramapo.edu
Received August 15, 2005. Revised October 8, 2005. Accepted October 8, 2005.
Guanine-rich nucleic acids are known to form highly stable G-quadruplex structures, also known as G-quartets. Recently, there has been a tremendous amount of interest in studying G-quadruplexes owing to the realization of their biological importance. G-rich sequences (GRSs) capable of forming G-quadruplexes are found in the vicinity of polyadenylation regions and are involved in regulating 3' end processing of mammalian pre-mRNAs. G-rich motifs are also known to play an important role in alternative, tissue-specific splicing by interacting with hnRNP H protein subfamily. Whether quadruplex structure directly plays a role in regulating RNA processing events requires further investigation. To date there has not been a comprehensive effort to study G-quadruplexes near RNA processing sites. We have applied a computational approach to map putative Quadruplex forming GRSs within the transcribed regions of a large number of alternatively processed human and mouse gene sequences that were obtained as fully annotated entries from GenBank and RefSeq. We have used the computed data to build the GRSDB database that provides a unique avenue for studying G-quadruplexes in the context of RNA processing sites. GRSDB website offers visual comparison of G-quadruplex distribution patterns among all the alternative RNA products of a gene with the help of dynamic graphics. At present, GRSDB contains data from 1310 human and mouse genes, of which 1188 are alternatively processed. It has a total of 379 223 predicted G-quadruplexes, of which 54 252 are near RNA processing sites. GRSDB is a good resource for researchers interested in investigating the functional relevance of G-quadruplexes, especially in the context of alternative RNA processing. It can be accessed at http://bioinformatics.ramapo.edu/grsdb/.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. C. Darnell, C. E. Fraser, O. Mostovetsky, and R. B. Darnell Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs Hum. Mol. Genet., September 1, 2009; 18(17): 3164 - 3177. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. D. Creacy, E. D. Routh, F. Iwamoto, Y. Nagamine, S. A. Akman, and J. P. Vaughn G4 Resolvase 1 Binds Both DNA and RNA Tetramolecular Quadruplex with High Affinity and Is the Major Source of Tetramolecular Quadruplex G4-DNA and G4-RNA Resolving Activity in HeLa Cell Lysates J. Biol. Chem., December 12, 2008; 283(50): 34626 - 34634. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. L. Huppert, A. Bugaut, S. Kumari, and S. Balasubramanian G-quadruplexes: the beginning and end of UTRs Nucleic Acids Res., November 1, 2008; 36(19): 6260 - 6268. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Arora, M. Dutkiewicz, V. Scaria, M. Hariharan, S. Maiti, and J. Kurreck Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif RNA, July 1, 2008; 14(7): 1290 - 1296. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Todd and S. Neidle The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements Nucleic Acids Res., May 1, 2008; 36(8): 2700 - 2704. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Zhang, Y. Lin, and C.-T. Zhang Greglist: a database listing potential G-quadruplex regulated genes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D372 - D376. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. K. Yadav, J. K. Abraham, P. Mani, R. Kulshrestha, and S. Chowdhury QuadBase: genome-wide database of G4 DNA occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D381 - D385. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Kikin, Z. Zappala, L. D'Antonio, and P. S. Bagga GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs Nucleic Acids Res., January 11, 2008; 36(suppl_1): D141 - D148. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Patel, A. T. Phan, and V. Kuryavyi Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics Nucleic Acids Res., December 3, 2007; 35(22): 7429 - 7455. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Todd, S. M. Haider, G. N. Parkinson, and S. Neidle Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter Nucleic Acids Res., September 27, 2007; 35(17): 5799 - 5808. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Wang, N. Dimova, and F. Cambi PLP/DM20 ratio is regulated by hnRNPH and F and a novel G-rich enhancer in oligodendrocytes Nucleic Acids Res., June 12, 2007; (2007) gkm387v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Burge, G. N. Parkinson, P. Hazel, A. K. Todd, and S. Neidle Quadruplex DNA: sequence, topology and structure Nucleic Acids Res., November 14, 2006; 34(19): 5402 - 5415. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Kikin, L. D'Antonio, and P. S Bagga QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W676 - W682. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Scaria, M. Hariharan, A. Arora, and S. Maiti Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W683 - W685. [Abstract] [Full Text] [PDF]
|
|