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Database: Splice Site Matrices of Different Species

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Faculty of Graduate Studies

Department of Physiology & Pathophysiology

College of Medicine

Faculty of Health Sciences

University of Manitoba

Splice Site Matrices/Constraints of >1000 Species/Lineages

Here you can download the consensus sequences of the splice sites of each species from the matrices.

List of SS Matrices/Constraints	Ensembl (Genome) Release #	Last updated
3SS_5SS_Matrices_R43/R96	R43/R96	6-07-2019
3SS_5SS_Matrices_R40/R93	R40/R93	9-26-2018
3SS_5SS_Matrices_R38/R91	R38/R91	5-09-2018
3SS_5SS_Matrices/ConstraintsR36/R90	R36/R90	3-26-2018

MEME motifs of the 5' splice sites (-5 - +10) of ensembl releases 42/95.

The 5' splice site of protist Acanthamoeba_castellanii_str_neff

MEME motifs of the 3' splice sites (-30 - +2) of ensembl releases 42/95 (including the branch point, polypyrimidine tract and 3' AG regions, and 5' GT in rare cases, depending on the species). In total, 1,453 genomes of different species/strains of fungi, metazoa, plants and protists.

The branchpoint motif of fungus R. taiwanensis

MEME motifs of the 3' splice sites (-12 - +2) of ensembl releases 42/95 (including the polypyrimidine tract and 3' AG regions, and branchpoints in some cases, of most species)

The 3' splice site of humans
B maylayi 3' splice
site MEME

The 3' splice site of nematode Brugia_malayi

The 3' splice site (BP & 3' AG) of protist Babesia_microti_ri

The relatively fixed position of the branchpoint motif TNAY explains the unusual 3' splice site Y-8 and R-6 nucleotides in this species in Nguyen, et al., Gene, 2018, 660:92-101, and Frontiers in Genetics, doi: 10.3389/fgene.2018.00741. |PDF|.

What else could these matrices be used for in so many species? Here are some examples:

To assess the effect of a mutation on a splice site in any of the species.
To assess the effect of a SNP on a splice site.
To assess the possibility for a cryptic splice site(s) in the genome to cause aberrant splicing of any of the species.
To help make mutations within a splice site for splicing reporter or other assays.
To assess the effect of different consensuses of splice sites of different species on the heterologous expression of splicing reporters.
To help identify potentially unusual U snRNAs or splicing factors based on the matrices and consensus of the splice sites of a species.
To compare the common and different consensus sequences of splice sites of different species or branches of life for their evolutionary changes.
The splice site constraints could be used to predict the abundance of alternative splicing in any of these species.

Questions or suggestions? E-mail.

References:

Nguyen H, Das U, Xie J. Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity. RNA Biology, Dec. 2019, http://dx.doi.org/10.1080/15476286.2019.1697548.
Nguyen H, Das U, Wang B, Xie J, The matrices and constraints of GT/AG splice sites of more than 1000 species/lineages. Gene, 2018, 660:92-101.
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009. [full text]

Research in this lab has been supported by CIHR , NCIC, CBCF, NSERC, MMSF, MHRC and CFI.

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CONTACT:
Prof. Jiuyong Xie
Department of Physiology
University of Manitoba
440 Basic Medical Sciences Bldg
745 Bannatyne Avenue
Winnipeg, MB CANADA
R3E 0J9
Tel +1-204 975-7774 (O),
+1-204 975 7740 (lab)