Laboratory of RNA Biology

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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]

Keywords: molecular biology, RNA, processing, alternative splicing, cryptic splicing, transcriptome integrity, hnRNP, gene regulation, gene expression, evolution, proteomic diversity, complexity, splicing factors, protein kinases, cell signaling, neurons, endocrine cells, SNP, mutation, cancer, GWAS, human health/genetic diseases

Highlights of some of the findings by the lab:

Splice Site Matrices of >1000 Species/lineages

REPAG_GenomesR38R91

(Right-click image to view details)

The REPAG element specifically among mammals
(Sohail M., and Xie J. Molecular & Cellular Biology, 2015, 35(12): 2203-2214)

(Right-click to view details)
Adaptive splicing

(Right-click image to view details)

The CaRRE element among vertebrates (Liu GD, et al., J. Biol. Chem. 2012, 287:22709–22716)

Molecular basis of the depolarization-regulated alternative splicing of the STREX exon of the Slo1 gene

Importance of proper splicing control in hormone production: aberrant splice variant of prolactin (right) due to the loss of hnRNP L

A new group of introns: REPA element 'inserted' between the Py and 3'AG and its effects on alternative splicing

Consensus of 1000 human REPAG intron ends (Credit: Aydan Wang)

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

Misce. links:

WES, EXON, Exome and Protein-Coding Regions, Non-coding regions, UTR

Eradication of Polio in China
RNA Meeting in Winnipeg, June 23-26, 2019 Some RNA/DNA literature/history:
Why are the snRNAs in splicing called U1, U2, U4, U5, U6 snRNAs? Here is the original paper that describes the use of Us in the names for some of the small nuclear RNAs that are Uridylic acid-rich, by James L. Hodnett and Harris Busch of the Baylor University College of Medicine in 1968: Hodnett JL, Busch H. Isolation and characterization of uridylic acid-rich 7 S ribonucleic acid of rat liver nuclei. J Biol Chem. 1968 Dec 25;243(24):6334-42. |PDF|
125 Questions in Science, which ones are related to Alternative Splicing?
How to present a clean, highlight revision text without the deleted words in the text or balloons after tracking changes in WORD?
Albert Einstein the mediocre: Why the h-index is a bogus measure of academic impact (Reader discretion is advised).
Sequencing RNA and its modifications Webinar
Opinions about the term non-coding RNA
谁翻译了基因一词？维基百科

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