Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Methods Protoc
2022 Jun 24;54:. doi: 10.3390/mps5040053.
Show Gene links
Show Anatomy links
Imaging Intron Evolution.
Panaro MA
,
Calvello R
,
Miniero DV
,
Mitolo V
,
Cianciulli A
.
???displayArticle.abstract???
Intron evolution may be readily imaged through the combined use of the "dot plot" function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate "Multiz" alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.
Abril,
Comparison of splice sites in mammals and chicken.
2005, Pubmed
Abril,
Comparison of splice sites in mammals and chicken.
2005,
Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Betancur-R,
The tree of life and a new classification of bony fishes.
2013,
Pubmed
Bourgeois,
On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements.
2019,
Pubmed
Broughton,
Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution.
2013,
Pubmed
Calvello,
Conservation/Mutation in the splice sites of cytokine receptor genes of mouse and human.
2013,
Pubmed
Calvello,
Unusual structure and splicing pattern of the vertebrate mitochondrial solute carrier SLC25A3 gene.
2018,
Pubmed
Chasin,
Searching for splicing motifs.
2007,
Pubmed
De Conti,
Exon and intron definition in pre-mRNA splicing.
2013,
Pubmed
Dolce,
The sequences of human and bovine genes of the phosphate carrier from mitochondria contain evidence of alternatively spliced forms.
1994,
Pubmed
Fedorova,
Introns in gene evolution.
2003,
Pubmed
Fiermonte,
Identification of the human mitochondrial oxodicarboxylate carrier. Bacterial expression, reconstitution, functional characterization, tissue distribution, and chromosomal location.
2001,
Pubmed
Fiermonte,
Expression in Escherichia coli, functional characterization, and tissue distribution of isoforms A and B of the phosphate carrier from bovine mitochondria.
1998,
Pubmed
Foote,
Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals.
1999,
Pubmed
Irimia,
Origin of spliceosomal introns and alternative splicing.
2014,
Pubmed
Kastner,
Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes.
2019,
Pubmed
Kohany,
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
2006,
Pubmed
Koonin,
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?
2006,
Pubmed
Koszul,
Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments.
2004,
Pubmed
Krayev,
Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing.
1982,
Pubmed
Lee,
Molecular clock calibrations and metazoan divergence dates.
1999,
Pubmed
Lin,
Growth Hormone Receptor Mutations Related to Individual Dwarfism.
2018,
Pubmed
Matlin,
Spliceosome assembly and composition.
2007,
Pubmed
Nei,
Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms.
2001,
Pubmed
Nobrega,
Comparative genomic analysis as a tool for biological discovery.
2004,
Pubmed
Palmieri,
The mitochondrial transporter family SLC25: identification, properties and physiopathology.
2013,
Pubmed
Palmieri,
Diseases Caused by Mutations in Mitochondrial Carrier Genes SLC25: A Review.
2020,
Pubmed
Panaro,
5' and 3' splicing signals evolution in vertebrates: Analysis in a conserved gene family.
2020,
Pubmed
Penny,
An overview of the introns-first theory.
2009,
Pubmed
Poverennaya,
Spliceosomal Introns: Features, Functions, and Evolution.
2020,
Pubmed
Rogozin,
Origin and evolution of spliceosomal introns.
2012,
Pubmed
Rose,
Introns as Gene Regulators: A Brick on the Accelerator.
2018,
Pubmed
Roy,
The origin of recent introns: transposons?
2004,
Pubmed
Schwartz,
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes.
2008,
Pubmed
Shaul,
How introns enhance gene expression.
2017,
Pubmed
Shi,
Mechanistic insights into precursor messenger RNA splicing by the spliceosome.
2017,
Pubmed
Sievers,
Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions.
2021,
Pubmed
Zhang,
The evolution mechanism of intron length.
2016,
Pubmed
