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Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome

https://doi.org/10.1155/2012/596274

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bies.080092openalex-snapshot

Quantitative regulation of alternative splicing in evolution and development

inferredcites →https://doi.org/10.1002/bies.20390openalex-snapshot

Unbalanced alternative splicing and its significance in cancer

inferredcites →https://doi.org/10.1002/bies.20692openalex-snapshot

Alternative splicing: current perspectives

inferredcites →https://doi.org/10.1006/dbio.2001.0379openalex-snapshot

Duplicate mitf Genes in Zebrafish: Complementary Expression and Conservation of Melanogenic Potential

inferredcites →https://doi.org/10.1006/jmbi.2000.4315openalex-snapshot

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen

inferredcites →https://doi.org/10.1007/s00239-008-9113-5openalex-snapshot

The Evolution of Alternative Splicing in the Pax Family: The View from the Basal Chordate Amphioxus

inferredcites →https://doi.org/10.1007/s10709-007-9223-9openalex-snapshot

Alternative splicing, gene duplication and connectivity in the genetic interaction network of the nematode worm Caenorhabditis elegans

inferredcites →https://doi.org/10.1007/s11427-010-4040-2openalex-snapshot

Spatiotemporal expression of Pax genes in amphioxus: Insights into Pax-related organogenesis and evolution

inferredcites →https://doi.org/10.1016/0092-8674(77)90180-5openalex-snapshot

An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA

inferredcites →https://doi.org/10.1016/0092-8674(80)90615-7openalex-snapshot

Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3′ ends

inferredcites →https://doi.org/10.1016/0092-8674(80)90617-0openalex-snapshot

Two mRNAs can be produced from a single immunoglobulin μ gene by alternative RNA processing pathways

inferredcites →https://doi.org/10.1016/j.biocel.2007.02.016openalex-snapshot

Alternative splicing in cancer: Noise, functional, or systematic?

inferredcites →https://doi.org/10.1016/j.cell.2008.10.046openalex-snapshot

Dynamic Regulation of Alternative Splicing by Silencers that Modulate 5′ Splice Site Competition

inferredcites →https://doi.org/10.1016/j.cell.2010.11.056openalex-snapshot

Epigenetics in Alternative Pre-mRNA Splicing

inferredcites →https://doi.org/10.1016/j.clinbiochem.2004.05.015openalex-snapshot

Splice variants as cancer biomarkers

inferredcites →https://doi.org/10.1016/j.febslet.2005.02.047openalex-snapshot

Are splicing mutations the most frequent cause of hereditary disease?

inferredcites →https://doi.org/10.1016/j.gde.2011.03.004openalex-snapshot

More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation

inferredcites →https://doi.org/10.1016/j.gene.2004.10.022openalex-snapshot

Function of alternative splicing

inferredcites →https://doi.org/10.1016/j.gene.2008.09.002openalex-snapshot

The evolutionary relationship between gene duplication and alternative splicing

inferredcites →https://doi.org/10.1016/j.jmb.2004.05.028openalex-snapshot

Improved Prediction of Signal Peptides: SignalP 3.0

inferredcites →https://doi.org/10.1016/j.tig.2004.12.004openalex-snapshot

Alternative splicing of conserved exons is frequently species-specific in human and mouse

inferredcites →https://doi.org/10.1016/j.tig.2006.01.001openalex-snapshot

Regulation of gene expression by alternative untranslated regions

inferredcites →https://doi.org/10.1016/j.tig.2007.10.001openalex-snapshot

Insights into the connection between cancer and alternative splicing

inferredcites →https://doi.org/10.1016/j.ygeno.2008.11.003openalex-snapshot

ASTD: The Alternative Splicing and Transcript Diversity database

inferredcites →https://doi.org/10.1016/j.ygeno.2009.02.006openalex-snapshot

AspAlt: A tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes

inferredcites →https://doi.org/10.1016/s0168-9525(00)02176-4openalex-snapshot

Alternative splicing: increasing diversity in the proteomic world

inferredcites →https://doi.org/10.1016/s0168-9525(03)00048-9openalex-snapshot

Duplication, degeneration and subfunctionalization of the nested synapsin–Timp genes in Fugu

inferredcites →https://doi.org/10.1016/s0378-1119(99)00339-xopenalex-snapshot

PAX3 gene structure, alternative splicing and evolution

inferredcites →https://doi.org/10.1016/s0968-0004(98)01336-xopenalex-snapshot

PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

inferredcites →https://doi.org/10.1021/cr068304copenalex-snapshot

Comparative Genomics and Evolution of Alternative Splicing: The Pessimists' Science

inferredcites →https://doi.org/10.1038/35057062openalex-snapshot

Initial sequencing and analysis of the human genome

inferredcites →https://doi.org/10.1038/76118openalex-snapshot

Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence

inferredcites →https://doi.org/10.1038/nature07509openalex-snapshot

Alternative isoform regulation in human tissue transcriptomes

inferredcites →https://doi.org/10.1038/nature08909openalex-snapshot

Expansion of the eukaryotic proteome by alternative splicing

inferredcites →https://doi.org/10.1038/nature09000openalex-snapshot

Deciphering the splicing code

inferredcites →https://doi.org/10.1038/nature09715openalex-snapshot

The developmental transcriptome of Drosophila melanogaster

inferredcites →https://doi.org/10.1038/nature10442openalex-snapshot

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

inferredcites →https://doi.org/10.1038/nature10523openalex-snapshot

Spatio-temporal transcriptome of the human brain

inferredcites →https://doi.org/10.1038/nbt.2153openalex-snapshot

BLUEPRINT to decode the epigenetic signature written in blood

inferredcites →https://doi.org/10.1038/ng.259openalex-snapshot

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

inferredcites →https://doi.org/10.1038/ng0893-332openalex-snapshot

dbEST — database for “expressed sequence tags”

inferredcites →https://doi.org/10.1038/ng1575openalex-snapshot

Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms

inferredcites →https://doi.org/10.1038/ng803openalex-snapshot

Alternative splicing and genome complexity

inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot

Mapping and quantifying mammalian transcriptomes by RNA-Seq

inferredcites →https://doi.org/10.1038/nmeth.1517openalex-snapshot

De novo assembly and analysis of RNA-seq data

inferredcites →https://doi.org/10.1038/nrg1204openalex-snapshot

The origin of new genes: glimpses from the young and old

inferredcites →https://doi.org/10.1038/nrg1451openalex-snapshot

How did alternative splicing evolve?

inferredcites →https://doi.org/10.1038/nrg2164openalex-snapshot

Splicing in disease: disruption of the splicing code and the decoding machinery

inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot

RNA-Seq: a revolutionary tool for transcriptomics

inferredcites →https://doi.org/10.1038/nrg2795openalex-snapshot

Next-generation genomics: an integrative approach

inferredcites →https://doi.org/10.1038/nrg2934openalex-snapshot

RNA sequencing: advances, challenges and opportunities

inferredcites →https://doi.org/10.1038/nrg3068openalex-snapshot

Next-generation transcriptome assembly

inferredcites →https://doi.org/10.1038/nrm2777openalex-snapshot

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

inferredcites →https://doi.org/10.1038/nsmb0109-13openalex-snapshot

Alternative splicing: regulation without regulators

inferredcites →https://doi.org/10.1073/pnas.0136770100openalex-snapshot

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

inferredcites →https://doi.org/10.1073/pnas.0602039103openalex-snapshot

Genomewide comparative analysis of alternative splicing in plants

inferredcites →https://doi.org/10.1073/pnas.102691299openalex-snapshot

Iris hypoplasia in mice that lack the alternatively spliced Pax6(5a) isoform

inferredcites →https://doi.org/10.1073/pnas.74.8.3171openalex-snapshot

Spliced segments at the 5′ terminus of adenovirus 2 late mRNA

inferredcites →https://doi.org/10.1074/jbc.272.51.32115openalex-snapshot

Tissue-specific Alternative Splicing of Ascidian Troponin I Isoforms

inferredcites →https://doi.org/10.1093/bib/bbl015openalex-snapshot

A hitchhiker's guide to expressed sequence tag (EST) analysis

inferredcites →https://doi.org/10.1093/bioinformatics/17.9.847openalex-snapshot

InterProScan – an integration platform for the signature-recognition methods in InterPro

inferredcites →https://doi.org/10.1093/bioinformatics/btg1015openalex-snapshot

Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes

inferredcites →https://doi.org/10.1093/genetics/161.1.259openalex-snapshot

Subfunctionalization of DuplicatemitfGenes Associated With Differential Degeneration of Alternative Exons in Fish

inferredcites →https://doi.org/10.1093/hmg/ddr370openalex-snapshot

Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts

inferredcites →https://doi.org/10.1093/icb/icq048openalex-snapshot

Alternative Splicing in Development and Function of Chordate Endocrine Systems: A Focus on Pax Genes

inferredcites →https://doi.org/10.1093/molbev/msm262openalex-snapshot

Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis

inferredcites →https://doi.org/10.1093/molbev/msr127openalex-snapshot

The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates

inferredcites →https://doi.org/10.1093/nar/30.1.276openalex-snapshot

The Pfam Protein Families Database

inferredcites →https://doi.org/10.1093/nar/gkg355openalex-snapshot

Conservation of human alternative splice events in mouse

inferredcites →https://doi.org/10.1093/nar/gkg786openalex-snapshot

Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences

inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot

Database resources of the National Center for Biotechnology Information: update

inferredcites →https://doi.org/10.1093/nar/gkh121openalex-snapshot

The Pfam protein families database

inferredcites →https://doi.org/10.1093/nar/gkl884openalex-snapshot

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species

inferredcites →https://doi.org/10.1093/nar/gkl924openalex-snapshot

Different levels of alternative splicing among eukaryotes

inferredcites →https://doi.org/10.1093/nar/gkl992openalex-snapshot

ECgene: an alternative splicing database update

inferredcites →https://doi.org/10.1093/nar/gkn741openalex-snapshot

Database resources of the National Center for Biotechnology Information

inferredcites →https://doi.org/10.1101/gr.093302.109openalex-snapshot

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

inferredcites →https://doi.org/10.1101/gr.099226.109openalex-snapshot

Sex-specific and lineage-specific alternative splicing in primates

inferredcites →https://doi.org/10.1101/gr.113803.110openalex-snapshot

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

inferredcites →https://doi.org/10.1101/gr.4197006openalex-snapshot

Evolution of alternative splicing after gene duplication

inferredcites →https://doi.org/10.1101/gr.4236606openalex-snapshot

Evolution of exon–intron structure and alternative splicing in fruit flies and malarial mosquito genomes

inferredcites →https://doi.org/10.1101/gr.764102openalex-snapshot

Selecting for Functional Alternative Splices in ESTs

inferredcites →https://doi.org/10.1126/science.1058040openalex-snapshot

The Sequence of the Human Genome

inferredcites →https://doi.org/10.1126/science.1089370openalex-snapshot

The Origins of Genome Complexity

inferredcites →https://doi.org/10.1126/science.1090100openalex-snapshot

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

inferredcites →https://doi.org/10.1126/science.1184208openalex-snapshot

Regulation of Alternative Splicing by Histone Modifications

inferredcites →https://doi.org/10.1186/1471-2229-8-18openalex-snapshot

Characterization of paralogous protein families in rice

inferredcites →https://doi.org/10.1186/1741-7007-7-23openalex-snapshot

Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay

inferredcites →https://doi.org/10.1261/rna.2460411openalex-snapshot

Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster

inferredcites →https://doi.org/10.1371/journal.pbio.0030314openalex-snapshot

Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate

inferredcites →https://doi.org/10.1371/journal.pbio.1000001openalex-snapshot

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits

inferredcites →https://doi.org/10.1371/journal.pcbi.0030033openalex-snapshot

The (In)dependence of Alternative Splicing and Gene Duplication

inferredcites →https://doi.org/10.1371/journal.pgen.1001080openalex-snapshot

Did Genetic Drift Drive Increases in Genome Complexity?

inferredcites →https://doi.org/10.1371/journal.pgen.1001236openalex-snapshot

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

inferredcites →https://doi.org/10.1371/journal.pone.0003587openalex-snapshot

Width of Gene Expression Profile Drives Alternative Splicing

inferredcites →https://doi.org/10.1373/clinchem.2014.237016openalex-snapshot

The Sequence of the Human Genome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species

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Composition and evolutionary importance of transposable elements in humans and primates

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Insertion of 275-bp SINE into first intron of PDIA4 gene is associated with litter size in Xiang pigs

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Alternative splicing of mutually exclusive exons—A review

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Comparative landscape of alternative splicing in fruit plants

inferred← citeshttps://doi.org/10.1016/j.drup.2020.100728openalex-snapshot

The role of alternative splicing in cancer: From oncogenesis to drug resistance

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Identification and functional regulation of three alternative splicing isoforms of the fthl27 gene in miiuy croaker, Miichthys miiuy

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2020.04.143openalex-snapshot

Properties of two spliceoforms of major ampullate spidroin 1 reveal unique functions of N-linker region

inferred← citeshttps://doi.org/10.1016/j.isci.2024.111626openalex-snapshot

Alternative splicing of EZH2 regulated by SNRPB mediates hepatocellular carcinoma progression via BMP2 signaling pathway

inferred← citeshttps://doi.org/10.1016/j.neuro.2015.04.006openalex-snapshot

Perinatal methylmercury exposure perturbs the expression of Plp1 and Cnp splice variants in cerebellum of rat pups

inferred← citeshttps://doi.org/10.1016/j.plantsci.2024.112236openalex-snapshot

Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops

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Genome-wide identification and characterisation of hevein precursor genes in Hevea brasiliensis

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Identification and characterization of genic simple sequence repeats from the leaf and stem transcriptomes of Stevia rebaudiana Bertoni

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Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

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Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

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Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis

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Single-molecule long-read sequencing facilitates shrimp transcriptome research

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Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)

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Principles and correction of 5’-splice site selection

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Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae

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Are all of the human exons alternatively spliced?

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Full-length hybrid transcriptome of the olfactory rosette in Senegalese sole ( Solea senegalensis ): an essential genomic resource for improving reproduction on farms

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Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity

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Genome-wide Analysis of Alternative Gene Splicing Associated with Virulence in the Brown Planthopper Nilaparvata lugens (Hemiptera: Delphacidae)

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Presence–Absence Variation in A. thaliana Is Primarily Associated with Genomic Signatures Consistent with Relaxed Selective Constraints

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Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity

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Alternative Splice in Alternative Lice

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Transcription-Associated Mutation Promotes RNA Complexity in Highly Expressed Genes—A Major New Source of Selectable Variation

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MeDAS: a Metazoan Developmental Alternative Splicing database

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High-resolution genome mapping and functional dissection of chlorogenic acid production in Lonicera maackii

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Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

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Polyploidy and novelty: Gottlieb's legacy

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Alternative splicing and the evolution of phenotypic novelty

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Species-specific deployment of Runx2 isoforms and differential regulation of target genes during avian jaw development and evolution

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An axonemal intron splicing program sustains Plasmodium male development

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Lineage‐specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana

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Molecular mechanisms of Eda‐mediated adaptation to freshwater in threespine stickleback

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Genome‐wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families

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Alternative splicing of lncRNA LAIR fine‐tunes the regulation of neighboring yield‐related gene LRK1 expression in rice

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Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly

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Exploration of alternative splicing events in ten different grapevine cultivars

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Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL

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Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice

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In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue

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Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

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NFAT1 and NFAT3 Cooperate with HDAC4 during Regulation of Alternative Splicing of PMCA Isoforms in PC12 Cells

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Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing

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Comparison of Alternative Splicing Junction Detection Tools Using RNASeq Data

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Pax2/5/8 and Pax6 alternative splicing events in basal chordates and vertebrates: a focus on paired box domain

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A Bioinformatics-Based Alternative mRNA Splicing Code that May Explain Some Disease Mutations Is Conserved in Animals

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RNA-Seq Perspectives to Improve Clinical Diagnosis

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Mitochondrial Genome Sequence of the Legume Vicia faba

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Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

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Trans-Disciplinary Responses to Climate Change: Lessons from Rice-Based Systems in Asia

inferred← citeshttps://doi.org/10.3390/genes11101228openalex-snapshot

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

inferred← citeshttps://doi.org/10.3390/ijms161126017openalex-snapshot

Abnormalities in Alternative Splicing of Apoptotic Genes and Cardiovascular Diseases

inferred← citeshttps://doi.org/10.4137/ebo.s20772openalex-snapshot

Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs

inferred← citeshttps://doi.org/10.4172/jcsb.1000156openalex-snapshot

A Systems Biology View of the Spliceosome Component Phf5a in Relation to Estrogen and Cancer

inferred← citeshttps://doi.org/10.5812/gct.14832openalex-snapshot

Individuals With Normal GLA Gene Sequence May Present Abnormally Spliced Alpha-Galactosidase mRNA Transcripts

inferred← citeshttps://doi.org/10.6084/m9.figshare.21213428openalex-snapshot

Additional file 1 of Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice

inferred← citeshttps://doi.org/10.6084/m9.figshare.21213431openalex-snapshot

Additional file 2 of Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice

inferred← citeshttps://doi.org/10.6084/m9.figshare.21213434openalex-snapshot

Additional file 6 of Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice

inferred← citeshttps://doi.org/10.64898/2026.04.28.720569openalex-snapshot

A high-resolution, sex-stratified atlas of transcriptional and alternative splicing dynamics in the fasting mouse liver

inferred← citeshttps://doi.org/10.7554/elife.94802openalex-snapshot

Alternative splicing across the tree of life

inferred← citeshttps://doi.org/10.7554/elife.94802.1openalex-snapshot

Evolutionary trends of alternative splicing

inferred← citeshttps://doi.org/10.7554/elife.94802.2openalex-snapshot

Alternative Splicing Across the Tree of Life: A Comparative Study

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