(Q33791162)

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Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

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scholarly article

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Europe PubMed Central

29 July 2017

Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals (English)

1 reference

Europe PubMed Central

29 July 2017

protein evolution

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4

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Eugene V Koonin

1 reference

Europe PubMed Central

29 July 2017

author name string

Svetlana A Shabalina

1

1 reference

Europe PubMed Central

29 July 2017

Aleksey Y Ogurtsov

2

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Europe PubMed Central

29 July 2017

Nikolay A Spiridonov

3

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Europe PubMed Central

29 July 2017

language of work or name

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publication date

3 May 2014

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Europe PubMed Central

29 July 2017

Nucleic Acids Research

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Europe PubMed Central

29 July 2017

42

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Europe PubMed Central

29 July 2017

11

1 reference

Europe PubMed Central

29 July 2017

7132-7144

1 reference

Europe PubMed Central

29 July 2017

Landscape and variation of RNA secondary structure across the human transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Exonic transcription factor binding directs codon choice and affects protein evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

The UCSC Genome Browser database: 2014 update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Transcriptome and genome sequencing uncovers functional variation in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Counting on co-transcriptional splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

The impact of splicing on protein domain architecture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Dynamic integration of splicing within gene regulatory pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing: a pivotal step between eukaryotic transcription and translation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

A complex network of factors with overlapping affinities represses splicing through intronic elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Transcriptional elongation and alternative splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Landscape of transcription in human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

A quantitative atlas of polyadenylation in five mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

CDD: a Conserved Domain Database for the functional annotation of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Connections between alternative transcription and alternative splicing in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Genome-wide functional analysis of human 5' untranslated region introns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

DBTSS provides a tissue specific dynamic view of Transcription Start Sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Evolution of alternative and constitutive regions of mammalian 5'UTRs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Expansion of the human mu-opioid receptor gene architecture: novel functional variants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative isoform regulation in human tissue transcriptomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Expression patterns of protein kinases correlate with gene architecture and evolutionary rates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative promoters influence alternative splicing at the genomic level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing: current perspectives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Functional coupling of last-intron splicing and 3'-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

The UCSC genome browser database: update 2007.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Intron size, abundance, and distribution within untranslated regions of genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing in human transcriptome: functional and structural influence on proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing: new insights from global analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

A periodic pattern of mRNA secondary structure created by the genetic code

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Hearing silence: non-neutral evolution at synonymous sites in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Multiple links between transcription and splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

The mammalian transcriptome and the function of non-coding DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Complex controls: the role of alternative promoters in mammalian genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Increase of functional diversity by alternative splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

On the importance of being co-transcriptional

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Transcriptional activators differ in their abilities to control alternative splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

The mRNA assembly line: transcription and processing machines in the same factory

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

An extensive network of coupling among gene expression machines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Selective constraint in intergenic regions of human and mouse genomes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Analysis of expressed sequence tags indicates 35,000 human genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Evolution of the Zfx and Zfy genes: rates and interdependence between the genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Poly(A) site choice rather than splice site choice governs the regulated production of IgM heavy-chain RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

4 July 2018

Tissue-specific alternative splicing remodels protein-protein interaction networks.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

Systematic analysis of alternative promoters correlated with alternative splicing in human genes.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

Assessing the impact of alternative splicing on domain interactions in the human proteome

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https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

DBTSS: database of transcription start sites, progress report 2008.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

OWEN: aligning long collinear regions of genomes.

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https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

Linear motifs confer functional diversity onto splice variants

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

The evolutionary landscape of alternative splicing in vertebrate species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4066770

30 October 2018

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU342

21 January 2018

Classification of common conserved sequences in mammalian intergenic regions

1 reference

https://pubmed.ncbi.nlm.nih.gov/24792168

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKU342

1 reference

Europe PubMed Central

29 July 2017

1 reference

Europe PubMed Central

29 July 2017

1 reference

Europe PubMed Central

29 July 2017

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