Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. (Q34474706)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

title

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

alternative mRNA splicing, via spliceosome

7 March 2020

main subject

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

Zahra Ayatollahi

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

publication date

1 May 2015

1 reference

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7 March 2020

1 reference

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7 March 2020

volume

1 reference

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7 March 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

page(s)

995-1007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

Widespread intron retention in mammals functionally tunes transcriptomes

7 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Mass-spectrometry-based draft of the human proteome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Widespread inhibition of posttranscriptional splicing shapes the cellular transcriptome following heat shock

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Alternative splicing at the intersection of biological timing, development, and stress responses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Complexity of the alternative splicing landscape in plants.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

RBM5 is a male germ cell splicing factor and is required for spermatid differentiation and male fertility

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

RNA sequencing of cancer reveals novel splicing alterations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Dynamic integration of splicing within gene regulatory pathways

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Solution structure of the second RRM domain of RBM5 and its unusual binding characters for different RNA targets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Alternative splicing in plants--coming of age.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Functional consequences of developmentally regulated alternative splicing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

HMMER web server: interactive sequence similarity searching

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

ANCHOR: web server for predicting protein binding regions in disordered proteins.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

MEME SUITE: tools for motif discovery and searching

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Discovery and revision of Arabidopsis genes by proteogenomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Where do introns come from?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Alternative isoform regulation in human tissue transcriptomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Up-regulation of the proapoptotic caspase 2 splicing isoform by a candidate tumor suppressor, RBM5

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Altered splicing in exon 8 of the DNA replication factor CIZ1 affects subnuclear distribution and is associated with Alzheimer's disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Splicing regulation: from a parts list of regulatory elements to an integrated splicing code

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

On the expansion of the pentatricopeptide repeat gene family in plants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

PlantGDB: a resource for comparative plant genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Regulation of retention of FosB intron 4 by PTB

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Alternative RNA splicing regulation in the testis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

The connection between splicing and cancer.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Length-dependent prediction of protein intrinsic disorder.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

The evolution of spliceosomal introns: patterns, puzzles and progress

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

The DEAD-box protein family of RNA helicases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Exploiting heterogeneous sequence properties improves prediction of protein disorder.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Variation in alternative splicing across human tissues

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Single nucleotide polymorphism-based validation of exonic splicing enhancers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Protein domains correlate strongly with exons in multiple eukaryotic genomes--evidence of exon shuffling?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Intrinsic differences between authentic and cryptic 5' splice sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

FosB is highly expressed in normal mammary epithelia, but down-regulated in poorly differentiated breast carcinomas

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

A computational analysis of sequence features involved in recognition of short introns

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

A family of human RNA-binding proteins related to the Drosophila Bruno translational regulator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Introns and reading frames: correlation between splicing sites and their codon positions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Orchestrated intron retention regulates normal granulocyte differentiation.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Bruno-like proteins modulate flowering time via 3' UTR-dependent decay of SOC1 mRNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Removal of retained introns regulates translation in the rapidly developing gametophyte of Marsilea vestita

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

The evolutionary landscape of alternative splicing in vertebrate species

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Extensive structural renovation of retrogenes in the evolution of the Populus genome

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Intron retention is a major phenomenon in alternative splicing in Arabidopsis.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Origin of introns by ‘intronization’ of exonic sequences

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484396

Translational control of intron splicing in eukaryotes

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25934563

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A role for exon sequences and splice-site proximity in splice-site selection

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25934563

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Function of alternative splicing

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25934563

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.186585.114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

PubMed publication ID

25934563

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25934563%20AND%20SRC:MED&resulttype=core&format=json