Predicting the impact of alternative splicing on plant MADS domain protein function (Q34147600)

31 July 2017

title

Predicting the impact of alternative splicing on plant MADS domain protein function (English)

1 reference

protein function prediction

31 July 2017

main subject

0 references

alternative mRNA splicing, via spliceosome

1 reference

inferred from title

author

Roeland C H J van Ham

object named as

Roeland C H J van Ham

1 reference

31 July 2017

Edouard I Severing

1 reference

31 July 2017

Aalt D J van Dijk

1 reference

31 July 2017

Giuseppa Morabito

1 reference

31 July 2017

Jacqueline Busscher-Lange

1 reference

31 July 2017

Richard G H Immink

1 reference

31 July 2017

language of work or name

English

0 references

publication date

25 January 2012

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

31 July 2017

page(s)

e30524

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

start time

25 January 2012

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Cytoscape 2.8: new features for data integration and network visualization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Analysis and design of RNA sequencing experiments for identifying isoform regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Single amino acid change alters the ability to specify male or female organ identity.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Alternative splicing and evolution: diversification, exon definition and function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Internal and external paralogy in the evolution of tropomyosin genes in metazoans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Expansion of the eukaryotic proteome by alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

The 'ABC' of MADS domain protein behaviour and interactions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Floral organ identity: 20 years of ABCs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Temperature Induced Flowering in Arabidopsis thaliana

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Splicing variation at a FLOWERING LOCUS C homeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Structural implication of splicing stochastics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

The Sequence Alignment/Map format and SAMtools

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

TopHat: discovering splice junctions with RNA-Seq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

SEPALLATA3: the 'glue' for MADS box transcription factor complex formation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

PtFLC homolog from trifoliate orange (Poncirus trifoliata) is regulated by alternative splicing and experiences seasonal fluctuation in expression level.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Database resources of the National Center for Biotechnology Information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Genome-wide analyses of alternative splicing in plants: opportunities and challenges.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Choose your partners: dimerization in eukaryotic transcription factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Clustal W and Clustal X version 2.0

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

The implications of alternative splicing in the ENCODE protein complement

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Evolutionary conservation of the FLOWERING LOCUS C-mediated vernalization response: evidence from the sugar beet (Beta vulgaris).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Potent induction of Arabidopsis thaliana flowering by elevated growth temperature.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Genomewide comparative analysis of alternative splicing in plants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Pfam: clans, web tools and services

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

INCOMPOSITA: a MADS-box gene controlling prophyll development and floral meristem identity in Antirrhinum.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

PlantGDB, plant genome database and analysis tools

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

The major clades of MADS-box genes and their role in the development and evolution of flowering plants.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

And then there were many: MADS goes genomic

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Large scale study of protein domain distribution in the context of alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Common exon duplication in animals and its role in alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Physiological and molecular basis of thyroid hormone action

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Identification of a MADS-box gene, FLOWERING LOCUS M, that represses flowering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

EMBOSS: the European Molecular Biology Open Software Suite

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Rose MADS-box genes 'MASAKO C1 and D1' homologous to class C floral identity genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

An ancestral MADS-box gene duplication occurred before the divergence of plants and animals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

CAP3: A DNA sequence assembly program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

MADS domain proteins in plant development

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Eucalyptus has functional equivalents of the Arabidopsis AP1 gene

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

ZEMa, a member of a novel group of MADS box genes, is alternatively spliced in maize endosperm

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Identification of common molecular subsequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

A general method applicable to the search for similarities in the amino acid sequence of two proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

The neighbor-joining method: a new method for reconstructing phylogenetic trees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

A small-scale procedure for the rapid isolation of plant RNAs.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Origin of alternative splicing by tandem exon duplication

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Comprehensive interaction map of the Arabidopsis MADS Box transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

A repressor complex governs the integration of flowering signals in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Two paralogous genes encoding small subunits of ADP-glucose pyrophosphorylase in maize, Bt2 and L2, replace the single alternatively spliced gene found in other cereal species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Evolution of alternative splicing after gene duplication

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Complex Rearrangements Lead to Novel Chimeric Gene Fusion Polymorphisms at the Arabidopsis thaliana MAF2-5 Flowering Time Gene Cluster

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

Evolution in action: following function in duplicated floral homeotic genes

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266260

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

28 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0030524

Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts

21 January 2018

1 reference

12 December 2020

Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins

1 reference

12 December 2020

The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat

1 reference

12 December 2020

Context analysis of termination codons in mRNA that are recognized by plant NMD

1 reference

12 December 2020

A BsisterMADS-box gene involved in ovule and seed development in petunia and Arabidopsis

1 reference

12 December 2020

Evidence for alternative splicing of MADS-box transcripts in developing cotton fibre cells

1 reference

12 December 2020

Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses

1 reference

12 December 2020

A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0030524

Identifiers

DOI

1 reference

31 July 2017

0 references

1 reference

31 July 2017

1 reference