Known and novel post-transcriptional regulatory sequences are conserved across plant families (Q35775748)

10 August 2017

title

Known and novel post-transcriptional regulatory sequences are conserved across plant families (English)

1 reference

10 August 2017

Justin N Vaughn

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10 August 2017

Sally R Ellingson

series ordinal

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10 August 2017

Flavio Mignone

series ordinal

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10 August 2017

Albrecht von Arnim

series ordinal

1 reference

10 August 2017

language of work or name

English

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publication date

11 January 2012

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10 August 2017

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10 August 2017

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10 August 2017

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10 August 2017

page(s)

368-384

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High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

10 August 2017

cites work

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

12 July 2018

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Conserved noncoding sequences (CNSs) in higher plants

12 July 2018

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Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

12 July 2018

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Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs

12 July 2018

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Revisiting the principles of microRNA target recognition and mode of action

12 July 2018

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Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

12 July 2018

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RNA target specificity of the embryonic cell fate determinant POS-1.

12 July 2018

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Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

12 July 2018

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Conserved upstream open reading frames in higher plants

12 July 2018

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Conserved secondary structures in Aspergillus

12 July 2018

1 reference

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Widespread translational inhibition by plant miRNAs and siRNAs

12 July 2018

1 reference

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Towards deciphering the principles underlying an mRNA recognition code

12 July 2018

1 reference

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PlantGDB: a resource for comparative plant genomics

12 July 2018

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Update of ASRP: the Arabidopsis Small RNA Project database

12 July 2018

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Conservation and evolution of miRNA regulatory programs in plant development

12 July 2018

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Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes

12 July 2018

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RNA regulons: coordination of post-transcriptional events

12 July 2018

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Frequent gain and loss of functional transcription factor binding sites

12 July 2018

1 reference

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Deep conservation of microRNA-target relationships and 3'UTR motifs in vertebrates, flies, and nematodes

12 July 2018

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Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast

12 July 2018

1 reference

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Identification of plant promoter constituents by analysis of local distribution of short sequences

12 July 2018

1 reference

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High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes

12 July 2018

1 reference

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Detecting non-coding selective pressure in coding regions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Conservation of noncoding microsatellites in plants: implication for gene regulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups

12 July 2018

1 reference

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Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster

12 July 2018

1 reference

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Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes

12 July 2018

1 reference

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PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

12 July 2018

1 reference

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OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

12 July 2018

1 reference

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Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

12 July 2018

1 reference

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Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes

12 July 2018

1 reference

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Begin at the beginning: predicting genes with 5' UTRs

12 July 2018

1 reference

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Genome wide analysis of Arabidopsis core promoters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Plant conserved non-coding sequences and paralogue evolution

12 July 2018

1 reference

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In silico representation and discovery of transcription factor binding sites

12 July 2018

1 reference

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Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes

12 July 2018

1 reference

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Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

12 July 2018

1 reference

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Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter

12 July 2018

1 reference

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Combining phylogenetic data with co-regulated genes to identify regulatory motifs

12 July 2018

1 reference

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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

12 July 2018

1 reference

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12 July 2018

1 reference

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AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Discovery of regulatory elements by a computational method for phylogenetic footprinting

12 July 2018

1 reference

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The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study

12 July 2018

1 reference

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Characterization of monocot and dicot plant S-adenosyl-l-methionine decarboxylase gene families including identification in the mRNA of a highly conserved pair of upstream overlapping open reading frames

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Characterization and translational regulation of the arginine decarboxylase gene in carnation (Dianthus caryophyllus L.).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Subcellular localization of expansin mRNA in xylem cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

In vivo evaluation of the context sequence of the translation initiation codon in plants

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Inhibition of CCAAT/enhancer-binding protein alpha and beta translation by upstream open reading frames

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

PAML: a program package for phylogenetic analysis by maximum likelihood

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

UGA suppression by tRNACmCATrp occurs in diverse virus RNAs due to a limited influence of the codon context

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

The translational cis-regulatory element of mammalian ribosomal protein mRNAs is recognized by the plant translational apparatus

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Vertebrate mRNAs with a 5'-terminal pyrimidine tract are candidates for translational repression in quiescent cells: characterization of the translational cis-regulatory element.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Translation start site multiplicity of the CCAAT/enhancer binding protein alpha mRNA is dictated by a small 5' open reading frame.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons

12 July 2018

1 reference

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Regulatory element identification in subsets of transcripts: comparison and integration of current computational methods.

12 July 2018

1 reference

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Participation of leaky ribosome scanning in protein dual targeting by alternative translation initiation in higher plants

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Dual modes of natural selection on upstream open reading frames.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

A dual upstream open reading frame-based autoregulatory circuit controlling polyamine-responsive translation

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

BASIC PENTACYSTEINE1, a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285926

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis

15 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22237150

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Subcellular Visualization of Gene Transcripts Encoding Key Proteins of the Chlorophyll Accumulation Process in Developing Chloroplasts

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22237150

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The 5'-untranslated region of the ntp303 gene strongly enhances translation during pollen tube growth, but not during pollen maturation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22237150

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.031179.111

1 reference

10 August 2017

1 reference

10 August 2017

1 reference