Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability (Q21266616)

Dimensions Publication ID

Dimensions

19 August 2022

L Aravind

2

L

Aravind

1 reference

Dimensions Publication ID

Dimensions

1009042846

Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions

19 August 2022

language of work or name

English

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publication date

16 July 2004

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published in

BMC Genomics

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volume

5

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issue

1

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page(s)

45

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cites work

1 reference

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Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing

19 March 2017

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The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci

19 March 2017

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Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein

19 March 2017

1 reference

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Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins

19 March 2017

1 reference

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Comparative genomics and evolution of proteins involved in RNA metabolism

19 March 2017

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Functional organization of the yeast proteome by systematic analysis of protein complexes

19 March 2017

1 reference

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RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex

19 March 2017

1 reference

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The Sm domain is an ancient RNA-binding motif with oligo(U) specificity

19 March 2017

1 reference

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Initial sequencing and analysis of the human genome

19 March 2017

1 reference

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Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach

19 March 2017

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A Sm-like protein complex that participates in mRNA degradation

19 March 2017

1 reference

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Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin

19 March 2017

1 reference

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Horizontal gene transfer among genomes: the complexity hypothesis

19 March 2017

1 reference

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

19 March 2017

1 reference

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Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors

19 March 2017

1 reference

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SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins

19 March 2017

1 reference

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Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box

19 March 2017

1 reference

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Global analysis of protein localization in budding yeast

19 March 2017

1 reference

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Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Structure and assembly of an augmented Sm-like archaeal protein 14-mer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Solution structure and function of a conserved protein SP14.3 encoded by an essential Streptococcus pneumoniae gene

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

The Pfam protein families database

19 March 2017

1 reference

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A comprehensive two-hybrid analysis to explore the yeast protein interactome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

T-Coffee: A novel method for fast and accurate multiple sequence alignment

19 March 2017

1 reference

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The genome sequence of Drosophila melanogaster

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

The enhancer of decapping proteins, Edc1p and Edc2p, bind RNA and stimulate the activity of the decapping enzyme

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Yeast Sm-like proteins function in mRNA decapping and decay

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Novel predicted RNA-binding domains associated with the translation machinery

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Arginine/serine-rich domains of the su(wa) and tra RNA processing regulators target proteins to a subnuclear compartment implicated in splicing

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Functional genomic analysis of C. elegans chromosome I by systematic RNA interference

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Prediction of protein secondary structure at better than 70% accuracy

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Evolution and classification of P-loop kinases and related proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

G-quartet-dependent recognition between the FMRP RGG box and RNA.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

An EVH1/WH1 domain as a key actor in TGFbeta signalling

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Suppressors of cdc25p overexpression identify two pathways that influence the G2/M checkpoint in fission yeast

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Topology prediction for helical transmembrane proteins at 86% accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Non-globular domains in protein sequences: automated segmentation using complexity measures

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Identification of a novel mRNA-associated protein in oocytes of Pleurodeles waltl and Xenopus laevis

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

The snRNP core assembly pathway: identification of stable core protein heteromeric complexes and an snRNP subcore particle in vitro

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

PCMA: fast and accurate multiple sequence alignment based on profile consistency.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

A biochemical function for the Sm complex.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

PIN domains in nonsense-mediated mRNA decay and RNAi

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=503384

Ataxin-2, global regulators of bacterial gene expression, and spliceosomal snRNP proteins share a conserved domain

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15257761

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The PWI motif: a new protein domain in splicing factors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15257761