Pick one, but be quick: 5' splice sites and the problems of too many choices

scientific article published on January 2013

Pick one, but be quick: 5' splice sites and the problems of too many choices is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P356DOI10.1101/GAD.209759.112
P932PMC publication ID3566305
P698PubMed publication ID23348838

P50authorAdrian Robert KrainerQ40473018
Xavier RocaQ42177767
Ian C EperonQ55137400
P2860cites workThe SR protein familyQ21183897
The apoptosis-promoting factor TIA-1 is a regulator of alternative pre-mRNA splicingQ24290594
Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMsQ24317191
Functional expression of cloned human splicing factor SF2: homology to rna-binding proteins, U1 70K, and drosophila splicing regulatorsQ24317722
The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5' splice sitesQ24337164
Phosphorylation-dephosphorylation differentially affects activities of splicing factor ASF/SF2.Q24533375
Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNAQ24535910
Congenital end-plate acetylcholinesterase deficiency caused by a nonsense mutation and an A-->G splice-donor-site mutation at position +3 of the collagenlike-tail-subunit gene (COLQ): how does G at position +3 result in aberrant splicing?Q24540131
Spliced segments at the 5′ terminus of adenovirus 2 late mRNAQ24561528
Functional domains of the human splicing factor ASF/SF2Q24564249
The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificitiesQ24598907
Identification of functional exonic splicing enhancer motifs recognized by individual SR proteinsQ24600148
The spliceosome assembly pathway in mammalian extractsQ24601223
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expressionQ24633499
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcriptsQ24651972
SR proteins in vertical integration of gene expression from transcription to RNA processing to translationQ24654094
General and specific functions of exonic splicing silencers in splicing controlQ24673220
Extended base pair complementarity between U1 snRNA and the 5' splice site does not inhibit splicing in higher eukaryotes, but rather increases 5' splice site recognitionQ24812684
Genetic variation of pre-mRNA alternative splicing in human populationsQ26858897
Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolutionQ27654469
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureQ27860806
Functional mammalian spliceosomal complex E contains SMN complex proteins in addition to U1 and U2 snRNPs.Q27865260
The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairingQ27933790
Interaction of the U1 snRNP with nonconserved intronic sequences affects 5' splice site selection.Q27936014
Genetic therapies for RNA mis-splicing diseasesQ28235690
Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencersQ28247879
Protein-protein interactions and 5'-splice-site recognition in mammalian mRNA precursorsQ28251112
Specific interactions between proteins implicated in splice site selection and regulated alternative splicingQ28257351
Splicing of a rare class of introns by the U12-dependent spliceosomeQ28275293
Are snRNPs involved in splicing?Q28281898
Role of the snRNAs in spliceosomal active siteQ28282063
Short/branched-chain acyl-CoA dehydrogenase deficiency due to an IVS3+3A>G mutation that causes exon skippingQ28284385
The RNA-binding protein TIA-1 is a novel mammalian splicing regulator acting through intron sequences adjacent to a 5' splice siteQ28609616
Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definitionQ40078319
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sitesQ40088295
A novel approach to describe a U1 snRNA binding site.Q40315328
HMGA1a trapping of U1 snRNP at an authentic 5' splice site induces aberrant exon skipping in sporadic Alzheimer's diseaseQ40334418
U1 snRNP-ASF/SF2 interaction and 5' splice site recognition: characterization of required elements.Q40395456
Stabilization of RNA stacking by pseudouridineQ40397122
The SR protein family: pleiotropic functions in pre-mRNA splicingQ41083714
A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5' cleavage site.Q41107145
U1 snRNA promotes the selection of nearby 5' splice sites by U6 snRNA in mammalian cellsQ41235244
Evidence against a scanning model of RNA splicingQ41454583
An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28pQ41607972
hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicingQ41679293
A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitroQ41728182
Comparative analysis detects dependencies among the 5' splice-site positionsQ41807332
Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomicsQ41824436
DExD/H-box Prp5 protein is in the spliceosome during most of the splicing cycleQ41870184
hnRNP A1 and hnRNP H can collaborate to modulate 5' splice site selectionQ41873390
Cis-acting elements distinct from the 5' splice site promote U1-independent pre-mRNA splicingQ41898179
Dynamic regulation of alternative splicing by silencers that modulate 5' splice site competitionQ41984492
High-affinity hnRNP A1 binding sites and duplex-forming inverted repeats have similar effects on 5' splice site selection in support of a common looping out and repression mechanismQ41993441
Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse waysQ42000836
Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotidesQ42177704
Quantitative evaluation of all hexamers as exonic splicing elementsQ42181233
The transition in spliceosome assembly from complex E to complex A purges surplus U1 snRNPs from alternative splice sitesQ42264162
The SR protein SC35 is responsible for aberrant splicing of the E1alpha pyruvate dehydrogenase mRNA in a case of mental retardation with lactic acidosisQ42709929
Ordered and dynamic assembly of single spliceosomesQ42726090
Stoichiometry of a regulatory splicing complex revealed by single-molecule analysesQ42730959
Ab initio identification of functionally interacting pairs of cis-regulatory elementsQ43012647
U1-like snRNAs lacking complementarity to canonical 5' splice sites.Q43054877
U1-independent pre-mRNA splicing contributes to the regulation of alternative splicingQ43150426
Electrophoretic separation of complexes involved in the splicing of precursors to mRNAsQ43517287
Early organization of pre-mRNA during spliceosome assembly.Q44046358
5' splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirementsQ44055786
An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathwayQ44540184
Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cellsQ44744396
Influences of separation and adjacent sequences on the use of alternative 5′ splice sitesQ45103471
A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assemblyQ45138449
RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition.Q46050971
Mutations in U6 snRNA that alter splice site specificity: implications for the active siteQ46572305
A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA.Q47070080
Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicingQ48084485
Prediction of human mRNA donor and acceptor sites from the DNA sequenceQ48219047
Saccharomyces cerevisiae has a U1-like small nuclear RNA with unexpected propertiesQ48338318
Pseudouridine residues in the 5′-terminus of uridine-rich nuclear RNA I (U1 RNA)Q48410567
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signalsQ48531006
Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.Q49947386
Properties of a U1/mRNA 5' splice site duplex containing pseudouridine as measured by thermodynamic and NMR methodsQ50136284
hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencerQ28609663
A compensatory base change in U1 snRNA suppresses a 5' splice site mutationQ29618292
The SR protein family of splicing factors: master regulators of gene expressionQ29619935
Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2Q29620278
Exon Identity Established through Differential Antagonism between Exonic Splicing Silencer-Bound hnRNP A1 and Enhancer-Bound SR ProteinsQ30040281
A mutation in a rare type of intron in a sodium-channel gene results in aberrant splicing and causes myotoniaQ30584867
Defining a 5' splice site by functional selection in the presence and absence of U1 snRNA 5' end.Q30827740
Deletion of the N-terminus of SF2/ASF permits RS-domain-independent pre-mRNA splicingQ33297016
Selection of alternative 5' splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1.Q33605355
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencingQ33740599
Competing upstream 5' splice sites enhance the rate of proximal splicingQ33769266
A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers.Q33890073
Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancersQ33935979
Identification of a bidirectional splicing enhancer: differential involvement of SR proteins in 5' or 3' splice site activationQ33959923
Deciphering the splicing codeQ34022324
An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA.Q34064140
Functional analysis of pre-mRNA splicing factor SF2/ASF structural domainsQ34070174
Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H'/F/2H9 familyQ34092482
Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome projectQ34311043
In vivo selection reveals combinatorial controls that define a critical exon in the spinal muscular atrophy genesQ34365948
Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequencesQ34389747
Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5' splice sitesQ34487822
G Run-mediated recognition of proteolipid protein and DM20 5' splice sites by U1 small nuclear RNA is regulated by context and proximity to the splice site.Q34575659
Cryptic splice site usage in exon 7 of the human fibrinogen Bbeta-chain gene is regulated by a naturally silent SF2/ASF binding site within this exonQ34625741
RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humansQ34863401
Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping.Q34921189
Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assemblyQ35002838
Comprehensive splice-site analysis using comparative genomicsQ35013128
Pre-mRNA splicing in the absence of an SR protein RS domainQ35209029
The A1 and A1B proteins of heterogeneous nuclear ribonucleoparticles modulate 5' splice site selection in vivoQ35604494
The SRSF1 linker induces semi-conservative ESE binding by cooperating with the RRMsQ35620904
A U1-U2 snRNP interaction network during intron definitionQ35665670
Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1.Q35764716
Broad specificity of SR (serine/arginine) proteins in the regulation of alternative splicing of pre-messenger RNA.Q35813276
Suppression of mammalian 5' splice-site defects by U1 small nuclear RNAs from a distanceQ35857085
Low U1 snRNP dependence at the NF1 exon 29 donor splice site.Q51764906
Correlation of hnRNP structure and nascent transcript cleavageQ52516604
Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5' splice-site disruption.Q52577158
Alternative splicing caused by RNA secondary structure.Q54198854
Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1.Q55476319
Resolving the functions of overlapping viral genes by site-specific mutagenesis at a mRNA splice siteQ58451157
Complexities of 5'splice site definition: Implications in clinical analysesQ58454175
Structural and functional defects in beta-thalassemiaQ58485020
An RNA Splicing Enhancer that Does Not Act by LoopingQ58830805
Effects of RNA secondary structure on alternative splicing of Pre-mRNA: Is folding limited to a region behind the transcribing RNA polymerase?Q58830817
The role of nucleotide sequences in splice site selection in eukaryotic pre-messenger RNAQ58830821
Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicingQ64378031
SR proteins can compensate for the loss of U1 snRNP functions in vitroQ64383400
Unusual splice sites revealed by mutagenic inactivation of an authentic splice site of the rabbit β-globin geneQ67260093
A role for exon sequences and splice-site proximity in splice-site selectionQ68970669
Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNAQ69660486
Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicingQ69829038
Mammalian heterogeneous ribonucleoprotein A1 and its constituent domains. Nucleic acid interaction, structural stability and self-associationQ70591313
3' splice site recognition in S. cerevisiae does not require base pairing with U1 snRNAQ70732949
A functional association between the 5' and 3' splice site is established in the earliest prespliceosome complex (E) in mammalsQ70744375
hnRNP A1 selectively interacts through its Gly-rich domain with different RNA-binding proteinsQ71176264
A U6 snRNA:pre-mRNA interaction can be rate-limiting for U1-independent splicingQ71738198
Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNPQ72202030
A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP bindingQ72638665
Involvement of U6 snRNA in 5' splice site selectionQ72669455
The 5′ terminus of the RNA moiety of U1 small nuclear ribonucleoprotein particles is required for the splicing of messenger RNA precursorsQ72821863
The 5' end of U2 snRNA is in close proximity to U1 and functional sites of the pre-mRNA in early spliceosomal complexesQ79749517
An exonic splicing silencer represses spliceosome assembly after ATP-dependent exon recognitionQ80336614
Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificityQ36268125
A mechanism for RNA splicingQ36362761
Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms.Q36481243
G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selectionQ36570227
Differentially expressed, variant U1 snRNAs regulate gene expression in human cellsQ36580574
SR proteins promote the first specific recognition of Pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle in a general splicing enhancer complexQ36670430
Modulation of exon skipping and inclusion by heterogeneous nuclear ribonucleoprotein A1 and pre-mRNA splicing factor SF2/ASF.Q36682707
Multiple interactions between the splicing substrate and small nuclear ribonucleoproteins in spliceosomesQ36833512
Amount of RNA secondary structure required to induce an alternative spliceQ36921027
Spliceosome assembly pathways for different types of alternative splicing converge during commitment to splice site pairing in the A complex.Q37099916
Heterogeneous nuclear ribonucleoproteins H and F regulate the proteolipid protein/DM20 ratio by recruiting U1 small nuclear ribonucleoprotein through a complex array of G runsQ37160862
Diagnostics of pathogenic splicing mutations: does bioinformatics cover all bases?Q37175054
Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA.Q37285454
Splice site strength-dependent activity and genetic buffering by poly-G runsQ37397927
U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repressionQ37597322
New insights into RNA secondary structure in the alternative splicing of pre-mRNAsQ37874082
Intrinsic U2AF binding is modulated by exon enhancer signals in parallel with changes in splicing activityQ38298431
Pathways for selection of 5' splice sites by U1 snRNPs and SF2/ASF.Q38316542
Modulation of exon skipping by high-affinity hnRNP A1-binding sites and by intron elements that repress splice site utilizationQ38325989
Primary structure of the human splicing factor asf reveals similarities with drosophila regulatorsQ38334210
An intronic splicing enhancer binds U1 snRNPs to enhance splicing and select 5' splice sitesQ39540203
Role of SR protein modular domains in alternative splicing specificity in vivoQ39607577
The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cellsQ39648201
Efficient use of a 'dead-end' GA 5' splice site in the human fibroblast growth factor receptor genesQ39744889
Cooperative-binding and splicing-repressive properties of hnRNP A1.Q39814580
hnRNP H binding at the 5' splice site correlates with the pathological effect of two intronic mutations in the NF-1 and TSHbeta genesQ39946083
Stabilization of the tau exon 10 stem loop alters pre-mRNA splicingQ39958205
Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosomeQ40025470
P433issue2
P921main subjectsmall nuclear RNAQ284578
P304page(s)129-144
P577publication date2013-01-01
P1433published inGenes & DevelopmentQ1524533
P1476titlePick one, but be quick: 5' splice sites and the problems of too many choices
P478volume27

Reverse relations

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