Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 24

System / cell line: splice ✕ Assay: binding ✕ Clear

Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Comprehensive splice-site analysis using comparative genomics.

PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

refseq u2-type genes comparative information phylogenetic
Rbfox2 controls autoregulation in RNA-binding protein networks.

PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

Has reproduction · 48

Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

v6.5 fhfox2 top introns iclip sequencing rt-pcr
Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish
Optimized mixed Markov models for motif identification.

PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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OMiMa can incorporate more than NNSplice's pairwise dependencies

simulated regulatory splice biological motif pairwise
Advances in the study of SR protein family.

PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

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SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

nuclear bovine drosophila caenorhabditis selex rna-binding splicing
Mutational analysis of steroidogenic factor 1 (NR5a1) in 24 boys with bilateral anorchia: a French collaborative study.

PMID 17940071 · PMC2990861 · Human reproduction (Oxford, England) · 2007 · 8 claims · 7 setups

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A novel heterozygous V355M missense mutation in SF1 was identified in one boy with micropenis and testicular regression syndrome (bilateral anorchia)

peripheral tsa201 tm3 cho sanger transient mammalian
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
Expression and Secretion of Circular RNAs in the Parasitic Nematode, Ascaris suum.

PMID 35711944 · PMC9194832 · Frontiers in genetics · 2022 · 8 claims · 7 setups

Has reproduction · 20

A. suum expresses 1,997 distinct circRNAs identified via next-generation sequencing in adult female body wall and ovary-enriched tissue

suum circrna qrt-pcr drug
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

chromosome user-submitted hannon-elledge gene linkage rnai shrna
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

PMID 41056017 · PMC12646653 · The Journal of clinical investigation · 2025 · 8 claims · 8 setups

Has reproduction · 67

Heterozygous CDKL1 missense variants (Cys143Arg, Ser206Leu, Thr135Met) were identified in 6 patients from 3 families with TAAD spectrum disorders

patients cohort cdkl1 aortic exome gene structural
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
Rho GTPases in human breast tumours: expression and mutation analyses and correlation with clinical parameters.

PMID 12237774 · PMC2364248 · British journal of cancer · 2002 · 8 claims · 8 setups

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RhoA, RhoB, Rac1 and Cdc42 protein levels are markedly overexpressed in breast tumours compared to matched normal tissue from the same patient

breast western c3-mediated 32p-gtp
F-SNP: computationally predicted functional SNPs for disease association studies.

PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

genome protein-coding genomic genome-wide non-synonymous exonic nonsense
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time

Experiments

Mutation analysis of the MSMB gene in familial prostate cancer.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Comprehensive splice-site analysis using comparative genomics.

Rbfox2 controls autoregulation in RNA-binding protein networks.

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

Optimized mixed Markov models for motif identification.

Advances in the study of SR protein family.

Mutational analysis of steroidogenic factor 1 (NR5a1) in 24 boys with bilateral anorchia: a French collaborative study.

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

Expression and Secretion of Circular RNAs in the Parasitic Nematode, Ascaris suum.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

Mutation analysis of the MDM4 gene in German breast cancer patients.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

Splicing bioinformatics to biology.

CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

Rho GTPases in human breast tumours: expression and mutation analyses and correlation with clinical parameters.

F-SNP: computationally predicted functional SNPs for disease association studies.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.