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 20

System / cell line: transcripts ✕ Assay: splicing ✕ Clear

Alternative splicing and bioinformatic analysis of human U12-type introns.

PMID 17332017 · PMC1874599 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The long, evolutionarily conserved polypyrimidine (Py) tract of the JNK2 U2-U12 hybrid intron provides the signal for default inclusion of the downstream alternative exon 6b in non-neuronal cells

hela hek293 genome jnk2 rt-pcr minigene bioinformatic
Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

gria2 drosophila nova1 cd45 splicing sirna hits-clip
ECgene: an alternative splicing database update.

PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

nine genome sage cdna genome-based chi-squared sage
Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.

PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 7 setups

Has reproduction · 76

Multiple partially or fully intron-spliced intermediates co-exist within an organelle, and both cis- and trans-splicing introns are spliced randomly (no fixed order), generating diverse intermediates.

nymphaea liriodendron pacbio illumina strand-specific
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

Has reproduction · 80

DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

transcripts platforms bacillus multi-subcellular simulated negative benchmark
A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

PMID 11476670 · PMC35353 · BMC genetics · 2001 · 8 claims · 7 setups

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The Q279R missense mutation acts as a splicing mutation in vivo, causing skipping of exon 9 (alone or with exon 8) rather than simply altering the encoded amino acid.

microdissected resected non-tumor liver pcr-rflp immunohistochemistry western
Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

PMID 19795481 · PMC3501199 · Human mutation · 2009 · 7 claims · 8 setups

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BRCA2 c.6853A>G (p.I2285V) co-occurs in trans with the deleterious founder mutation c.5946delT, supporting classification as a neutral variant

lymphocytes brca2 brca2-null ashkenazi rt-pcr splicing allelic
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Biased exon/intron distribution of cryptic and de novo 3' splice sites.

PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

disease authentic hek293t nuclear literature shapiro-senapathy splicing
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

Has reproduction · 83

The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

intestine colon dss distal bulk phenotypic h&e
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

PMID 18978773 · PMC2597294 · Nature · 2008 · 8 claims · 8 setups

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HITS-CLIP, combining CLIP with high-throughput sequencing, provides a genome-wide, unbiased method to map protein-RNA interactions in vivo.

neocortex brain 293t hits-clip traditional exon
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
Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

Has reproduction

An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.

udn blood skin snvs whole-genome bulk splice-altering
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

Has reproduction · 57

ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

arabidopsis pacbio randomly illumina pacbio nanopore
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Visualizing the genome: techniques for presenting human genome data and annotations.

PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

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Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups

Has reproduction · 30

Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.

tall tobacco illumina smrt electrolyte
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based

Experiments

Alternative splicing and bioinformatic analysis of human U12-type introns.

Computational analysis of splicing errors and mutations in human transcripts.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

ECgene: an alternative splicing database update.

Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

Identification of common genetic variation that modulates alternative splicing.

Biased exon/intron distribution of cryptic and de novo 3' splice sites.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

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

Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Visualizing the genome: techniques for presenting human genome data and annotations.

SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.