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 119

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

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
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
Does distance matter? Variations in alternative 3' splicing regulation.

PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

intronic human-mouse same comparative polypyrimidine branch
Mutations in transglutaminase 1 gene in autosomal recessive congenital ichthyosis in Egyptian families.

PMID 15665393 · PMC3839340 · Disease markers · 2004 · 8 claims · 4 setups

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An intron-5/exon-6 splice acceptor mutation in TGM1, detectable by MspI digestion, was identified in two Egyptian families at a frequency of 9.6% (5/52 alleles)

genomic arci pcr clinical pedigree
Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

genomic encode entire chromosome multi-species hmm-based classifier
Identification of two novel OPA1 mutations in Chinese families with autosomal dominant optic atrophy.

PMID 19112530 · PMC2610289 · Molecular vision · 2008 · 8 claims · 5 setups

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Two novel heterozygous OPA1 mutations were identified: a splice-site mutation c.985-2A>G in family F1 and a nonsense mutation c.2197C>T (p.R733X) in family F2

genomic available leukocytes affected linkage pcr single
A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family.

PMID 18432314 · PMC2329669 · Molecular vision · 2008 · 6 claims · 5 setups

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A novel homozygous splice-site mutation, c.1495+2_1495+3insT, in the donor splice-site of TULP1 intron 14 underlies autosomal recessive early-onset RP in family TB13.

genomic tulp1 y79 haplotype direct mismatch-primer
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
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
Evaluation of SCN8A as a candidate gene for autosomal dominant essential tremor.

PMID 18718804 · PMC2877193 · Parkinsonism & related disorders · 2009 · 7 claims · 6 setups

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Mutations in the coding sequence and splice sites of human SCN8A do not appear to be a common cause of autosomal dominant essential tremor in Caucasian patients.

genomic neurologically ethnically scn8a heteroduplex pcr snp
Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

genomic sequenced korean common sanger sequence population
Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

PMID 19901218 · PMC3514888 · Archives of ophthalmology (Chicago, Ill. : 1960) · 2009 · 8 claims · 4 setups

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No COL2A1 mutations were found, making ocular Stickler syndrome an unlikely diagnosis for this family

genomic family complete pcr clinical
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

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The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

hnrpr specified comparative algorithm
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
Pegasys: software for executing and integrating analyses of biological sequences.

PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

eukaryotic formatted genomic input initio sequence gene
High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

PMID 16086836 · PMC1190179 · BMC medical genetics · 2005 · 8 claims · 6 setups

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IVS2-2A>G allele frequency does not differ significantly between hearing-impaired cases and controls among Hispanics and Caucasians (p=0.45)

genomic mitochondrial slc26a5 pcr sequence splice
Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

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Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr
The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

PMID 19926015 · PMC2880864 · Journal of the American College of Cardiology · 2009 · 8 claims · 6 setups

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Comprehensive open-reading-frame RYR2 mutational analysis reveals possible CPVT1 mutations located outside the three canonical hot-spot domains

genomic hair-root reference patients pcr screening multi-tissue

Experiments

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

Comprehensive splice-site analysis using comparative genomics.

Does distance matter? Variations in alternative 3' splicing regulation.

Mutations in transglutaminase 1 gene in autosomal recessive congenital ichthyosis in Egyptian families.

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

Identification of two novel OPA1 mutations in Chinese families with autosomal dominant optic atrophy.

A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

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

Evaluation of SCN8A as a candidate gene for autosomal dominant essential tremor.

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

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

Pegasys: software for executing and integrating analyses of biological sequences.

High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.