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 41

System / cell line: intron ✕ Assay: cdna ✕ Clear

RPS4Y gene family evolution in primates.

PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

primate chromosomes rps4x concatenated pcr fluorescence repeat
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
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
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

human-mouse adjacent est genome splice
Identification of herpesvirus transcripts from genomic regions around the replication origins.

PMID 37773348 · PMC10541914 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 59

Herpesviruses display distinct patterns of transcriptional overlaps near or at the replication origins (Oris)

nine same vzv prv direct cage-seq qrt-pcr
Atypical haemolytic uraemic syndrome associated with a hybrid complement gene.

PMID 17076561 · PMC1626556 · PLoS medicine · 2006 · 6 claims · 7 setups

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Affected members of a previously genetically unsolved aHUS family carry a heterozygous CFH/CFHL1 hybrid gene (exons 1-21 from CFH, exons 22/23 from CFHL1)

peripheral genomic convalescent cdna genomic breakpoint-spanning
AceView: a comprehensive cDNA-supported gene and transcripts annotation.

PMID 16925834 · PMC1810549 · Genome biology · 2006 · 8 claims · 4 setups

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At the mRNA level, AceView transcripts are the closest match to Gencode transcripts among all evaluated methods, including alternative splice variants

genome encode caenorhabditis comparative n-to-n cds
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
Non-EST based prediction of exon skipping and intron retention events using Pfam information.

PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

refseq dbest genome pfam initio est comparative
Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

genomic electronic pcr pcr-restriction
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

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Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
A novel matrix metalloproteinase 2 (MMP2) terminal hemopexin domain mutation in a family with multicentric osteolysis with nodulosis and arthritis with cardiac defects.

PMID 18985071 · PMC2721823 · European journal of human genetics : EJHG · 2009 · 7 claims · 8 setups

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A novel homozygous frameshift mutation (1732delA) in exon 11 of MMP2 causes MONA in this Turkish family by deleting the terminal (third and fourth) hemopexin domains.

blood-derived patient-derived serum genomic direct rt-pcr gelatin
MutScreener: primer design tool for PCR-direct sequencing.

PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

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MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

sim4 cdna gene comparative sequence pcr
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

random trans-acting tpo fibronectin minigene selex cdna
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome

Experiments

RPS4Y gene family evolution in primates.

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

Computational analysis of splicing errors and mutations in human transcripts.

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

Identification of herpesvirus transcripts from genomic regions around the replication origins.

Atypical haemolytic uraemic syndrome associated with a hybrid complement gene.

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

Non-EST based prediction of exon skipping and intron retention events using Pfam information.

Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

A novel matrix metalloproteinase 2 (MMP2) terminal hemopexin domain mutation in a family with multicentric osteolysis with nodulosis and arthritis with cardiac defects.

MutScreener: primer design tool for PCR-direct sequencing.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.