APPRIS

Names
More detailed information about this field from each metasource.

APPRIS
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

appris
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

Other names: appris

This source may no longer be available. No known URL could be resolved successfully.

Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.

Webpage:

http://appris-tools.org

Publications:

Publications
More detailed information about this field from each metasource.

APPRIS: annotation of principal and alternative splice isoforms
PMID: 23161672
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

APPRIS WebServer and WebServices
PMID: 25990727
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

http://dx.doi.org/10.1093/nar/gkx997
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

APPRIS: annotation of principal and alternative splice isoforms PubMed citations: 96.

96 articles citing: APPRIS: annotation of principal and alternative splice isoforms

Enhanced protein isoform characterization through long-read proteogenomics. PMID:35241129
Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data. PMID:35205403
Homozygous duplication identified by whole genome sequencing causes LRBA deficiency. PMID:34795304
APPRIS: selecting functionally important isoforms. PMID:34755885
Molecular and functional profiling identifies therapeutically targetable vulnerabilities in plasmablastic lymphoma. PMID:34465776
Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells. PMID:34389041
ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses. PMID:34297039
Assessing conservation of alternative splicing with evolutionary splicing graphs. PMID:34266979
catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions. PMID:34086933
Assessing the functional relevance of splice isoforms. PMID:34046593
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. PMID:33836063
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
Improving CLIP-seq data analysis by incorporating transcript information. PMID:33334306
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. PMID:33261662
Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression. PMID:33087347
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. PMID:33080218
Extensive germline genome engineering in pigs. PMID:32958897
Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay. PMID:32941650
Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins. PMID:32890404
The role of exome sequencing in newborn screening for inborn errors of metabolism. PMID:32778825
Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5' leader regions. PMID:32766783
Nuclease-mediated depletion biases in ribosome footprint profiling libraries. PMID:32503920
Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3'UTR intron-containing NMD targets. PMID:32502192
Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. PMID:32487729
Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA. PMID:32467309
Mapping and characterization of structural variation in 17,795 human genomes. PMID:32460305
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. PMID:32423416
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms. PMID:32393825
ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping. PMID:32284880
Design and analysis of CRISPR-Cas experiments. PMID:32284587
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms. PMID:32272892
ISOGO: Functional annotation of protein-coding splice variants. PMID:31974522
Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. PMID:31971508
Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome. PMID:31825849
A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus. PMID:31745551
Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias. PMID:31714939
Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. PMID:31619139
Network-based method for drug target discovery at the isoform level. PMID:31554914
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing. PMID:31413257
Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer. PMID:31328753
New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients. PMID:31175170
Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. PMID:31160636
methyl-ATAC-seq measures DNA methylation at accessible chromatin. PMID:31160376
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. PMID:30925859
O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1-dependent mitochondrial dysfunction in the retina. PMID:30733333
Intronic CNVs and gene expression variation in human populations. PMID:30677042
Sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs. PMID:30572815
Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes. PMID:30553725
PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations. PMID:30445568
GENCODE reference annotation for the human and mouse genomes. PMID:30357393
The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. PMID:30068703
Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. PMID:30029003
TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response. PMID:29932418
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Maternal 5mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. PMID:29545821
SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. PMID:29440222
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition. PMID:29284518
Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. PMID:29202200
Am I ready for CRISPR? A user's guide to genetic screens. PMID:29199283
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
APPRIS 2017: principal isoforms for multiple gene sets. PMID:29069475
Alternative RNA Splicing in the Pathogenesis of Liver Disease. PMID:28680417
Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge. PMID:28497567
Transcription factor-DNA binding: beyond binding site motifs. PMID:28359978
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. PMID:27964752
Ensembl 2017. PMID:27899575
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. PMID:27875984
The BLUEPRINT Data Analysis Portal. PMID:27863955
Pre-mRNA mis-splicing of sarcomeric genes in heart failure. PMID:27825848
The state of play in higher eukaryote gene annotation. PMID:27773922
Alternative Splicing May Not Be the Key to Proteome Complexity. PMID:27712956
The Ensembl Variant Effect Predictor. PMID:27268795
CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes. PMID:27111720
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PMID:27100087
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Potential Gene Interactions in the Cell Cycles of Gametes, Zygotes, Embryonic Stem Cells and the Development of Cancer. PMID:26442212
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. PMID:26297486
Identifying and characterising key alternative splicing events in Drosophila development. PMID:26275604
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. PMID:26216192
Creating reference gene annotation for the mouse C57BL6/J genome assembly. PMID:26187010
Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse. PMID:26121354
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. PMID:26110515
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
APPRIS WebServer and WebServices. PMID:25990727
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. PMID:25953081
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets. PMID:25858286
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. PMID:25765346
Cis-Expression Quantitative Trait Loci Mapping Reveals Replicable Associations with Heroin Addiction in OPRM1. PMID:25744370
Most highly expressed protein-coding genes have a single dominant isoform. PMID:25732134
Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. PMID:25265570
Analysis of stop-gain and frameshift variants in human innate immunity genes. PMID:25058640
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PMID:24244129
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. PMID:23815980
The alternative heart: impact of alternative splicing in heart disease. PMID:23775418
Alternative splicing for diseases, cancers, drugs, and databases. PMID:23766705
APPRIS WebServer and WebServices PubMed citations: 13.

13 articles citing: APPRIS WebServer and WebServices

APPRIS: selecting functionally important isoforms. PMID:34755885
Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. PMID:31886458
GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. PMID:30862647
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Isoform-level gene expression patterns in single-cell RNA-sequencing data. PMID:29490015
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
APPRIS 2017: principal isoforms for multiple gene sets. PMID:29069475
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
Differential molecular regulation of processing and membrane expression of Type-I BMP receptors: implications for signaling. PMID:28357470
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. PMID:27965389
ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins. PMID:27153567
Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences. PMID:26833483
Ensembl 2016. PMID:26687719
http://dx.doi.org/10.1093/nar/gkx997

Tags:

Tags
More detailed information about this field from each metasource.

nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

gene structure, introns and exons, splice sites
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

rna splicing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276

nucleic acid sequence gene structure, introns and exons, splice sites sequence analysis rna splicing gene transcripts

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