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34-564: GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants”. The result will be

68-667: A high or low level of support based on a new method developed to score the quality of transcripts. The current GENCODE Human gene set version (GENCODE Release 20) includes annotation files (in GTF and GFF3 formats), FASTA files and METADATA files associated with the GENCODE annotation on all genomic regions (reference-chromosomes/patches/scaffolds/haplotypes). The annotation data is referred on reference chromosomes and stored in separated files which include: Gene annotation, PolyA features annotated by HAVANA, (Retrotransposed) pseudogenes predicted by

102-514: A higher throughput on the 454 “ next-generation ” sequencing platform. In 2008, barcode multiplexing was added to the DeepCAGE protocol (Maeda et al. , 2008). In nanoCAGE (Plessy et al. , 2010), the 5′ ends or RNAs were captured with the template-switching method instead of CAP Trapper, in order to analyze smaller starting amounts of total RNA. Longer tags were cleaved with the type III restriction enzyme EcoP15I and directly sequenced on

136-537: A major paper discussing the results from a major release – GENCODE Release 7, which was frozen in December 2011. 2018 In 2018, one of the latest additions to the GENCODE project was the CRISPR/Cas9 track on human and model organism assemblies. CRISPR is a genome editing technique that uses sequences of RNA that successfully bind to the region edited with high specificity. The new track was designed to assist in

170-577: A mounting challenge for the GENCODE project to come up with an updated notion of a gene. The Human Genome Project was an international research effort to determine the sequence of the human genome and identify the genes that it contains. The Project was coordinated by the National Institutes of Health and the U.S. Department of Energy. Additional contributors included universities across the United States and international partners in

204-455: A set of annotation covers the complete genome rather than just the regions that have been manually annotated, a merged data set is created using manual annotations from HAVANA, together with automatic annotations from the Ensembl automatically annotated gene set. This process also adds unique full-length CDS predictions from the Ensembl protein coding set into manually annotated genes, to provide

238-559: A set of annotations including all protein-coding loci with alternatively transcribed variants , non-coding loci with transcript evidence, and pseudogenes . GENCODE is currently progressing towards its goals in Phase 2 of the project. The most recent release of the Human geneset annotations is Gencode 36, with a freeze date of December 2020. This release utilises the latest GRCh38 human reference genome assembly. The latest release for

272-402: A similar technique serial analysis of gene expression (SAGE) in which tags come from other parts of transcripts, CAGE is primarily used to locate exact transcription start sites in the genome. This knowledge in turn allows a researcher to investigate promoter structure necessary for gene expression. CAGE tags tend to start with an extra guanine (G) that is not encoded in the genome, which

306-464: Is a set of short nucleotide sequences (often called tags in analogy to expressed sequence tags ) with their observed counts. Copy numbers of CAGE tags provide a digital quantification of the RNA transcript abundances in biological samples. Using a reference genome, a researcher can usually determine, with some confidence, the original mRNA (and therefore which gene ) the tag was extracted from. Unlike

340-421: Is an important new source of evidence, but generating complete gene models from it is a difficult problem. As part of GENCODE, a competition was run to assess the quality of predictions produced by various RNAseq prediction pipelines (Refer to RGASP below). To confirm uncertain models, GENCODE also has an experimental validation pipeline using RNA sequencing and RACE. For GENCODE 7, transcript models are assigned

374-405: Is attributed to the template-free 5′-extension during the first-strand cDNA synthesis or reverse-transcription of the cap itself. When not corrected, this can induce erroneous mapping of CAGE tags, for instance to nontranscribed pseudogenes. On the other hand, this addition of Gs was also utilised as a signal to filter more reliable TSS peaks. The original CAGE method (Shiraki et al. , 2003)

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408-563: The Solexa (then Illumina) platform without concatenation. The CAGEscan methodology (Plessy et al. , 2010), where the enzymatic tag cleavage is skipped, and the 5′ cDNAs sequenced paired-end , was introduced in the same article to connect novel promoters to known annotations. With HeliScopeCAGE (Kanamori-Katayama et al. , 2011), the CAP-trapped CAGE protocol was changed to skip the enzymatic tag cleavage and sequence directly

442-546: The nAnTi-CAGE protocol, where capped 5′ ends are sequenced on the Illumina platform with no PCR amplification and no tag cleavage. In 2017, Poulain et al. updated the nanoCAGE protocol to use the tagmentation method (based on Tn5 transposition ) for multiplexing. In 2018, Cvetesic et al. increased the sensitivity of CAP-trapped CAGE by introducing selectively degradable carrier RNA (SLIC-CAGE, "Super-Low Input Carrier-CAGE"). In 2021, Takahashi et al. simplified

476-647: The pilot project were published in June 2007. The findings highlighted the success of the pilot project to create a feasible platform and new technologies to characterise functional elements in the human genome, which paves the way for opening research into genome-wide studies. 2007 October New funding was part of NHGRI's endeavour to scale-up the ENCODE Project to a production phase on the entire genome along with additional pilot-scale studies. 2012 September In September 2012, The GENCODE consortium published

510-716: The 44 ENCODE regions was frozen on 29 April 2005 and was used in the first ENCODE Genome Annotation Assessment Project (E-GASP) workshop. GENCODE Release 1 contained 416 known loci, 26 novel (coding DNA sequence) CDS loci, 82 novel transcript loci, 78 putative loci, 104 processed pseudogenes and 66 unprocessed pseudogenes. 2005 October A second version (release 02) was frozen on 14 October 2005, containing updates following discoveries from experimental validations using RACE and RT-PCR techniques. GENCODE Release 2 contained 411 known loci, 30 novel CDS loci, 81 novel transcript loci, 83 putative loci, 104 processed pseudogenes and 66 unprocessed pseudogenes. 2007 June The conclusions from

544-561: The COVID-19 pandemic during 2020, there has been an urge to support research responding to the situation, so GENCODE has reviewed and improved the annotation for a set of protein-coding genes associated with SARSCoV-2 infection. The key participants of the GENCODE project have remained relatively consistent throughout its various phases, with the Wellcome Trust Sanger Institute now leading the overall efforts of

578-573: The GENCODE consortium that run pipelines that aid the manual annotators in producing models in unannotated regions, and to identify potential missed or incorrect manual annotation, including completely missing loci, missing alternative isoforms, incorrect splice sites and incorrect biotypes. These are fed back to the manual annotators using the AnnoTrack tracking system. Some of these pipelines use data from other ENCODE subgroups including RNASeq data, histone modification and CAGE and Ditag data. RNAseq data

612-458: The GENCODE website contains a Genome Browser for human and mouse where you can reach any genomic region by giving the chromosome number and start-end position (e.g. 22:30,700,000..30,900,000), as well as by ENS transcript id (with/without version), ENS gene id (with/without version) and gene name. The browser is powered by Biodalliance. The definition of a "gene" has never been a trivial issue, with numerous definitions and notions proposed throughout

646-524: The United Kingdom, France, Germany, Japan, and China. The Human Genome Project formally began in 1990 and was completed in 2003, 2 years ahead of its original schedule. Ensembl is part of the GENCODE project. A key research area of the GENCODE project was to investigate the biological significance of long non-coding RNAs (lncRNA). To better understand the lncRNA expression in Humans, a sub project

680-541: The Yale & UCSC pipelines, but not by HAVANA, long non-coding RNAs, and tRNA structures predicted by tRNA-Scan. Some examples of the lines in the GTF format are shown below: The columns within the GENCODE GTF file formats are described below. Format description of GENCODE GTF file. TAB-separated standard GTF columns Description of key-value pairs in 9th column of the GENCODE GTF file (format: key "value") Also,

714-669: The accuracy and completeness of GENCODE annotations have been continuously refined through its iteration of releases. A comparison of key statistics from 3 major GENCODE releases until 2014 is shown below. It is evident that although the coverage, in terms of total number of genes discovered, is steady increasing, the number of protein-coding genes has actually decreased. This is mostly attributed to new experimental evidence obtained using Cap Analysis Gene Expression (CAGE) clusters, annotated PolyA sites, and peptide hits. Putative loci can be verified by wet-lab experiments and computational predictions are analysed manually. Currently, to ensure

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748-514: The advent of the ENCODE/GENCODE project, even more problematic aspects of the definition have been uncovered, including alternative splicing (where a series of exons are separated by introns), intergenic transcriptions, and the complex patterns of dispersed regulation, together with non-genic conservation and the abundance of noncoding RNA genes. As GENCODE endeavours to build an encyclopaedia of genes and gene variants, these problems presented

782-654: The capped 5′ ends on the HeliScope platform, without PCR amplification. It was then automated by Itoh et al. in 2012. In 2012, the standard CAGE protocol was updated by Takahashi et al. to cleave tags with EcoP15I and sequence them on the Illumina-Solexa platform. In 2013, Batut et al. combined CAP trapper, template switching, and 5′-phosphate-dependent exonuclease digestion in RAMPAGE to maximize promoter specificity. In 2014, Murata et al. published

816-485: The feasibility of automated genome annotations based on transcriptome sequencing. RGASP is organised in a consortium framework modelled after the EGASP (ENCODE Genome Annotation Assessment Project) gene prediction workshop, and two rounds of workshops have been conducted to address different aspects of RNA-seq analysis as well as changing sequencing technologies and formats. One of the main discoveries from rounds 1 & 2 of

850-416: The human genome. As part of this stage, the GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. It was envisaged that the results of the first two phases will be used to determine the best path forward for analysing the remaining 99% of the human genome in a cost-effective and comprehensive production phase. 2005 April The first release of the annotation of

884-461: The most complete and up-to-date annotation of the genome possible. Ensembl transcripts are products of the Ensembl automatic gene annotation system (a collection of gene annotation pipelines), termed the Ensembl gene build. All Ensembl transcripts are based on experimental evidence and thus the automated pipeline relies on the mRNAs and protein sequences deposited into public databases from the scientific community. There are several analysis groups in

918-592: The mouse geneset annotations is Gencode M25, also with a freeze date December 2020. Since September 2009, GENCODE has been the human gene set used by the Ensembl project and each new GENCODE release corresponds to an Ensembl release. 2003 September The project was designed with three phases - Pilot, Technology development and Production phase. The pilot stage of the ENCODE project aimed to investigate in great depth, computationally and experimentally, 44 regions totaling 30 Mb of sequence representing approximately 1% of

952-409: The off-target and the guide. 2020 Among other achievements, it has been completed the first pass manual annotation of the mouse reference genome, it has started a cooperation with RefSeq and Uniprot reference annotation databases toward achieving annotation convergence, and the annotation of lncRNAs has been improved via the discovery of novel loci and novel transcripts at existing loci. Also, given

986-673: The project was the importance of read alignment on the quality of gene predictions produced. Hence, a third round of RGASP workshop is currently being conducted (in 2014) to focus primarily on read mapping to the genome. Genome Too Many Requests If you report this error to the Wikimedia System Administrators, please include the details below. Request from 172.68.168.151 via cp1112 cp1112, Varnish XID 938441803 Upstream caches: cp1112 int Error: 429, Too Many Requests at Thu, 28 Nov 2024 08:02:41 GMT Cap analysis gene expression The output of CAGE

1020-550: The project. A summary of key participating institutions of each phase is listed below: Source: Since its inception, GENCODE has released 36 versions of the Human gene set annotations (excluding minor updates). The key summary statistics of the most recent GENCODE Human gene set annotation ( Release 36, December 2020 freeze ) is shown below: Through advancements in sequencing technologies (such as RT-PCR-seq), increased coverage from manual annotations (HAVANA group), and improvements to automatic annotation algorithms using Ensembl,

1054-428: The search for appropriate guide sentences by listing potential binding sites for the CRISPR/Cas9 complex that are next to transcribed regions, or within 200 bp of one. For each site, the track provides possible guide sequences along with a collection of predicted efficiency and specificity scores for those guide sequences. It also provides information about potential off-targets, grouped by the number of missmatches between

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1088-435: The years since the discovery of the human genome. First, genes were conceived in the 1900s as discrete units of heredity, then it was thought as the blueprint for protein synthesis, and in more recent times, it was being defined as genetic code that is transcribed into RNA. Although the definition of a gene has evolved greatly over the last century, it has remained a challenging and controversial subject for many researchers. With

1122-735: Was created by GENCODE to develop custom microarray platforms capable of quantifying the transcripts in the GENCODE lncRNA annotation. A number of designs have been created using the Agilent Technologies eArray system, and these designs are available in a standard custom Agilent format. The RNA-seq Genome Annotation Assessment Project (RGASP) project is designed to assess the effectiveness of various computational methods for high quality RNA-sequence data analysis. The primary goals of RGASP are to provide an unbiased evaluation for RNA-seq alignment, transcript characterisation (discovery, reconstruction and quantification) software, and to determine

1156-462: Was using CAP Trapper for capturing the 5′ ends, oligo-dT primers for synthesizing the cDNAs, the type IIs restriction enzyme MmeI for cleaving the tags, and the Sanger method for sequencing them. Random reverse-transcription primers were introduced in 2006 by Kodzius et al. to better detect the non-polyadenylated RNAs. In DeepCAGE (Valen et al. , 2008), the tag concatemers were sequenced at

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