Nature 381, 661666 (1996). Journal of Translational Medicine Measuring around 191 megabases in length, chromosome 4 contains 186 million base pairs, or 6% of our DNA. We identified 5,737 putative protein-coding genes that result from mRNA modified by human polymorphisms and have significant homology to known proteins. 2008;3:20. Other parameters such as exon/intron mean and extreme length appear to have reached a stability that is unlikely to be substantially modified by future updates of the human genome data, which appear to be approachinga plateau on the curve of new added data, at least where protein-coding genes are concerned [6]. This lncRNA sequence is 2,913 nucleotides long and is found in Homo sapiens. 2023 Jan 25;31:398-410. doi: 10.1016/j.omtn.2023.01.010. doi: 10.1093/nar/gky1095. Chromosome 1 (human) Chromosome 2 (human) Chromosome 3 (human) Chromosome 4 (human) Chromosome 5 (human) Chromosome 6 (human) Chromosome 7 (human) Chromosome 8 (human) Chromosome 9 (human) Chromosome 10 (human) The following is a partial list of genes on human chromosome 3. The entire human mitochondrial DNA molecule has been mapped [1] [2] . Baker, S. J. et al. Front Genet. List of human protein-coding genes page 2 covers genes EPHA2-MTNR1B List of human protein-coding genes page 3 covers genes MTO1-SLC22A6 List of human protein-coding genes page 4 covers genes SLC22A7-ZZZ3 NB: Each list page contains 5000 human protein-coding genes, sorted alphanumerically by the HGNC-approved gene symbol. 2014;23:586678. Pseudogenes: 606 to 879. The .gov means its official. Protein-coding genes: 1,961 to 2,093 Google Scholar. Several miRNA variants from different populations are known to be associated with an increased risk of rheumatoid arthritis (RA). This can be served as a reference for cell line selection for in vitro experiments when studying a specific cancer type. The lists below constitute a complete list of all known human protein-coding genes. Pseudogenes: 666 to 839. Sign up for the Nature Briefing: Translational Research newsletter top stories in biotechnology, drug discovery and pharma. Due to the continuous increase of data deposited in genomic repositories, a revision and analysis of their content is recommended. We aim to name protein-coding genes based on a key normal function of the gene product. The data presented in the Genes.xlsx, Transcripts.xlsx and Gene_Table.xlsx have been counter-checked with the complete, original data included in the GeneBase software. The human genome is conventionally divided into the "coding" genome, which generates the ~20,000 annotated human protein coding genes, and the "dark" genome, which does not encode. Non-coding RNA genes: 318 to 1,202 Pseudogenes: 247 to 333. This is the list of human protein-coding genes linked to SARS-CoV-2 infection and / or COVID-19 disease currently being targeted for re-annotation by GENCODE. The 83 million base pairs in chromosome 17 (almost 3%) plays a vital role in the development of physiological balance and generation of internal organs. The data are updated as of January 2019, 3years after the last published analysis of human gene features [6] and pre-filtered according to public annotation about the review or validation of the records to ensure reliability of the data. Bethesda, MD 20894, Web Policies Nucleic Acids Res. Main summarized data derived from the analysis of our updated and standard-formatted data sets are also provided here, while the data tables remain available for human genome studies. An official website of the United States government. doi: 10.1093/iob/obac008. How many protein-coding genes in the human genome? The genome sequence is an organism's blueprint: the set of instructions dictating its biological traits. Data in the Gene_Table.xlsx table are derived from the Gene Table section of the NCBI Gene resourceparsed by GeneBaseGene_Table table and include, along with NCBI Gene identifier, official Gene Symbol and Gene Type, along with data about each gene exon/intron represented in each row: chromosome sequence RefSeq GenBank accession number, start and end coordinates, chromosome strand and length in bp for the gene to which the exon/intron belongs; length in bp for the relative transcript; coordinates and length in bp of the 5 UTR, CDS and 3 UTR of the transcript to which the exon/intron belong; RefSeq status, label and GenBank accession number for that transcript; start and end coordinates, length in bp and serial number for each exon, coding exon and intron; last exon annotation which shows Yes if that exon or coding exon is the last in the transcript; protein RefSeq label and GenBank accession number; non-redundant annotation, which shows Yes to label each exon/coding exon/intron a single time (YesMerged meaning that the same element appears to be repeated in the data, YesUnique meaning that the element is unique in the data set); live status, genome annotation status and gene RefSeq status for the genederived from the GeneBase Gene_Summary related table. Contains encoding instructions for Acylamino-acid-releasing enzyme, 5-azacytidine-induced protein 2 and protein C3orf23. So far, about 19,000 lncRNAs genes have been annotated in the human genome (Gencode 41), nearly matching the number of protein-coding genes. Click on a cluster or Go to interactive expression cluster page to view an interactive UMAP and details about all cluster annotations. We first performed a protein-centric transcriptomics scan to define a revised set of human secreted proteins (secretome) based on 19,670 protein-coding genes predicted by Ensembl ().For each protein-coding gene, all protein isoforms (splice variants) were annotated on the basis of the presence of a signal peptide, transmembrane regions, or both, and each protein isoform was classified as being . Human protein-coding genes and gene feature statistics in 2019, https://doi.org/10.1186/s13104-019-4343-8, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/. The length of the bars visualizes the number of elevated genes in each tissue compared to the tissue with the maximum amount of elevated genes (brain). Piovesan A, Caracausi M, Ricci M, Strippoli P, Vitale L, Pelleri MC. 99.4% of the bodys euchromatic DNA is located in chromosome 20. Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. (2021)). Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH. Nature 312, 767768 (1984). National Center for Biotechnology Information, highly restricted Down Syndrome critical region. Maddon, P. J. et al. Follow . Voshall A, Moriyama EN. MCP and MC supervised the project. 2012 Oct;22(10):2079-87. doi: 10.1101/gr.139170.112. volume12, Articlenumber:315 (2019) Symp. Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Genome Biol. Gene expression data were processed in the same way as for PROGENy analysis. Estimates of the current updates are closer to 20,000 protein-coding genes, as well as an expanding number of functional, non-coding RNA sequences. volume551,pages 427431 (2017)Cite this article. Deng, H. et al. Genetic code variants [ edit] 1. All authors agreed both to be personally accountable for the authors own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. Comparison with a previous report of 3years ago [6], which in turn demonstrated important differences with the first analysis of the human genome sequence [10, 11], reveals some substantial changes in relevant parameters such as the number of known, characterized nuclear protein-coding genes (from 18,255 to 19,116), thus now approaching a limit theorized 5years ago [12]; the protein-coding non-redundant transcriptome space (from 53,827,863 to 59,281,518bp, with an increase of 10.1%); number of exons (from 412,641 to 562,164, plus 36.2%, when this number is not collapsed to eliminate redundant exons appearing in more than one mRNA) due to a relevant increase of the number of mRNA isoforms recorded. Protein-coding genes: 516 to 555 Non-coding DNA. Higher-order chromatin conformation forms a scaffold upon which epigenetic mechanisms converge to regulate gene expression [1, 2].Many genes are expressed in an allele-specific manner in the human genome, and this phenomenon is an important contributor to heritable differences in phenotypic traits and can be cause of congenital and acquired diseases including cancer [3, 4]. Measuring 82 megabases, chromosome 13 accounts for up to 3.5% of the human genome. Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. The entire molecule is regulated by only one regulatory region which contains the origins of replication of both heavy and light strands. The expression for all protein-coding genes in all major tissues and organs in the human body can be explored in this interactive database, including numerous catalogs of proteins expressed in a tissue-restricted manner. Biol Direct. Pseudogenes: 931 to 1,207. Despite its massive size of 155 megabases, chromosome X only accounts for 5% of the human genome. (ii) The enrichment of the TCGA cohort elevated genes (i.e., the union of enriched, group enriched, and enhanced genes in the TCGA cohort) in cell lines was evaluated by gene set enrichment analysis (GSEA). Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. Nature AP and PS designed the study, collected the data and performed the analysis. Intron data are presented as companions to the relative upstream exon, there will therefore be no intron data in the rows with Last_Exon field showing Yes. Based on the transcriptomics profiles, cell lines were evaluated for their consistency to the corresponding TCGA (The Cancer Genome Atlas) disease cohort to help researchers to select the best cell lines as in vitro models for cancer research. 2003, 460464 (2003). Fully mapped in 2001, this chromosome of 63 million nucleotides is known for its injurious effects involving heart diseases. GENCODE - Human Release 43 Human Release 43 (GRCh38.p13) Statistics of this release More information about this assembly (including patches, scaffolds and haplotypes) Go to GRCh37 version of this release GTF / GFF3 files Fasta files Metadata files Search model organisms. Jobs People Learning Dismiss Dismiss. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. 28S ribosomal protein L42, mitochondrial is a protein that in humans is encoded by the MRPL42 gene. Non-coding RNA genes: 355 to 1,207 Pseudogenes: 736 to 911. 83, 21252130 (1989). The read counts of the 1055 cell lines were normalized by DESeq2 with respect to the size factor of each cell line and were further transformed by variance stabilizing transformation into log2 space. The largest of its kind, the Human Reference Interactome (HuRI) map charts 52,569 interactions between 8,275 human proteins, as described in a study published in Nature. Nature. 2016;44:D73345. 2023 BioMed Central Ltd unless otherwise stated. 2019;47:D74551. For TCGA disease cohorts previously analyzed by the HPA pathology project also the ranking list of the cell lines based on gene expression similarity to the corresponding diseaase cohort is shown. 22 June 2021, Receive 51 print issues and online access, Get just this article for as long as you need it, Prices may be subject to local taxes which are calculated during checkout. Nucleic Acids Res. Following validation by the software Splign [8], we confirm that there are no human (and possibly of any species) introns shorter than 30bp (Table2). This optimistic trend culminated with ~ 550 new gene function . It is also not too different from chromosome 9 found in baboons and macaques. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. The functionality of these genes is supported by both transcriptional and proteomic . We are grateful to Kirsten Welter for her kind and expert revision of the manuscript. Get what matters in translational research, free to your inbox weekly. Next-generation transcriptome assembly: strategies and performance analysis. The three data tables Genes.xlsx, Transcripts.xlsx and Gene_Table.xlsx have been released in the public repository Open Science Framework and they can be freely downloaded at the address: https://osf.io/mhda7/. We are profoundly grateful to the Fondazione Umano Progresso, Milano, Italy for their fundamental support to our research on trisomy 21 and to this study. Protein-coding genes: 862 to 984 The result of the cluster analysis is presented as a UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes. A number of 2685 genes are classified as brain elevated and 202 genes were only detected in the brain. 2017;232:75970. Funded by the National Human Genome Research Institute (NHGRI), the ENCODE Project set out to systematically identify and catalog all functional elements parts of the genetic blueprint that may be crucial in directing how our cells function present in our DNA. The team followed up with a detailed molecular analysis which confirmed that the variant affects the expression of several cytoskeletal proteins and smooth muscle cell function. In fact, scientists have estimated that there may be as many as 500,000 or more different human proteins, all coded by a mere 20,000 protein-coding genes. The clustering of 19023 genes expressed in tissues resulted in 89 expression clusters, which have been manually annotated to describe common features in terms of function and specificity. Ensembl 2019. We have generated general descriptive statistics for human nuclear protein-coding genes and messenger RNAs (mRNAs) (Table1), exons, coding-exons and introns (Table2). The unfolding of these instructions is initiated by the transcription of the DNA into RNA sequences. Nucleic Acids Res. protein-L-isoaspartate (D-aspartate) O-methyltransferase: 5: 20: PCNA: 113: proliferating cell nuclear antigen: 12: 67: PDGFB: 47: platelet-derived growth factor beta . Explore the proteomes of specific tissues and organs, The Human Protein Atlas project is funded, protein localization in tissues at a single-cell level, if a gene is enriched in a particular tissue (specificity), which genes have a similar expression profile across tissues (expression cluster). Protein-coding genes: 739 to 822 Epub 2012 Jun 18. https://doi.org/10.1038/d41586-017-07291-9, DOI: https://doi.org/10.1038/d41586-017-07291-9. It is expected that cell lines showing high concordance to the matched TCGA cancer type should present high log2 fold changes of the elevated genes of that TCGA cohort relative to the disease baseline expression. The two initial human genome papers reported 31,000 [ 2] and 26,588 protein-coding genes [ 3 ], and when the more . 2001;107:88191. Database. Considering only upregulated DEGs or. The 985 cancer cell lines were analyzed for their representability of the corresponding TCGA disease cohorts. Article Human, non-human primates, domestic species and default for everything that is not a mouse, rat, fish, worm, or fly Full gene names are not italicized and Greek symbols are not used eg: insulin-like growth factor 1 Gene symbols Greek symbols are never used (e.g., TNFA, not TNF; PPARG, not PPAR ;) hyphens are almost never used Data in the Transcripts.xlsx table include the same first five types of information provided in the Genes.xlsx table, plus RefSeq GenBank accession number for each transcript, length in bp of the whole transcript as well as of its 5 untranslated region UTR, coding sequence (CDS) and 3 UTR, number of exons and coding exons for that transcript, derived from the GeneBaseTranscripts table. The Pathology section contains mRNA and protein expression data from 17 different forms of human cancer. Bioinformatics in the Era of Post Genomics and Big Data. Pseudogenes: 513 to 598. Using the spreadsheet filtering and summarization functions (Excel for Mac 2011, Microsoft) or exploiting the search and calculation functions in GeneBase (FileMaker Pro) provided identical results in all cases. AMIA Annu. Chromosome 11, which contains a little over 4% of our building blocks, is incredibly critical to our olfactory system as 40% of the 856 olfactory receptor genes in our body are clustered here. Pseudogenes: 539 to 682. The resulting file has been imported according to the user guide of GeneBase 1.1, available for free at http://apollo11.isto.unibo.it/software/ and including a FileMaker Pro runtime (FileMaker, Santa Clara, CA) at its core. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. OLeary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, et al. Summary. The human genome began with the assumption that our genome contains 100,000 protein-coding genes, and estimates published in the 1990s revised this number slightly downward, usually reporting values between 50,000 and 100,000. In the absence of functional data, protein-coding genes may be named in the following ways: Based on recognized structural domains and motifs encoded by the gene (e.g. In order to provide reliable data, we focused on a curated subset of human nuclear protein-coding genes with a REVIEWED or VALIDATED Reference Sequence (RefSeq) status [1, 7]. Friedrich, G. & Soriano, P. Genes Dev. At that time, Consortium researchers had confirmed the existence of 19,599 protein-coding genes in the human genome and identified another 2,188 DNA segments that are predicted to be protein-coding genes. Protein-coding genes: 790 to 886 The description of each field is included in the first row of the spreadsheet table. Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y. Sci Adv. A-proteins have hydrophobic amino acid compositions . The red circles connected to each tissue name indicates the number of tissue enriched genes associated with that particular tissue. Around 890 diseases such as Alzheimer's, glaucoma and hearing loss have been linked to genetic disorders found in chromosome 1. Piovesan, A., Antonaros, F., Vitale, L. et al. We use cookies to enhance the usability of our website. In 3 sisters with isolated pituitary hormone deficiency (CPHD7; 618160), Argente et al. Dismiss. (2014) identified compound heterozygosity for mutations in the RNPC3 gene: the first was a c.1420C-A transversion, resulting in a pro474-to-thr (P474T) substitution at a highly conserved residue in a turn position between the beta-3 strand and alpha-2 helix, and the second was a c.1504C-T transition . Provided by the Springer Nature SharedIt content-sharing initiative, Nature (Nature) Part of When expanded it provides a list of search options that will switch the search inputs to match the current selection. A key scientific priority is the functional characterization of lncRNAs, a major challenge in molecular biology that has encouraged many high-throughput efforts. The UCSC genome browser database: 2019 update. Below is a list of articles on human chromosomes, each of which contains an incomplete list of genes located on that chromosome. All authors read and approved the final manuscript. Piovesan A, Vitale L, Pelleri MC, Strippoli P. Universal tight correlation of codon bias and pool of RNA codons (codonome): the genome is optimized to allow any distribution of gene expression values in the transcriptome from bacteria to humans. The genes in chromosome 2 span 242 million nucleotide base pairs, which also amounts to about 8% of the human DNA. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). eCollection 2022. Here we provide a tabulated set of data about human nuclear protein-coding genes (genes, transcripts and gene features such as exons, coding portion of the exons and introns) derived from advanced parsing of NCBI Gene web site offered in a standard, ready-to-use spreadsheet format. The expression for all protein-coding genes in all major tissues and organs in the human body can be explored in this interactive database, including numerous catalogs of proteins expressed in a tissue-restricted manner. While the basic approach to obtain the data we present here is similar to the one followed in our previous study about the subject [6], there are two main differences. The sequence of the human genome. government site. USA 90, 19771981 (1993). Careers. 8600 Rockville Pike Cell 42, 93104 (1985). Other parameters such as gene, exon or intron mean and extreme length appear to have reached a stability that is unlikely to be substantially modified by human genome data updates, at least regarding protein-coding genes. Mitchell, J. LncRNA studies have been stimulated by the . Correlation tests were used to identify relationships between gene length and other gene and protein characteristics. Integrated transcriptome map highlights structural and functional aspects of the normal human heart. Dismiss. This sex chromosome (allosome) is only present in males. To obtain The cell lines were then ranked based on Spearmans () and NES from high to low, respectively. Sci. Open Access articles citing this article. Non-coding RNA genes: 191 to 594 -, Piovesan A, Vitale L, Pelleri MC, Strippoli P. Universal tight correlation of codon bias and pool of RNA codons (codonome): the genome is optimized to allow any distribution of gene expression values in the transcriptome from bacteria to humans. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al. "One reason for this might be that practically all genetic testing performed today focuses on protein coding genes. Show all. Pseudogenes: 433 to 594. Google Scholar. The various subproteomes can be explored in this interactive database including numerous catalogs of protein-coding genes with detailed information regarding expression and localization of the corresponding proteins.