CAS 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. 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. Contains encoding instructions for Acylamino-acid-releasing enzyme, 5-azacytidine-induced protein 2 and protein C3orf23. Springer Nature. Ensembl 2019. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 2015;22:495503. Morgan, T. H. Science 32, 120122 (1910). All rights reserved. In addition, based on biological data mining, for each cell line, the relative activity of 14 cancer-related pathways and 43 cytokines were inferred and presented to characterize the phenotype of the cell line. 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. The UniProtKB/Swiss-Prot Homo sapiens proteome contains one representative . 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. Comparison with previous reports reveals substantial change in the number of known nuclear protein-coding genes (now 19,116), the protein-coding non-redundant transcriptome space [now 59,281,518 base pair (bp), 10.1% increase], the number of exons (now 562,164, 36.2% increase) due to a relevant increase of the RNA isoforms recorded. How has the classification of all protein-coding genes been done? PubMed Central Finally, we confirm that there are no human introns shorter than 30bp. This article is an index of lists of human genes. Pseudogenes: 736 to 911. Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y. Sci Adv. 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: 583 to 820 A key scientific priority is the functional characterization of lncRNAs, a major challenge in molecular biology that has encouraged many high-throughput efforts. Google Scholar. Mol Ther Nucleic Acids. Protein-coding genes: 739 to 822 Protein-coding genes: 739 to 822 Non-coding RNA genes: 246 to 830 Pseudogenes: 590 to 738 Chromosome 9 accounts for between 4% and 4.5% of our DNA cells. Integr Org Biol. By using this website, you agree to our A gene is a string of DNA that encodes the information necessary to make a protein, which then goes on to perform some function within our cells. Human protein-coding genes and gene feature statistics in 2019. TABLE 9.5 HUMAN GENOME AND HUMAN GENE STATISTICS SIZE OF GENOME COMPONENTS Mitochondrial genome Nuclear genome Euchromatic component . 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. Initial sequencing and analysis of the human genome. Non-coding RNA genes: 483 to 1,158 A study published last month (May 29) on BioRxiv provides an expanded database of approximately 5,000 novel genesof those, around 1,000 code for proteins, expanding the estimated number of protein-coding genes from around 20,000 to 21,000. Non-coding RNA genes: 355 to 1,207 In addition, data can be exported in other formats and imported in other applications (database management systems, statistical software, genomic tools) for further analysis. Provided by the Springer Nature SharedIt content-sharing initiative. Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. These data might also be used in comparative genomic studies when compared to similar data sets generated from different species to uncover specific and significant differences in genome and gene organization. Human mtDNA consists of 16,569 nucleotide pairs. Journal of Translational Medicine Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype. Finally the two ranking lists were combined, and cell lines were reordered according to their average rank. Pseudogenes: 606 to 879. 2003, 460464 (2003). NCBI Resource Coordinators. In this work, we used human genome data to identify possible functions associated with gene size, with a focus on protein-coding regions and genes. 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: 559 to 629 What can you learn from the Cell Lines section? Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization. Invest. Accounts for up to 5.5% of our nucleotide base pairs, chromosome 7 has encoded instructions for the manufacturing of proteins such as Poliovirus and RNF216, which are responsible for viral RNA replication. Researchers often turn to model organisms to understand the complex molecular mechanisms of the human body. Coding Region Position: hg38 chr20:63,488,023-63,497,763 Size: 9,741 Coding . Open Access Non-coding DNA. Caracausi M, Piovesan A, Vitale L, Pelleri MC. Genomics. -, Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. (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). 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. Finally, we confirm that there are no human introns shorter than 30 bp. Clipboard, Search History, and several other advanced features are temporarily unavailable. Based on transcriptomics analysis across all major organs and tissue types in the human body, all putative 20090 protein coding genes have been classified with regard to abundance and distribution of transcribed mRNA molecules, including 10986 proteins showing a significantly elevated level of expression in a particular tissue or a group of related tissues and 8776 proteins detected in all organs and tissues. Pseudogenes: 433 to 594. Now, let's filter to get only protein-coding genes, group by the ensembl gene ID, summarize to count how many transcripts are in each gene, inner join that result back to the original gene list, so we can select out only the gene, number of transcripts, symbol, and description, mutate the description column so that it isn't so wide that it'll break the display, arrange the returned data . Genes that make proteins are called protein-coding genes. Protein-coding genes: 1,224 to 1,327 The genome sequence is an organism's blueprint: the set of instructions dictating its biological traits. The activity of 43 CytoSig cytokines was inferred based on the gene expression profile of the 1055 cell lines by the package CytoSig (Jiang P et al. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Article We are grateful to Kirsten Welter for her kind and expert revision of the manuscript. "There are 3000 human proteins whose function is unknown," says Wood. To obtain For this, read counts for HPA and CCLE cell lines quantified by Kallisto were re-analyzed without filtering out the non-protein-coding genes to ensure a broadened coverage of cancer pathway responsive genes. Pseudogenes: 666 to 839. Next-generation transcriptome assembly: strategies and performance analysis. All these kinds of analyses depend on the chosen gene entry subset, the RefSeq classification system and are subject to the accuracy of the input dataset. Dismiss. Open Access In order to provide a curated set of updated statistics regarding human nuclear protein-coding genes and transcripts through GeneBase 1.1 Human, we considered only NCBI Gene records retrieved bysearching for protein-coding gene type, with REVIEWED or VALIDATED RefSeq gene status, with at least one REVIEWED or VALIDATED transcript, excluding records annotated as not in current annotation release records (Genome_Annotation_Status field). 17 January 2023, Mammalian Genome Chromosome 13, with 3% of the bodys mapped human genome, is usually blamed for childhood obesity and delay in speech development. Chromosome 10, which makes up almost 4.5% of our DNA, is almost identical to chromosome 10 found in gorilla, orangutan and chimps. 2019;47:D853D858. Genome Biol. protein-L-isoaspartate (D-aspartate) O-methyltransferase: 5: 20: PCNA: 113: proliferating cell nuclear antigen: 12: 67: PDGFB: 47: platelet-derived growth factor beta . doi: 10.1093/iob/obac008. A-proteins have hydrophobic amino acid compositions . A description about the classification of genes into the tissue enriched and group enriched categories is found here. Actually, apart from three introns estimated to be of 13bp long due to NCBI Gene Gene Table artifacts [5], there is one unique intron smaller than 30bp, intron 14 of XBP1 gene, in these data. London: IntechOpen; 2018. p. 1536. The results were represented as the normalized enrichment score (NES), with a positive value showing high consistency between a cell line and a disease-matched TCGA cohort. Non-coding RNA genes: 260 to 639 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. Piovesan A, Caracausi M, Antonaros F, Pelleri MC, Vitale L. Database (Oxford). volume12, Articlenumber:315 (2019) 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/. PubMed Central Pseudogenes: 545 to 693. Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy, Allison Piovesan,Francesca Antonaros,Lorenza Vitale,Pierluigi Strippoli,Maria Chiara Pelleri&Maria Caracausi, You can also search for this author in 2019;47:D745D751. Pseudogenes: 381 to 400. 2013;101:2829. and transmitted securely. 2001;107:88191. The reasons for the choice of the NCBI Gene database as a reference data source have been previously discussed in detail [6]. Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, et al. Gene Status; AAR2: updated: AASS: updated: AATF: updated: ABCC1: updated: ABHD17A: updated: ABO pending: ACAD9: updated: ACADM: updated: ACBD5: updated: Epub 2006 Mar 9. Proc. Nature 312, 763767 (1984). Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. 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]. The data sets were created by exporting the data from each relative table of GeneBase as a spreadsheet. Members of this family maint ain homeostasis by neutralizing overexpressed proteinase activity through their function as suicide substrates. Cell. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Then, for each TCGA cohort, Spearmans was calculated between the averaged FPKM values and the nTPM values of the disease-matched cell lines based on the common 19,760 protein-coding genes. PubMed The Cell Lines section contains information on genome-wide RNA expression profiles of human protein-coding genes in human cell lines. NB: Each list page contains 5000 human protein-coding genes, sorted alphanumerically by the, Learn how and when to remove this template message, List of human protein-coding genes page 1, List of human protein-coding genes page 2, List of human protein-coding genes page 3, List of human protein-coding genes page 4, Entrez-Cross Database Query Search System, https://en.wikipedia.org/w/index.php?title=Lists_of_human_genes&oldid=1095516146, This page was last edited on 28 June 2022, at 20:15. The red circles connected to each tissue name indicates the number of tissue enriched genes associated with that particular tissue. ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended.