Springer Nature. CAS All the currently (alive/live qualification) available human nuclear gene entries were downloaded from NCBI Gene web site on January 5th, 2019 using the following text query: Homo sapiens [Organism] AND source_genomic [properties] AND alive [property]. 2023 Feb;55(2):209-220. doi: 10.1038/s41588-022-01276-9. Gene Status; AAR2: updated: AASS: updated: AATF: updated: ABCC1: updated: ABHD17A: updated: ABO pending: ACAD9: updated: ACADM: updated: ACBD5: updated: For example, based on current genome annotations, there is one human SERPINA1 gene with five mouse homologs, presumably due to gene duplication in the mouse lineage. doi: 10.1126/sciadv.abq5072. (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). A genome-wide classification of the protein-coding genes with regard to cell line distribution across all cancer cell lines as well as specificity across 27 cancer types has been performed using between-sample normalized data (nTPM). Protein class Gene ontology Length & mass Signal peptide (predicted) Transmembrane regions (predicted) MAN1A2-001 ENSP00000348959 ENST00000356554: O60476 [Direct mapping] Mannosyl-oligosaccharide 1,2-alpha-mannosidase IB . 2016. https://doi.org/10.1093/database/baw153. AP and PS designed the study, collected the data and performed the analysis. Non-coding RNA genes: 355 to 1,207 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. Please enable it to take advantage of the complete set of features! Protein-coding genes: 45 to 73 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. 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. Both types of genes can produce non-coding transcripts, but non-coding RNA genes do not produce protein-coding transcripts. Non-coding RNA genes: 148 to 515 Measuring 90 megabases in length, Chromosome 16 has exceptionally high gene density, particularly relating to genetic diseases in humans, which numbers about 150 out of the 90 million nucleotide sequences. Protein-coding genes: 996 to 1,111 AB046579 - Homo sapiens teckvar mRNA for chemokine TECK variant precursor, . Protein-coding genes: 1,961 to 2,093 Genome Biol. and transmitted securely. National Library of Medicine The UMAP was generated by clustering genes based on expression patterns. The https:// ensures that you are connecting to the This small chromosome (less than 2.5%), measuring only 19 by 59 megabases in size, is pretty low key. A genome-wide expression analysis of 1055 human cell lines, including 985 cancer cell lines, was performed using RNA-seq with early-split samples as duplicates. On the cell line category specific pages, which are accessed by clicking on the piechart or the colored boxes on the Cell Line section page, plots showing the cancer-related pathway (PROGENy) and cytokine (CytoSig) activity relative to the average expression of all analyzed cell lines as the baseline are displayed. Responsible for overly large nose tip, nasal bridge and ear lobes. This lncRNA sequence is 2,913 nucleotides long and is found in Homo sapiens. The UCSC Genes track is a set of gene predictions based on data from RefSeq, GenBank, CCDS, Rfam, and the tRNA Genes track. This protein inhibits the neutrophil-derived proteinases neutrophil elastase, cathepsin G, and proteinase-3 and thus protects tissues from damage at inflammatory . Consensus pseudogenes predicted by the Yale and UCSC pipelines, Protein-coding transcript translation sequences, Genome sequence, primary assembly (GRCh38), It contains the comprehensive gene annotation on the reference chromosomes only, It contains the comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes), It contains the comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions, It contains the basic gene annotation on the reference chromosomes only, It contains the basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes), It contains the basic gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions, It contains the comprehensive gene annotation of lncRNA genes on the reference chromosomes, It contains the polyA features (polyA_signal, polyA_site, pseudo_polyA) manually annotated by HAVANA on the reference chromosomes, 2-way consensus (retrotransposed) pseudogenes predicted by the Yale and UCSC pipelines, but not by HAVANA, on the reference chromosomes, tRNA genes predicted by ENSEMBL on the reference chromosomes using tRNAscan-SE, Nucleotide sequences of all transcripts on the reference chromosomes, Nucleotide sequences of coding transcripts on the reference chromosomes, Transcript biotypes: protein_coding, nonsense_mediated_decay, non_stop_decay, IG_*_gene, TR_*_gene, polymorphic_pseudogene, protein_coding_LoF, Amino acid sequences of coding transcript translations on the reference chromosomes, Nucleotide sequences of long non-coding RNA transcripts on the reference chromosomes, Nucleotide sequence of the GRCh38.p13 genome assembly version on all regions, including reference chromosomes, scaffolds, assembly patches and haplotypes, The sequence region names are the same as in the GTF/GFF3 files, Nucleotide sequence of the GRCh38 primary genome assembly (chromosomes and scaffolds), Remarks made during the manual annotation of the transcript, Entrez gene ids associated to GENCODE transcripts (from Ensembl xref pipeline), Piece of evidence used in the annotation of an exon (usually peptides, mRNAs, ESTs), Source of the gene annotation (Ensembl, Havana, Ensembl-Havana merged model or imported in the case of small RNA and mitochondrial genes), HGNC approved gene symbol (from Ensembl xref pipeline), PDB entries associated to the transcript (from Ensembl xref pipeline), Manually annotated polyA features overlapping the transcript 3'-end, Pubmed ids of publications associated to the transcript (from HGNC website), RefSeq RNA and/or protein associated to the transcript (from Ensembl xref pipeline), Amino acid position of a selenocysteine residue in the transcript, UniProtKB/SwissProt entry associated to the transcript (from Ensembl xref pipeline), Piece of evidence used in the annotation of the transcript, UniProtKB/TrEMBL entry associated to the transcript (from Ensembl xref pipeline). Mahley, R. W. et al. 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. 2013;14:R36. Pseudogenes: 931 to 1,207. Bookshelf Data in the Genes.xlsx table are NCBI Gene identifier, official Gene Symbol, Chromosome, Gene Type, gene RefSeq status, transcript RefSeq status, Gene Length in bp. Dalgleish, A. G. et al. Piovesan, A., Antonaros, F., Vitale, L. et al. Nature 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. 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. 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. 99.4% of the bodys euchromatic DNA is located in chromosome 20. Protein-coding genes: 646 to 719 Human protein-coding genes and gene feature statistics in 2019. Ensembl 2019. 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. Nature 312, 767768 (1984). PubMed The authors declare that they have no competing interests. Filtering by the Yes annotation allows the retrieval of a non-redundant set of exons, coding exons and introns, respectively. Article 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/. The 985 cancer cell lines were analyzed for their representability of the corresponding TCGA disease cohorts. 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. You can filter the table results by gene type to show only protein-coding or non-coding genes, or search within the list of human genes by gene name or protein name. The lists below constitute a complete list of all known human protein-coding genes. The data sets were created by exporting the data from each relative table of GeneBase as a spreadsheet. Advances in the Exon-Intron Database (EID). 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/. Non-coding RNA genes: 242 to 1,052 Strittmatter, W. J. et al. The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria.These are usually treated separately as the nuclear genome and the mitochondrial genome. This site needs JavaScript to work properly. doi: 10.1093/nar/gkx1095. (2018)). Here, RNA-seq profiles of cell lines generated by the HPA (n = 69) and the Cancer Cell Line Encyclopedia (CCLE 2019; n = 1019) were integrated, with the 33 common cell lines averaged for their gene expression. 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. TABLE 9.5 HUMAN GENOME AND HUMAN GENE STATISTICS SIZE OF GENOME COMPONENTS Mitochondrial genome Nuclear genome Euchromatic component . Search model organisms. 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. 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. The downloading, parsing and import of gene entries are described in more detail in the software public documentation. In total, 16465 of all human protein coding genes (n= 20090) are detected in the human brain. Humans have about 20,000 protein-coding genes but scientists still know remarkably little about most of the proteins they encode. Read more about the different categories of elevated expression here. The RNA expression levels were determined for all protein-coding genes (n = 20090) across the 1055 human cell lines and the results are presented on the gene summary page of the Cell Lines section as exemplified in the figure below. Hum Mol Genet. Natl Acad. Gene disorders here are linked to diseases such as autism, EhlersDanlos syndrome and variants of dementia. (i) Spearmans correlation coefficient () between every cancer cell line and its corresponding TCGA cohorts was estimated at the gene level. Dismiss. The nucleotides in chromosome 3 accounts for 6.5% of our DNA, with over 200 million base pairs. volume551,pages 427431 (2017)Cite this article. The red circles connected to each tissue name indicates the number of tissue enriched genes associated with that particular tissue. Due to the continuous increase of data deposited in genomic repositories, a revision and analysis of their content is recommended. This selection retrieved 19,116 genes, 46,932 transcripts and 562,164 exons. However, rather than an intron excised via canonical splicing, this is a 26-nucleotide segment known to be removed in particular circumstances by a completely different mechanism, an excision mediated by the endonuclease inositol-requiring enzyme 1 (IRE1) [9]. Pseudogenes: 288 to 379. "There are 3000 human proteins whose function is unknown," says Wood. Google Scholar. 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. 2013;101:2829. When the first draft of the human genome sequence published in 2001, there were approximately 30,000-40,000 protein-coding sequences. All authors read and approved the final manuscript. The human genome is massive, and contains over 30,000 protein-coding genes, as well as thousands more pseudogenes and non-coding RNAs. Cell. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S . How many protein-coding genes in the human genome? 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). Non-coding RNA genes: 245 to 973 RT-PCR. CAS Non-coding RNA genes: 277 to 993 The data sets are provided in standard, open format.xlsx. 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. You are using a browser version with limited support for CSS. Extensive annotations were added to aid identification of differentially expressed genes, potential gene editing sites, and non-coding gene . If you continue, we'll assume that you are happy to receive all cookies. 2016;25:252538. The orange circles indicate the number of genes with enriched expression in a group of tissues, connected by lines. MCP and MC supervised the project. Klatzmann, D. et al. Accessibility 2015;22:495503. 5, 15131523 (1991). Chromosome 10, which makes up almost 4.5% of our DNA, is almost identical to chromosome 10 found in gorilla, orangutan and chimps. 2006 Jun;7(2):178-85. doi: 10.1093/bib/bbl003. 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) Protein-coding genes: 804 to 874 Chromosome 13, with 3% of the bodys mapped human genome, is usually blamed for childhood obesity and delay in speech development. Pseudogenes: 606 to 879. Here, a consensus z-score above 1 or below -1 was considered significant. 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. Proc. Mitchell, J. California Privacy Statement, Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, et al. 2019;47:D745D751. Pseudogenes: 365 to 502. The entire molecule is regulated by only one regulatory region which contains the origins of replication of both heavy and light strands. The functionality of these genes is supported by both transcriptional and proteomic . Chromosome 10 Protein-coding genes: 706 to 754 Non-coding RNA genes: 244 to 881 Pseudogenes: 568 to 654 28S ribosomal protein L42, mitochondrial is a protein that in humans is encoded by the MRPL42 gene. It contains 133 million base pairs of nucleotides, or over 4% of the total. Protein-coding genes: 706 to 754 Next-generation transcriptome assembly: strategies and performance analysis. The UDN has allowed us to delve much deeper, beyond standard clinical testing. and JavaScript. In an additional analysis of the 2415 protein-coding genes differentially expressed over time, we performed an ORA enrichment of genes related to immune functions. Non-coding RNA genes: 483 to 1,158 the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in About 4000 human protein-coding genes are not mentioned in any scientific publication at all. We use cookies to enhance the usability of our website. Getting a list of protein coding genes in human Getting a list of protein coding genes in human 0 3.3 years ago fi1d18 4.1k Hi I have raw read counts extracted by htseq from STAR alignment I have both data with both Ensembl IDs and gene symbols, but I need only a latest list of protein coding genes in human; I googled but I did not find Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Hum Mol Genet. statement and 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. -. Front Genet. (2021)). MeSH 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. Click to obtain the corresponding list of genes. Open Access Piovesan A, Caracausi M, Ricci M, Strippoli P, Vitale L, Pelleri MC. 2023 Jan 20;9(3):eabq5072. 2018;46:D813. Science. View/Edit Mouse. Here they are listed below in order of frequency (1 = most highly researched): TP53 - Encodes the tumour-suppressor protein p53, which is mutated in up to half of all human cancers. 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. The two initial human genome papers reported 31,000 [ 2] and 26,588 protein-coding genes [ 3 ], and when the more . 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. J Cell Physiol. Nucleic Acids Res. Print 2016. We aim to name protein-coding genes based on a key normal function of the gene product. Nature 381, 661666 (1996). 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.