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2023 Jan 10;13:1085139. doi: 10.3389/fgene.2022.1085139. Pseudogenes: 513 to 598. 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]. Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. Unmasking the biological function and regulatory mechanism of NOC2L: a novel inhibitor of histone acetyltransferase, Progress towards completing the mutant mouse null resource, Estrogen receptor- signaling in post-natal mammary development and breast cancers, p53 in ferroptosis regulation: the new weapon for the old guardian, Understudied proteins: opportunities and challenges for functional proteomics, An open invitation to the Understudied Proteins Initiative, Sign up for Nature Briefing: Translational Research. 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. The results are presented as an interactive UMAP plot in which mouse-over displays general information for the clusters and the clicking on a cluster will display more information and plots regarding that specific cluster, as well as, a clickable list of all clusters. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al. Finally the two ranking lists were combined, and cell lines were reordered according to their average rank. Search human. Once the taq polymerase starts to replicate DNA, the probe is destroyed and fluorescent material is released . Chromosome values were re-exported from GeneBase in text format and pasted into the relative column of Genes.xlsx file to avoid misinterpretation of X and Y values as numbers by Excel. Protein-coding genes: 1,194 to 1,292 Sci Rep. 2018;8:2977. 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. In: Abdurakhmonov IY, editor. After that, for every cell line, we calculated the fold change of every gene relative to the disease baseline expression, followed by the log2 transformation of the fold change. Galtier studied protein-coding genes in 44 metazoan species pairs to investigate the relationships between the rate of adaptive evolution (measured using and a) and N e. There was a positive relationship between and N e, but a negative relationship between the estimated rate of fixation of deleterious mutations ( na) and N e. Only about 1 percent of DNA is made up of protein-coding genes; the other 99 percent is noncoding. Protein-coding genes: 1,224 to 1,327 The UniProtKB/Swiss-Prot Homo sapiens proteome contains one representative . Genomics. AP and PS designed the study, collected the data and performed the analysis. Non-coding RNA genes: 138 to 608 Accessibility 83, 21252130 (1989). MeSH Clipboard, Search History, and several other advanced features are temporarily unavailable. They make up the elementary units of heredity and are passed down from parents to children. Extensive annotations were added to aid identification of differentially expressed genes, potential gene editing sites, and non-coding gene . Cookies policy. This optimistic trend culminated with ~ 550 new gene function . Science 244, 217221 (1989). 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. Nucleic Acids Res. Finally, a new classification has been introduced in which genes are clustered based on similarity in expression across the cell lines. Pseudogenes: 568 to 654. On the other hand, a genetic element could be transcribed, and thus identified as a functional gene, only under particular conditions such as a developmental stage, a disease or the exposure to specific stresses or drugs. Bioinformatics in the Era of Post Genomics and Big Data. Chromosome 9 accounts for between 4% and 4.5% of our DNA cells. Springer Nature. In order to make a protein, a molecule closely related to DNA called ribonucleic acid (RNA) first copies the code within DNA. This article is an index of lists of human genes. Then, the R package decoupleR was used to calculate the relative pathways activities based on the top 100 signature genes per pathway obtained from the R package progeny (Schubert M et al. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets. Below is a list of articles on human chromosomes, each of which contains an incomplete list of genes located on that chromosome. if a gene is enriched in cellines from a particular cancer type (specificity), which genes have a similar expression profile across the cell lines (expression cluster), the catalogue of genes elevated in each of the cell lines, which cell line has the most consistent expression profile to its corresponding TCGA disease cohort (i.e., the best cell lines for cancer study), cancer-related pathway and cytokine activity of each cell line, (i) classify the gene expression specificity in different cancer types and the distribution across all cell lines, (ii) evaluate the consistency between the cell lines and the corresponding TCGA disease cohort, (iii) estimate the cancer-related pathway (PROGENy) and cytokine (CytoSig) activity (with non-protein-coding genes included for calculation), (iv) find the highest correlating genes and further to classify all genes according to their cell line-specific expression. Terms and Conditions, The three most widely used human gene catalogs [Ensembl ( 4 ), RefSeq ( 5 ), and Vega ( 6 )] together contain a total of 24,500 protein-coding genes. The Cell Lines section contains information on genome-wide RNA expression profiles of human protein-coding genes in human cell lines. 2017-05-19 List of genes. A tour through the most studied genes in biology reveals some surprises. 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. 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. In addition, statistics based on these data and any subset generated from them may be used to tune genomic software requiring parameters about nuclear protein-coding gene, transcript or exon/intron number and length [15, 16]. 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. Non-coding RNA genes: 483 to 1,158 Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Its work is centred around internal organ development. Around 890 diseases such as Alzheimer's, glaucoma and hearing loss have been linked to genetic disorders found in chromosome 1. Epub 2006 Mar 9. Correlation tests were used to identify relationships between gene length and other gene and protein characteristics. This site needs JavaScript to work properly. The downloading, parsing and import of gene entries are described in more detail in the software public documentation. sharing sensitive information, make sure youre on a federal Get what matters in translational research, free to your inbox weekly. 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. Regarding the number of genes, it should in any casealways be kept in mind that positive, but not negative, evidence for the existence of a gene may be obtained because, from a structural point of view, a locus could be present, or amplified, due to a copy number variation (CNV) shared by only a limited number of subjects. doi: 10.1093/nar/gkx1095. Appended below is the summary of each of the chromosomes. Tissues and organs are divided into groups according to functional features they have in common. Finally, these data might be useful to design experiments for poorly characterized human genome regions, as in, for example, our current annotation effort of the recently defined highly restricted Down Syndrome critical region (HR-DSCR), which to date does not contain known genes [17], or to study transcription mechanisms such as alternative splicing or nonsense-mediated messenger RNA decay. Google Scholar. About 4000 human protein-coding genes are not mentioned in any scientific publication at all. Maria Chiara Pelleri. That leaves 2764 potential genes that may or may not be real. Careers. The nucleotides in chromosome 3 accounts for 6.5% of our DNA, with over 200 million base pairs. Use of a fluorescent probe which will bind to the target DNA if present (e. a specific gene's reverse transcribed mRNA). The lists below constitute a complete list of all known human protein-coding genes. Non-coding RNA genes: 165 to 404 Despite containing only up to 5.0% of the bodys DNA, chromosome 8 is quite important as over 8% of its genes are specialists in brain development. Finally, we confirm that there are no human introns shorter than 30 bp. A key scientific priority is the functional characterization of lncRNAs, a major challenge in molecular biology that has encouraged many high-throughput efforts. Coding Region Position: hg38 chr20:63,488,023-63,497,763 Size: 9,741 Coding . Accounting for just one and a half percent of the human genome, chromosome 21 is infamous for its role in Down syndrome. Pseudogenes: 736 to 911. J Cell Physiol. 2018;46:D813. The 985 cancer cell lines were analyzed for their representability of the corresponding TCGA disease cohorts. Please enable it to take advantage of the complete set of features! 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. Advances in the Exon-Intron Database (EID). A comprehensive catalog of functional elements in the human and mouse genomes provides a powerful resource for research into mammalian biology and mechanisms of human diseases. 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. 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]. Figure 1: Human species page. Abstract. 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. Protein-coding genes: 739 to 822 MCP and MC supervised the project. Fully mapped in 2001, this chromosome of 63 million nucleotides is known for its injurious effects involving heart diseases. 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. Sci. Proc. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Database resources of the national center for biotechnology information. Nucleic Acids Res. The red circles connected to each tissue name indicates the number of tissue enriched genes associated with that particular tissue. official website and that any information you provide is encrypted Federal government websites often end in .gov or .mil. 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. Protein-coding genes: 1,961 to 2,093 The functionality of these genes is supported by both transcriptional and proteomic . 2023 Jan 25;31:398-410. doi: 10.1016/j.omtn.2023.01.010. Around 27.9% of the nucleotide sequences inside exhibit no protein encoding. This small chromosome (less than 2.5%), measuring only 19 by 59 megabases in size, is pretty low key. Google Scholar. 2001;107:88191. The entire human mitochondrial DNA molecule has been mapped [1] [2] . Measures about 78 megabases in length and contains around 2.7% of our genetic library. Protein-coding genes: 308 to 343 ISTOCK, BLACKJACK3D T he human genome may contain more protein-coding genes than prior analyses suggested. A total of 155 protein-coding genes mapped to the GO term "regulation of immune system process"; 85 genes from C1, 32 genes from C3 and 38 genes from C5. 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. 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. Caracausi M, Piovesan A, Vitale L, Pelleri MC. J. Clin. Science. The Human Protein Atlas project is funded. 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 The genes were classified according to specificity into (i) cancer enriched genes with at least four-fold higher expression levels in one cell line cancer type as compared with any other analyzed cell line cancer types; (ii) group enriched genes with enriched expression in a small number of cell line cancer types (2 to 10); and (iii) cancer enhanced genes with only moderately elevated expression. This section of the Human Protein Atlas focuses on the expression profiles in human tissues of genes both on the mRNA and protein level. Measuring around 191 megabases in length, chromosome 4 contains 186 million base pairs, or 6% of our DNA. Friedrich, G. & Soriano, P. Genes Dev. "There are 3000 human . Dismiss. Genes that make proteins are called protein-coding genes. Morgan, T. H. Science 32, 120122 (1910). The new human gene database contains 43,162 genes, of which 21,306 are protein-coding and 21,856 are noncoding, and a total of 323,824 transcripts, for an average of 7.5 transcripts per gene. doi: 10.1093/database/baw153. 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). Contains encoding instructions for Acylamino-acid-releasing enzyme, 5-azacytidine-induced protein 2 and protein C3orf23. 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. p-arm Partial list of the genes located on p-arm (short arm) of human chromosome 3: . the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in 2685 5610 8170 2764 861 Elevated in brain Elevated in other but expressed in brain Low tissue specificity but expressed in brain Not detected in . The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). PhyloCSF is a method that determines the protein-coding potential of individual bases using alignments of the coding regions of multiple organisms representing a range of taxonomic groups. By using this website, you agree to our Article Dismiss. Coding Region Position: hg38 chr19:8,053,050-8,062,225 Size: 9,176 Coding Exon Count: . The cell lines were then ranked based on Spearmans () and NES from high to low, respectively. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. The authors declare that they have no competing interests. Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, et al. Hum Mol Genet. Members of this family maint ain homeostasis by neutralizing overexpressed proteinase activity through their function as suicide substrates. 2022 Apr 8;4(1):obac008. and JavaScript. A genomic coordinate list of these protein-coding genes is available as Table S1. For this, for each gene in a TCGA cohort, the FPKM values were averaged per cohort. Google Scholar. doi: 10.1016/j.ygeno.2013.02.009. Caracausi M, Ghini V, Locatelli C, Mericio M, Piovesan A, Antonaros F, Pelleri MC, Vitale L, Vacca RA, Bedetti F, et al. Non-coding RNA genes: 244 to 881 Below is a list of articles on human chromosomes, each of which contains an incomplete list of genes located on that chromosome. We have previously shown that GeneBase, a software with a graphical interface able to import and elaborate data available in the National Center for Biotechnology Information (NCBI) Gene database, allows users to perform original searches, calculations and analyses of the main gene-associated meta-information [5], and since the release of GeneBase 1.1, it can also provide descriptive statistical summarization such as median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features for any desired database subset [6]. PhyloCSF scores are calculated based on codon substitution frequencies. ISSN 0028-0836 (print). Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. In 3 sisters with isolated pituitary hormone deficiency (CPHD7; 618160), Argente et al. HHS Vulnerability Disclosure, Help "If people like our gene list, then maybe a . Cite this article. Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y. Sci Adv. Natl Acad. The https:// ensures that you are connecting to the Non-coding RNA genes: 323 to 622 AMIA Annu. qPCR: Uses a reporter probe to detect cDNA (complementary DNA to RNA). A-proteins have hydrophobic amino acid compositions . https://doi.org/10.1038/d41586-017-07291-9. 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 . National Library of Medicine Non-coding RNA genes: 277 to 993 volume551,pages 427431 (2017)Cite this article. doi: 10.1093/iob/obac008. AB451389 - Homo sapiens EEF1A2 mRNA for eukaryotic translation elongation factor 1 . Google Scholar. Article -, Piovesan A, Caracausi M, Ricci M, Strippoli P, Vitale L, Pelleri MC. Non-coding RNA genes: 355 to 1,207 2018;46:D8D13. But non-human genes do appear quite high on the list. The cell line cancer enriched and group enriched genes are displayed in the interactive plot below, in which clicking on the red and orange circles results in gene lists for the corresponding enriched and group enriched genes, respectively. 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. First, the data are now updated as of January 2019 rather than January 2016, exploiting novel information made available in the last 3years and thus showing how some parameters have been subjected to relevant changes, while others appear to be stable. Nature 312, 767768 (1984). Non-coding RNA genes: 242 to 1,052 The protein encoded by this gene is a member of the serpin family of proteinase inhibitors. USA 90, 19771981 (1993). Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. Bookshelf After the Human Genome Project, scientists found that there were around 20,000 genes within the genome, a number that some researchers had already predicted. In the current release, we collected and curated 2507 unique human genes, including 2267 protein-coding and 240 non-coding genes from comprehensive manual examination of 10,960 PubMed article abstracts. For complete list, see the link in the infobox on the right. To test this, for the 27 cell line cancer types, gene expression was averaged per disease, resulting in the mean expression for each of the 27 cell line cancer types. Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. 2013;101:282289. The human genome is massive, and contains over 30,000 protein-coding genes, as well as thousands more pseudogenes and non-coding RNAs. Epub 2012 Jun 18. PubMedGoogle Scholar, Dolgin, E. The most popular genes in the human genome. Pseudogenes: 373 to 481. 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. 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. 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. Following validation by the software Splign [8], we confirm that there are no human (and possibly of any species) introns shorter than 30bp (Table2). . (i) Spearmans correlation coefficient () between every cancer cell line and its corresponding TCGA cohorts was estimated at the gene level. 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. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S . Pseudogenes: 413 to 528. 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). Epub 2023 Jan 12. We have generated general descriptive statistics for human nuclear protein-coding genes and messenger RNAs (mRNAs) (Table1), exons, coding-exons and introns (Table2). It is one of the only two allosome chromosomes (gender-determining chromosomes) in the human body. 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. Open Access In 2008, a draft of the complete human proteome was released from UniProtKB/Swiss-Prot: the approximately 20,000 putative human protein-coding genes were represented by one UniProtKB/Swiss-Prot entry each, tagged with the keyword 'Complete proteome' (now obsolete) and later linked to proteome identifier UP000005640.. Filtering by the Yes annotation allows the retrieval of a non-redundant set of exons, coding exons and introns, respectively. Protein-coding genes: 45 to 73 London: IntechOpen; 2018. p. 1536. The entire molecule is regulated by only one regulatory region which contains the origins of replication of both heavy and light strands. Ensembl 2019. Integrated transcriptome map highlights structural and functional aspects of the normal human heart. 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. Protein-coding genes: 215 to 256 The genes in chromosome 2 span 242 million nucleotide base pairs, which also amounts to about 8% of the human DNA. The assemblage of genes ND5 and ND6 was the worst of all, for which the length was 16% and 27% of the length of the whole gene, respectively. 2017;232:75970. Protein-coding genes: 988 to 1,036 Further analysis of transcriptome data and clinical data from cancer patients showed that recurrently p53-regulated lncRNAs are associated with patient survival. 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 For the remaining protein-coding genes, 39 to 86% of the length was assembled. Non-coding RNA genes: 318 to 1,202 Annotated by 9 databases (GeneCards, MalaCards, Ensembl/GENCODE, NONCODE, Ensembl, HGNC, LNCipedia, Expression Atlas, RefSeq). Article The description of each field is included in the first row of the spreadsheet table. Thank you for visiting nature.com. This protein inhibits the neutrophil-derived proteinases neutrophil elastase, cathepsin G, and proteinase-3 and thus protects tissues from damage at inflammatory . Up to 50 of the genes in chromosome 18 are involved in birth defects, so it is not a particularly popular chromosome. 2004. Search model organisms. 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. Finally, for each cell line, gene log2 fold changes were sorted from high to low, followed by the GSEA of the TCGA cohort elevated genes against the sorted gene list. 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. DNA Res. Protein-coding genes: 516 to 555 One of the most interesting diseases caused by genetic disorders in chromosome 12 is stuttering or stammering. 2016;44:D73345. Baker, S. J. et al. Article Pseudogenes: 545 to 693. RT-PCR. Pseudogenes: 590 to 738. Protein-coding genes: 1,124 to 1,199 Pseudogenes: 761 to 902. The authors declare that they have no competing interests. protein-L-isoaspartate (D-aspartate) O-methyltransferase: 5: 20: PCNA: 113: proliferating cell nuclear antigen: 12: 67: PDGFB: 47: platelet-derived growth factor beta . The mRNA expression data is derived from deep sequencing of RNA (RNA-seq) from 256 different normal tissue types. Depending on the genome-sequencing center, OLNs are only attributed to protein-coding genes, or also to pseudogenes, and also to tRNA-coding genes and others. Cell 70, 431442 (1992). Protein-coding genes: 261 to 285 Aim: This study was undertaken with the aim to investigate the association of single nucleotide variants; namely . PubMed Central 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. CAS government site. Acidic ribosomal proteins, called A-proteins (acidic) or P-proteins (phosphorylated acidic), such as RPLP2, are generally present in multiple copies on the ribosome and have isoelectric points in the range of pH 3 to 5, in contrast to most ribosomal proteins, which are single copy and basic.