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. Non-coding RNA genes: 148 to 515 All authors read and approved the final manuscript. In addition, data can be exported in other formats and imported in other applications (database management systems, statistical software, genomic tools) for further analysis. Produces many zinc based proteins, such as ZBTB43 and ZNF79. How has the classification of all protein-coding genes been done? Piovesan A, Caracausi M, Antonaros F, Pelleri MC, Vitale L. GeneBase 1.1: a tool to summarize data from NCBI Gene datasets and its application to an update of human gene statistics. So what are the Top Ten researched human genes? Human mtDNA consists of 16,569 nucleotide pairs. -, 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. Bethesda, MD 20894, Web Policies Gene expression data were processed in the same way as for PROGENy analysis. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S . The UCSC genome browser database: 2019 update. Voshall A, Moriyama EN. 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. https://doi.org/10.1186/s13104-019-4343-8, DOI: https://doi.org/10.1186/s13104-019-4343-8. Non-coding RNA genes: 299 to 894 Open Access Dismiss. Pseudogenes: 590 to 738. Hum Mol Genet. The https:// ensures that you are connecting to the All underlying images of immunohistochemistry stained normal tissues are available together with knowledge-based annotation of protein expression levels. Protein-coding genes: 804 to 874 The colored bars represent number of genes with elevated expression in the associated tissue divided into tissue enriched (red), group enriched (orange) or tissue enhanced (purple) categories according to the transcriptomics based specificity classification. Dalgleish, A. G. et al. Science. 26 October 2021, Cellular and Molecular Life Sciences 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. Genomics. AB451389 - Homo sapiens EEF1A2 mRNA for eukaryotic translation elongation factor 1 . Mol Ther Nucleic Acids. All authors critically discussed the final manuscript. doi: 10.1126/sciadv.abq5072. Bookshelf Nature 312, 763767 (1984). For instance, it would easily become possible to explore hypotheses about the correlation of structural details of human nuclear protein-coding genes to their level of expression, exploiting quantitative descriptions of the human transcriptome [13], or to the dosage of metabolites related to enzyme proteins, exploiting quantitative representations of human metabolome in health and disease [14]. 2015;22:495503. AP and PS wrote the manuscript draft. Protein-coding genes: 559 to 629 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. Baker, S. J. et al. If you continue, we'll assume that you are happy to receive all cookies. Lowenstein, E. J. et al. 2013;101:2829. An official website of the United States government. 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. Cell. Nature 381, 661666 (1996). 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. 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. Klatzmann, D. et al. A curated database of candidate human ageing-related genes and genes associated with longevity and/or ageing in model organisms. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. On average 10% of these genes are located in genomic regions unannotated by 12 other gene catalogs. 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 TNF - Encodes tumour necrosis factor, an immune molecule that has been a major drug target for inflammatory disease. Database resources of the national center for biotechnology information. The transcriptomics analysis covers 1055 human cell lines, corresponding to 27 cancer types, one non-cancerous group and one uncategorised group of cellines, and includes classification based on specificity, distribution and expression clusters. Protein-coding genes: 706 to 754 Non-coding RNA genes: 328 to 992 "There are 3000 human . (2018)). More surprisingly, until about the year 2000, the fastest growing groups of human genes in the newly added literature were those that have never/rarely been reported about in previous years. volume551,pages 427431 (2017)Cite this article. 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. Non-coding RNA genes: 324 to 856 Integrated transcriptome map highlights structural and functional aspects of the normal human heart. Non-coding RNA genes: 260 to 639 A-proteins have hydrophobic amino acid compositions . 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. It is broadly suspected that a large fraction of these entries is simply spurious ORFs, because they show no evidence of evolutionary conservation. About 4000 human protein-coding genes are not mentioned in any scientific publication at all. Human protein-coding genes and gene feature statistics in 2019. 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. 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. AP and PS designed the study, collected the data and performed the analysis. 2016;25:252538. This selection retrieved 19,116 genes, 46,932 transcripts and 562,164 exons. The mRNA expression data is derived from deep sequencing of RNA (RNA-seq) from 256 different normal tissue types. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Protein-coding genes: 261 to 285 AMIA Annu. The data sets were created by exporting the data from each relative table of GeneBase as a spreadsheet. Non-coding RNA genes: 355 to 1,207 The primary growth genes for cell divisions, which makes them vulnerable to cancers. Non-coding RNA genes: 246 to 830 Co-authors David Sweetser, MD, PhD, and Lauren Briere, MS, CGC, narrowed the search to a single nucleotide variant in the gene MIR145, a microRNA gene. 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. Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, et al. Cell 70, 431442 (1992). The .gov means its official. 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. 8600 Rockville Pike Symp. doi: 10.1093/dnares/dsv028. J. Clin. [International Human Genome Sequencing Consortium. Non-coding RNA genes: 191 to 594 The protein data covers 15318 genes (76%) for which there are available antibodies. Provided by the Springer Nature SharedIt content-sharing initiative. https://doi.org/10.1038/d41586-017-07291-9. Pseudogenes: 513 to 598. Show all. Protein-coding genes: 795 to 912 BEND7, "BEN domain containing 7") The genome-wide RNA expression profiles of human protein-coding genes in 18 single cell immune cell types are presented covering various B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. MeSH 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. A tour through the most studied genes in biology reveals some surprises. 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 . Google Scholar. -, Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Proc. The best assembled were COX1, COX3, and ND4L, as they have collected more than 90% of the protein-coding-gene length. This site needs JavaScript to work properly. The UMAP was generated by clustering genes based on expression patterns. Pseudogenes: 666 to 839. Protein-coding genes: 1,357 to 1,469 Non-coding RNA genes: 450 to 1,598 2016 Dec 26;2016:baw153. "There are 3000 human proteins whose function is unknown," says Wood. Nature. We set out the expected frequency of ARE-containing genes at 25.55%, considering the ARE database (38) and 19,116 human protein coding genes (39). The UCSC Genes track is a set of gene predictions based on data from RefSeq, GenBank, CCDS, Rfam, and the tRNA Genes track. 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 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 . Provided by the Springer Nature SharedIt content-sharing initiative, Nature (Nature) 2023 Jan 10;13:1085139. doi: 10.3389/fgene.2022.1085139. Advances in the Exon-Intron Database (EID). Non-coding RNA genes: 244 to 881 Brief Bioinform. 2023 Jan 20;9(3):eabq5072. 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. The Human Protein Atlas project is funded. This can be served as a reference for cell line selection for in vitro experiments when studying a specific cancer type. The 985 cancer cell lines were analyzed for their representability of the corresponding TCGA disease cohorts. [Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes]. 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. 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 availability of the data sets presented here allows a ready update of main parameters about human genome, often cited in textbooks or reports without a source accounting for a rigorous method for extracting this information. This sex chromosome (allosome) is only present in males. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. Pseudogenes: 288 to 379. 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. 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. DNA Res. Initial sequencing and analysis of the human genome. Responsible for overly large nose tip, nasal bridge and ear lobes. 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.. 2003, 460464 (2003). ISTOCK, BLACKJACK3D T he human genome may contain more protein-coding genes than prior analyses suggested. Contains 249 million nucleotide base pairs, which amounts to 8% of the total DNA found in the human body. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets. 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. 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]. We have generated general descriptive statistics for human nuclear protein-coding genes and messenger RNAs (mRNAs) (Table1), exons, coding-exons and introns (Table2). Humans have about 20,000 protein-coding genes but scientists still know remarkably little about most of the proteins they encode. [Correction of five different types of errors of model REFSEQs appeared in NCBI human gene database only by using two novel human genes C17orf32 and ZNF362]. GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. These data allowed us to identify novel regulators of cambium activities and many non-coding RNAs that may tune the expression of protein-coding genes. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Maria Chiara Pelleri. Non-coding RNA genes: 277 to 993 Importantly, we identified multiple p53-responsive lncRNAs that are co-regulated with their protein-coding host genes, revealing an important mechanism by which p53 may regulate lncRNAs. The funding sources had no role in the design of this study and collection, analysis, and interpretation of data and in writing the manuscript. Nucleic Acids Res. It is possible to use calculation and statistical functions of the spreadsheet to analyze the data in any direction. The concept is that genes that have an elevated expression in a TCGA cohort can be considered as the cohort signature, and their high expression should be reflected by cell line models. Through comparative analyses with the cell-type-specific gene expression data in Arabidopsis roots [ 8 ], we identified co-expression gene-regulatory networks (GRNs) conserved in Arabidopsis and radish roots. Clipboard, Search History, and several other advanced features are temporarily unavailable. Google Scholar. Protein-coding genes: 1,124 to 1,199 The UCSC genome browser database: 2019 update. Each tissue name is clickable and redirects to the selected proteome. Keywords: Unauthorized use of these marks is strictly prohibited. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Protein-coding genes: 215 to 256 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. Aim: This study was undertaken with the aim to investigate the association of single nucleotide variants; namely . Click "View all genes" to view a table of human genes. Researchers often turn to model organisms to understand the complex molecular mechanisms of the human body. Correlation analysis based on mRNA expression levels of human genes in cancer tissue and the clinical outcome for almost 8000 cancer patients is presented in a gene-centric manner. Appended below is the summary of each of the chromosomes. You are using a browser version with limited support for CSS. The UniProtKB/Swiss-Prot Homo sapiens proteome contains one representative . Pseudogenes: 413 to 528. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. Protein coding genes. 2018;46:D8D13. The orange circles indicate the number of genes with enriched expression in a group of tissues, connected by lines. Gene statistics; Human genes; Protein-coding genes. The following is a partial list of genes on human chromosome 3. Non-coding RNA genes: 422 to 1,188 Among more than 60 different . DIMES N. 3997 24-11-2015/Fondazione Umano Progresso, NCBI Resource Coordinators Database resources of the national center for biotechnology information. Next-generation transcriptome assembly: strategies and performance analysis. The position of the longest intron is related to biological functions in some human genes. All rights reserved. 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. Further analysis of transcriptome data and clinical data from cancer patients showed that recurrently p53-regulated lncRNAs are associated with patient survival. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in How has the pathway and cytokine analysis been done? This article is an index of lists of human genes. Strittmatter, W. J. et al. Protein-coding genes: 790 to 886 Piovesan, A., Antonaros, F., Vitale, L. et al. 2016;44:D73345. 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. 2012 Oct;22(10):2079-87. doi: 10.1101/gr.139170.112. Front Genet. We identified 5,737 putative protein-coding genes that result from mRNA modified by human polymorphisms and have significant homology to known proteins. To calculate the relative pathways activities across all cell lines, the normalized values were centered by subtracting the mean value per gene. Epub 2023 Jan 12. 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. (2018)). Finally, we confirm that there are no human introns shorter than 30 bp. Non-coding RNA genes: 325 to 1,199 Coding Region Position: hg38 chr19:8,053,050-8,062,225 Size: 9,176 Coding Exon Count: . In the meantime, to ensure continued support, we are displaying the site without styles DNA Res. Klatzmann, D. et al. 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. Pseudogenes: 574 to 785. FOIA 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]. 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. Pseudogenes: 606 to 879. Disclaimer. Pseudogenes: 247 to 333. Piovesan A, Caracausi M, Antonaros F, Pelleri MC, Vitale L. Database (Oxford). 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) Non-coding RNA genes: 165 to 404 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 551, 427431 (2017). This optimistic trend culminated with ~ 550 new gene function . In total, 16465 of all human protein coding genes (n= 20090) are detected in the human brain. Around 890 diseases such as Alzheimer's, glaucoma and hearing loss have been linked to genetic disorders found in chromosome 1. 1. of the ORF-K1 gene encoding a highly variable glycoprotein related to the immunoglobulin receptor family that maps at the extreme left-hand end of the HHV-8 genome. doi: 10.1093/nar/gky1095. 2001;291:130451. It contains 133 million base pairs of nucleotides, or over 4% of the total. Epub 2012 Jun 18. View/Edit Mouse. Hum Mol Genet. For this, for each gene in a TCGA cohort, the FPKM values were averaged per cohort. For complete list, see the link in the infobox on the right. PubMedGoogle Scholar. Follow the Python code link for information about updates to the list of genes on these pages. Natl Acad. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. 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. Please enable it to take advantage of the complete set of features! 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]. Enzymes . 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. 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. High-throughput sequencing technologies and bioinformatic tools significantly expanded our knowledge about ncRNAs, highlighting their key role in gene regulatory networks, through their capacity to interact with coding and non-coding RNAs, DNAs and . Both types of genes can produce non-coding transcripts, but non-coding RNA genes do not produce protein-coding transcripts. Nature 312, 767768 (1984). This acrocentric chromosome measures 95 megabases long, and accounts for 3.5% of the human DNA. Correspondence to The data sets are provided in standard, open format.xlsx. Article Open Access articles citing this article. 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 human. Up to 50 of the genes in chromosome 18 are involved in birth defects, so it is not a particularly popular chromosome. 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. 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. Nature PhyloCSF scores are calculated based on codon substitution frequencies. MCP and MC supervised the project. 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. Noncoding DNA does not provide instructions for making proteins. 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.
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