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Genome Databases Genomics & Medicine http://biochem118.stanford.edu/ Doug Brutlag, Professor Emeritus of Biochemistry & Medicine (by courtesy) Stanford University School of Medicine © Doug Brutlag 2015 Components of a Typical Human Gene Regulatory Regions Promoter Exon Transcription Start Site Intron Exon Intron Exon Terminator Gene (DNA) Transcription Stop Site © Doug Brutlag 2015 Multiple Enhancer Sequences © Doug Brutlag 2015 Active Genes are Transcribed into RNA Regulatory Regions Promoter Exon Intron Exon Intron Exon Terminator Gene (DNA) Transcription Transcription Start Site Primary Transcript Transcription (RNA) Stop Site © Doug Brutlag 2015 Splicing Transcript Yields Mature mRNA Regulatory Regions Promoter Exon Intron Exon Intron Exon Terminator Gene (DNA) Transcription Transcript (RNA) Splicing 5’ 3’ mRNA (RNA) © Doug Brutlag 2015 Intron Splicing Mechanism © Michael King2015 © DougW. Brutlag Mature mRNA contains 7-Methyl-Guanylate 5’ Cap and 3’ Poly A Tail Regulatory Regions Promoter Exon Intron Exon Intron Exon Terminator Gene 7-Me-G-Cap 5’UTR 3’UTR 3’ Poly A Tail Transcript Splicing Spliced Transcript 5’UTR 7-Me-G-Cap Coding Region 3’UTR 3’ Poly A Tail mRNA © Doug Brutlag 2015 Mature mRNA contains 7-Methyl-Guanylate 5’ Cap © Doug Brutlag 2015 Mature mRNA contains 7-Methyl-Guanylate5’ Cap © Doug Brutlag 2015 PolyAdenylation of mRNAs © Michael King2015 © DougW. Brutlag Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions Promoter 7-Me-G-Cap Exon Intron Exon Intron Exon Transcription 5’UTR 3’UTR Terminator Gene (DNA) 3’ Poly A Tail Transcript (RNA) Splicing 5’ 7-Me-G-Cap 3’ 5’UTR Protein Coding Region 3’UTR 3’ Poly A Tail mRNA (RNA) Translation N-terminus C-terminus Protein © Doug Brutlag 2015 The Genetic Code © Doug Brutlag 2015 Alternative Splicing Generates Distinct Proteins in Different Tissues Promoter Exon Intron Exon Intron Exon Terminator Gene (DNA) Transcription Transcript (RNA) Splicing 3’ 5’ Transcript (RNA) Alternate Splicing 5’ mRNA-1 (RNA) 3’ mRNA-2 (RNA) © Doug Brutlag 2015 Messenger RNA (mRNA) Databases ESTs UniGene & Full Length cDNA RefSeq Promoter Exon Intron Exon Intron Exon Terminator Gene (DNA) Gene Database Transcript (RNA) Transcription Splicing 5’ 5’ ESTs 3’ mRNA Refseq Database 3’ ESTs UniGene Database Full Length cDNA RefSeq Database © Doug Brutlag 2015 ESTs, Full Length cDNA UniGene & RefSeq Databases Promoter Exon Intron Exon Intron Exon Terminator Gene 3‘ UTR Gene Database Transcription 5‘ UTR Transcript (RNA) Splicing 3’ 5’ mRNA RefSeq Database 3’ ESTs UniGene Database 5’ ESTs 5’ UTR 3‘ UTR Protein Full Length cDNA RefSeq Database Proteins Protein Database © Doug Brutlag 2015 GENSCAN Gene Model http://genes.mit.edu/GENSCAN.html Hidden Markov models of gene structure © Doug Brutlag 2015 Assembled contigs Genome Databases uniSTS A Mapping B Gene Prediction C Expression Data GrailEXP GenScan FGENESH FGENESH+ UniGene Human RefSeq Human Mouse ESTs Entrez Gene Mouse RefSeq Mouse NCBI Proteins E Additional Data F Summary dbSNP Human ESTs D Protein Similarity Genomic DNA GeneMark Ensembl cDNA UniProt Promoters Entrez Gene UCSC Browser Ensembl © Doug Brutlag 2015 Entrez Gene Loci http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene Proteins UniGene RefSeq GrailEXP FGENESH Genscan Entrez Gene © Doug Brutlag 2015 NCBI Genome http://www.ncbi.nlm.nih.gov/genome/ © Doug Brutlag 2015 Canis lupus familiaris Genome http://www.ncbi.nlm.nih.gov/genome/85 © Doug Brutlag 2015 Canis lupus familiaris http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615 © Doug Brutlag 2015 Human Genome Resources http://www.ncbi.nlm.nih.gov/genome/guide/human/ © Doug Brutlag 2015 NCBI Entrez Gene http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene © Doug Brutlag 2015 Human Beta-Hemoglobin Gene Entry http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Beta-Hemoglobin Gene Entry http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Hemoglobin Gene Entry http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Beta-Hemoglobin Phenotypes http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Beta-Hemoglobin Phenotypes http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Hemoglobin Interactions http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Beta-Hemoglobin Gene Entry http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Beta-Hemoglobin Biosystems http://www.ncbi.nlm.nih.gov/biosystems/152665 © Doug Brutlag 2015 Human Beta-Hemoglobin Conserved Domain http://www.ncbi.nlm.nih.gov/cdd?LinkName=gene_cdd&from_uid=3043 © Doug Brutlag 2015 Human Beta-Hemoglobin Homologene http://www.ncbi.nlm.nih.gov/homologene?LinkName=gene_homologene&from_uid=3043h © Doug Brutlag 2015 Human Beta-Hemoglobin Homologene http://www.ncbi.nlm.nih.gov/homologene?LinkName=gene_homologene&from_uid=3043h © Doug Brutlag 2015 Human Beta-Hemoglobin Genome Map Viewer http://www.ncbi.nlm.nih.gov/gene/3043 © Doug Brutlag 2015 Human Beta-Hemoglobin SNP Gene Viewer http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=3043 © Doug Brutlag 2015 Variation Viewer for Human Beta-Hemoglobin http://ww.ncbi.nlm.nih.gov/sites/varvu?gene=3043 © Doug Brutlag 2015 Ensembl Home Page http://www.ensembl.org/ © Doug Brutlag 2015 Ensembl Human Genome http://uswest.ensembl.org/Homo_sapiens/Info/Index © Doug Brutlag 2015 Ensembl Human HBB Gene Search http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=opsin © Doug Brutlag 2015 Ensembl Human HBB Gene http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244734;r=11:5246694-5 © Doug Brutlag 2015 Ensembl Human HBB Gene Transcripts http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244734;r=11:5246694-525062 © Doug Brutlag 2015 Ensembl Human HBB Protein Summary http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000244734;r=11:524 © Doug Brutlag 2015 Ensembl Tutorials http://uswest.ensembl.org/info/website/tutorials/index.html © Doug Brutlag 2015 UCSC Genome Home Page http://genome.ucsc.edu/ © Doug Brutlag 2015 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway © Doug Brutlag 2015 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway © Doug Brutlag 2015 HBB Gene in the UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:5246696-5248301&hgsid=349247439&refGene=pack& , © Doug Brutlag 2015 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203-153499469&hgsid=216983641&knownG © Doug Brutlag 2015 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203-153499469&hgsid=216983641&knownG © Doug Brutlag 2015 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203-153499469&hgsid=216983641&knownG © Doug Brutlag 2015 UCSC Help File http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html © Doug Brutlag 2015
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