Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics & Medicine
Doug Brutlag 2011 Components of a Typical Human GeneGene IntronIntronExonExonExonPromoterTerminator TFBS
Doug Brutlag 2011 Active Genes are Transcribed into RNA PrimaryTranscript Gene IntronIntronExon Exon Exon PromoterTerminator
Doug Brutlag 2011Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator 5’5’5’5’ 3’3’3’3’ Splicing Splicing Transcript Yields Mature mRNA
Doug Brutlag 2011 Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator 5’5’5’5’ 3’3’3’3’ Splicing Coding Region 5’UTR 3’UTR 5’UTR 3’UTR
Doug Brutlag 2011 Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator Splicing Coding Region 5’UTR 3’UTR 5’UTR 3’UTR 7-Me-G-Cap 3’ Poly A Tail
Doug Brutlag 2011 ESTs, Full Length cDNA UniGene & RefSeq Databases UniGeneRefSeq Transcript mRNA Gene Intron Exon PromoterTerminator 5’5’ 3’3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing
Doug Brutlag 2011 ESTs, Full Length cDNA UniGene & RefSeq Databases UniGeneRefSeq Transcript mRNA Gene Intron Exon PromoterTerminator 5’5’ 3’3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing Proteins 5’ UTR 3’ UTR Protein
Doug Brutlag 2011 GENSCAN Gene Model Hidden Markov models of gene structure
Doug Brutlag 2011 Promoters E Additional Data Genomic DNA Assembled contigs A Mapping uniSTS dbSNP Mouse ESTs Human ESTs C Expression Data Entrez Gene Mouse RefSeq Mouse UniGene Human RefSeq Human Ensembl cDNA Genome Databases nrPRO D Protein Similarity pFAM Motifs GrailEXP B Gene Prediction GenScanFGENESH FGENESH+ GeneMark F Summary Entrez Gene UCSC Browser Ensembl
Doug Brutlag 2011Inclusive Exon Prediction Entrez Gene Loci NR-Pro Genscan GrailEXP FGENESH Entrez Gene UniGene ESTs
Doug Brutlag 2011 Alternative Splicing Generates Distinct Proteins in Different Tissues Transcript mRNA-1 Gene Intron Exon PromoterTerminator 5’5’ 3’3’ Transcript mRNA-2 5’5’3’3’ Alternate Splicing Splicing
Doug Brutlag 2011 Alternative Splicing Detected in EST Libraries
Doug Brutlag 2011 NCBI Genomes
Doug Brutlag 2011 Eukaryote Genome Projects
Doug Brutlag 2011 Canis lupus familiaris Genome iew&list_uids= iew&list_uids=10726
Doug Brutlag 2011 NCBI Entrez Gene
Doug Brutlag 2011 NCBI Entrez Gene: Human Opsin
Doug Brutlag 2011 Entrez Gene: Human Opsin OPN1MW
Doug Brutlag 2011 Entrez Gene: Human Opsin OPN1MW
Doug Brutlag 2011 MapViewer: Human Opsin OPN1MW
Doug Brutlag 2011 Evidence Viewer for OPN1MW lid=2652&from= &to= lid=2652&from= &to=
Doug Brutlag 2011 OMIM Home Page
Doug Brutlag 2011 Colorblindness in OMIM
Doug Brutlag 2011 Colorblindness in OMIM
Doug Brutlag 2011 Colorblindness in OMIM
Doug Brutlag 2011 Human Genome Resources
Doug Brutlag 2011 RefSeq
Doug Brutlag 2011 RefSeq Gene
Doug Brutlag 2011 NCBI UniGene
Doug Brutlag 2011 NCBI Homologene Database
Doug Brutlag 2011 Comparative Genomics
Doug Brutlag 2011 Ensembl Home Page
Doug Brutlag 2011 EBI Genomes Home Page
Doug Brutlag 2011 Ensembl Human Genome
Doug Brutlag 2011 Ensembl Human Opsin Search x=;q=opsin x=;q=opsin
Doug Brutlag 2011 Ensembl Human Opsin Genes x=;q=opsin x=;q=opsin
Doug Brutlag 2011 Ensembl Human OPN1MW Gene ;r=X: ;r=X:
Doug Brutlag 2011 Ensembl Opsin OPN1MW Gene Location #r=X: #r=X:
Doug Brutlag 2011 Ensembl OPN1MW Transcripts #r=X: #r=X:
Doug Brutlag 2011 Ensembl OPN1MW Opsin Protein ;r=X: ;t=ENST ;r=X: ;t=ENST
Doug Brutlag 2011 Ensembl Tutorials
Doug Brutlag 2011 UCSC Genome Home Page
Doug Brutlag 2011 UCSC Genome Browser
Doug Brutlag 2011 UCSC Genome Browser
Doug Brutlag 2011 UCSC Genome Browser &hgsid= &knownGene=pack&hgFind.matches=uc004fkd.2, &hgsid= &knownGene=pack&hgFind.matches=uc004fkd.2,
Doug Brutlag 2011 UCSC Genome Browser &hgsid= &knownGene=pack&hgFind.matches=uc004fkd.2, &hgsid= &knownGene=pack&hgFind.matches=uc004fkd.2,
Doug Brutlag 2011 UCSC Proteome Browser
Doug Brutlag 2011 UCSC Proteome Browser
Doug Brutlag 2011 UCSC Help File