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Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy) Genome Databases Computational Molecular Biology Biochem 218 – BioMedical Informatics 231 http://biochem218.stanford.edu/ http://biochem218.stanford.edu/
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Components of a Typical Human Gene Gene Intron Exon PromoterTerminator TFBS
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GENSCAN Gene Model http://genes.mit.edu/GENSCAN.html http://genes.mit.edu/GENSCAN.html Hidden Markov Models of Gene Structure Hidden Markov models of gene structure
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ESTs, Full Length cDNA Gene mRNA Primary Transcript Intron Exon PromoterTerminator 5’ 3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing
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Alternative Splicing Generates Distinct Proteins in Different Tissues Transcript mRNA-1 Gene Intron Exon PromoterTerminator 5’ 3’ Transcript mRNA-25’3’ Alternate Splicing Splicing
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Alternative Splicing Detected in EST Libraries
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D Protein Similarity Promoters E Additional Data GenomicDNA NHGRI contigs A Mapping uniSTS dbSNP Mouse ESTs Human ESTs C Expression Data Entrez Gene Mouse RefSeq Mouse UniGene Human RefSeq Human Ensembl cDNA Annotating Genome Databases F Summary Entrez GeneGeneCards GrailEXP B Gene Prediction GenScanFGENESH FGENESH+ GeneMark nrPRO UniProt pFAM Motifs D Protein Data
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Entrez Gene Loci http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene NR-Pro RefSeq ESTs Entrez Gene Genscan GrailEXP FGENESH
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NCBI Genome Page http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome
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Human Genome Resources http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/ http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/
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Entrez Human Genome Projects http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView& TermToSearch=9558 http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView& TermToSearch=9558
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PCNA Gene in Entrez Gene http://www.ncbi.nlm.nih.gov/gene/5111 http://www.ncbi.nlm.nih.gov/gene/5111
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MapViewer of PCNA Gene
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OMIM Entry for PCNA http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176740 http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176740
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Hugo Nomenclature for PCNA http://www.genenames.org/data/hgnc_data.php?hgnc_id=8729 http://www.genenames.org/data/hgnc_data.php?hgnc_id=8729
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HUGO Home Page http://www.genenames.org/ http://www.genenames.org/
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Sequence View of PCNA Gene http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NT_011387.8&v=5035598..5047267 http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NT_011387.8&v=5035598..5047267
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Evidence Viewer for PCNA http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_011387.8&gene=PCNA& lid=5111 http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_011387.8&gene=PCNA& lid=5111
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SNP Polymorphisms in PCNA http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=5111 http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=5111
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Entrez Gene http://www.ncbi.nlm.nih.gov/gene http://www.ncbi.nlm.nih.gov/gene
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OMIM Home Page http://www.ncbi.nlm.nih.gov/omim http://www.ncbi.nlm.nih.gov/omim
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OMIM Coverage http://www.ncbi.nlm.nih.gov/Omim/mimstats.html http://www.ncbi.nlm.nih.gov/Omim/mimstats.html
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Colorblindness in OMIM
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Colorblindness in OMIM http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=303800 http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=303800
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Human Gene Mutation Database http://www.hgmd.cf.ac.uk/ac/gene.php?gene=OPN1MW http://www.hgmd.cf.ac.uk/ac/gene.php?gene=OPN1MW
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GeneTests http://www.genetests.org/ http://www.genetests.org/
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GeneReviews on Red-Green Color Vision Defects http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=rgcb http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=rgcb
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Genes & Disease http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd&part=gnd_book_info http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd&part=gnd_book_info
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Genes & Disease Table of Contents http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd
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Chromosome 7 http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd&part=A272#A279 http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd&part=A272#A279
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UCSC Genome Browser http://genome.ucsc.edu/ http://genome.ucsc.edu/ httphttp://genome.ucsc.edu/
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UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway http://genome.ucsc.edu/cgi-bin/hgGateway
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PCNA Entry at UCSC http://genome.cse.ucsc.edu/cgi-bin/hgTracks?insideX=115&revCmplDisp=0&hgsid=149552355&hgt.out1=1.5x&position=chr20%3A5043932- 5048444&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0& hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0&hgtgroup_encodeGenes_close=1&hgtgroup_encodeTxL evels_close=1&hgtgroup_encodeChip_close=1&hgtgroup_encodeChrom_close=1&hgtgroup_encodeCompAndVar_close=1 http://genome.cse.ucsc.edu/cgi-bin/hgTracks?insideX=115&revCmplDisp=0&hgsid=149552355&hgt.out1=1.5x&position=chr20%3A5043932- 5048444&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0& hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0&hgtgroup_encodeGenes_close=1&hgtgroup_encodeTxL evels_close=1&hgtgroup_encodeChip_close=1&hgtgroup_encodeChrom_close=1&hgtgroup_encodeCompAndVar_close=1
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UCSC Proteome Browser http://genome.ucsc.edu/cgi-bin/pbGlobal?proteinID=P12004 http://genome.ucsc.edu/cgi-bin/pbGlobal?proteinID=P12004
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UCSC Tutorials http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml
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Ensembl Genomes Home Page http://www.ensembl.org/ http://www.ensembl.org/
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Ensembl Human Genome http://www.ensembl.org/Homo_sapiens/ http://www.ensembl.org/Homo_sapiens/
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Ensembl DNA View of Human PCNA http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646 http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646
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Ensembl PCNA Transcripts http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646 http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646
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Ensembl PCNA Splice Variants http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646 http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646
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Ensembl PCNA Gene Tree (Pecan) http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646 http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646
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Ensembl PCNA Variations http://www.ensembl.org/H omo_sapiens/Gene/Sum mary?g=ENSG000001326 46
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Ensembl Protein View of PCNA
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Ensembl Tutorials http://www.ensembl.org/common/Workshops_Online http://www.ensembl.org/common/Workshops_Online
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Comparative Genomics
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UCSC PCNA Entry
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UCSC Comparative Genomics
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Ensembl Genome Alignments
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Ensembl Genome Alignments (PCNA)
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NCBI Homologene Database
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Homologene PCNA Entries
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