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Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy)

Computational Molecular Biology Biochem 218 – BioMedical Informatics 231 http://biochem218.stanford.edu/. Genome Databases. Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy). TFBS. Promoter. Terminator. Exon. Intron. Exon. Intron. Exon. Gene.

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Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy)

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  1. Computational Molecular BiologyBiochem 218 – BioMedical Informatics 231http://biochem218.stanford.edu/ Genome Databases Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy)

  2. TFBS Promoter Terminator Exon Intron Exon Intron Exon Gene Components of a Typical Human Gene

  3. GENSCAN Gene Modelhttp://genes.mit.edu/GENSCAN.html Hidden Markov Models of Gene Structure Hidden Markov models of gene structure

  4. Gene Exon Exon Intron Intron Promoter Exon Terminator Primary Transcript Splicing mRNA 3’ 5’ 3’ ESTs 5’ ESTs Full Length cDNA ESTs, Full Length cDNA

  5. Exon Exon Intron Intron Exon Promoter Terminator Gene Transcript Splicing 3’ mRNA-1 5’ Alternate Splicing Transcript 5’ 3’ mRNA-2 Alternative Splicing GeneratesDistinct Proteins in Different Tissues

  6. Alternative SplicingDetected in EST Libraries

  7. NHGRI contigs GenomicDNA uniSTS dbSNP A Mapping GrailEXP GenScan FGENESH FGENESH+ GeneMark BGene Prediction Human ESTs UniGene Human RefSeq Human Ensembl cDNA C Expression Data Mouse ESTs Entrez Gene Mouse RefSeq Mouse Promoters E Additional Data Annotating Genome Databases nrPRO pFAM Motifs UniProt DProtein Similarity D Protein Data Entrez Gene GeneCards F Summary

  8. NR-Pro RefSeq ESTs GrailEXP FGENESH Genscan Entrez Gene Loci http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene Entrez Gene

  9. NCBI Genome Pagehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=genome

  10. Human Genome Resourceshttp://www.ncbi.nlm.nih.gov/projects/genome/guide/human/

  11. Entrez Human Genome Projectshttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=9558

  12. PCNA Gene in Entrez Genehttp://www.ncbi.nlm.nih.gov/gene/5111

  13. MapViewer of PCNA Gene

  14. OMIM Entry for PCNAhttp://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176740

  15. Hugo Nomenclature for PCNAhttp://www.genenames.org/data/hgnc_data.php?hgnc_id=8729

  16. HUGO Home Pagehttp://www.genenames.org/

  17. Sequence View of PCNA Genehttp://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NT_011387.8&v=5035598..5047267

  18. Evidence Viewer for PCNAhttp://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_011387.8&gene=PCNA&lid=5111

  19. SNP Polymorphisms in PCNAhttp://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=5111

  20. Entrez Genehttp://www.ncbi.nlm.nih.gov/gene

  21. OMIM Home Pagehttp://www.ncbi.nlm.nih.gov/omim

  22. OMIM Coveragehttp://www.ncbi.nlm.nih.gov/Omim/mimstats.html

  23. Colorblindness in OMIM

  24. Colorblindness in OMIMhttp://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=303800

  25. Human Gene Mutation Databasehttp://www.hgmd.cf.ac.uk/ac/gene.php?gene=OPN1MW

  26. GeneTestshttp://www.genetests.org/

  27. GeneReviews on Red-Green Color Vision Defectshttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=rgcb

  28. Genes & Diseasehttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd&part=gnd_book_info

  29. Genes & Disease Table of Contentshttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd

  30. Chromosome 7http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd&part=A272#A279

  31. UCSC Genome Browserhttp://genome.ucsc.edu/ http://genome.ucsc.edu/

  32. UCSC Genome Browserhttp://genome.ucsc.edu/cgi-bin/hgGateway

  33. PCNA Entry at UCSChttp://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_encodeTxLevels_close=1&hgtgroup_encodeChip_close=1&hgtgroup_encodeChrom_close=1&hgtgroup_encodeCompAndVar_close=1

  34. UCSC Proteome Browserhttp://genome.ucsc.edu/cgi-bin/pbGlobal?proteinID=P12004

  35. UCSC Tutorialshttp://www.openhelix.com/downloads/ucsc/ucsc_home.shtml

  36. Ensembl Genomes Home Pagehttp://www.ensembl.org/

  37. Ensembl Human Genomehttp://www.ensembl.org/Homo_sapiens/

  38. Ensembl DNA View of Human PCNAhttp://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646

  39. Ensembl PCNA Transcriptshttp://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646

  40. Ensembl PCNA Splice Variantshttp://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646

  41. Ensembl PCNA Gene Tree (Pecan)http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646

  42. Ensembl PCNA Variations Ensembl PCNA Variations http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000132646

  43. Ensembl Protein View of PCNA

  44. Ensembl Tutorialshttp://www.ensembl.org/common/Workshops_Online

  45. Comparative Genomics

  46. UCSC PCNA Entry

  47. UCSC Comparative Genomics

  48. Ensembl Genome Alignments

  49. Ensembl Genome Alignments (PCNA)

  50. NCBI Homologene Database

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