1. 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/

2. Components of a Typical Human Gene Gene Intron Exon PromoterTerminator TFBS

3. 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

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

5. Alternative Splicing Generates Distinct Proteins in Different Tissues Transcript mRNA-1 Gene Intron Exon PromoterTerminator 5’ 3’ Transcript mRNA-25’3’ Alternate Splicing Splicing

6. Alternative Splicing Detected in EST Libraries

7. 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

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

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

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

11. 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

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

13. MapViewer of PCNA Gene

14. 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

15. 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

16. HUGO Home Page http://www.genenames.org/ http://www.genenames.org/

17. 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

18. 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

19. 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

20. Entrez Gene http://www.ncbi.nlm.nih.gov/gene http://www.ncbi.nlm.nih.gov/gene

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

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

23. Colorblindness in OMIM

24. 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

25. 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

26. GeneTests http://www.genetests.org/ http://www.genetests.org/

27. 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

28. 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

29. 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

30. 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

31. UCSC Genome Browser http://genome.ucsc.edu/ http://genome.ucsc.edu/ httphttp://genome.ucsc.edu/

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

33. 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

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

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

36. Ensembl Genomes Home Page http://www.ensembl.org/ http://www.ensembl.org/

37. Ensembl Human Genome http://www.ensembl.org/Homo_sapiens/ http://www.ensembl.org/Homo_sapiens/

38. 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

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

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

42. Ensembl PCNA Variations http://www.ensembl.org/H omo_sapiens/Gene/Sum mary?g=ENSG000001326 46

43. Ensembl Protein View of PCNA

44. Ensembl Tutorials http://www.ensembl.org/common/Workshops_Online http://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

51. Homologene PCNA Entries