| Category | Number of entries | Source | Example fields from this category |
|---|---|---|---|
| Genes | 20,503 | UCSC Genome Browser's track Human Refseq Genes. Click here for restrictions on use | orientation, exons, CDS |
| Genes with product and function data | 0 | Locus Link | product, biological process, cellular component, molecular function |
| Expression data | 0 | UniGene at NCBI | tissue, gene ID |
| Microarray expression data | 0 | GNF | tissue, expression level |
| Gene Orthologs | 0 | Database of evolutionary distances and Ensembl | species, gene symbol, coordinates in other species, percent CDS identity,percent protein identity |
| Alternate Gene Model: Ensembl Genes | 33,518 | UCSC Golden Path | orientation, exons, CDS |
| Alternate Gene Model: Geneid Genes | 27,656 | UCSC Golden Path | orientation, exons, CDS |
| Alternate Gene Model: Genscan Genes | 36,254 | UCSC Golden Path | orientation, exons, CDS |
| Alternate Gene Model: Twinscan Genes | 21,972 | UCSC Golden Path | orientation, exons, CDS |
| Chimp ESTs | 4,103 (11,108 exons) | UCSC Golden Path | matches, mismatches, ... |
| Chimp mRNAs | 574 (2,608 exons) | UCSC Golden Path | matches, mismatches, ... |
| NonChimp ESTs | 29,187,285 (87,294,078 exons) | UCSC Golden Path | matches, mismatches, ... |
| NonChimp mRNAs | 840,981 (4,160,021 exons) | UCSC Golden Path | matches, mismatches, ... |
| Spliced ESTs | 2,249 (8,661 exons) | UCSC Golden Path | matches, mismatches, ... |
| Multiple alignments | 0 | UCSC Golden Path and Penn State - Bioinformatics Group scoring using multiz | score |
| Local alignments chimp vs. human | 360,218 | UCSC Golden Path and Penn State - Bioinformatics Group | score, lav file sequence and header fields |
| Gap free alignments chimp vs. human | 4,936,978 | UCSC Golden Path and Penn State - Bioinformatics Group | percent identity, local alignment ID |
| 3-way conserved | 0 | Penn State - Bioinformatics Group | repetitive element |
| Fugu blat alignments | 703,106 | UCSC Golden Path | matches, mismatches, ... |
| Human net alignments | 5,549,139 | UCSC Genome Browser | score, level, gaps, repeat bases, N bases, ... |
| Regulatory potential score (based on hmr alignments) | 0 | Penn State - Bioinformatics Group | score |
| Transcription factor binding sites | 207,177,890 | Penn State - Bioinformatics Group and TRANSFAC (free registration required) |
factor, strand, score |
| Conserved Transcription factor binding sites | 0 | Penn State - Bioinformatics Group and TRANSFAC (free registration required) |
factor, strand, score |
| CpG islands | 22,587 | UCSC Golden Path | name |
| SNPs | 0 | dbSNP and UCSC Golden Path |
type, allele, frequency |
| Repeats | 4,249,477 | UCSC Golden Path | name, class, family |
| Recombination rates | 0 | deCODE Genetics Marshfield Genethon Downloaded from UCSC Golden Path |
recombination rate; sex averaged, F, and M |
| GC percent | 154,211 | UCSC Golden Path | percent |
| Isochore | 6,032 | Anton Nekrutenko's Group | percent |
| Restriction sites | 98,600,283 | Penn State - Bioinformatics Group | for 128 different enzymes |