| Category | Number of entries | Source | Example fields from this category |
|---|---|---|---|
| Genes | 39,842 | Locus Link and Refseq gene track at UCSC | orientation, exons, CDS |
| Genes with product and function data | 27,565 | Locus Link | product, biological process, cellular component, molecular function |
| Expression data | 977,705 | UniGene at NCBI | tissue, gene ID |
| Microarray expression data | 26,360 | GNF | tissue, expression level |
| Strain with Mutant Allele | 1,158 | The Jackson Laboratory | strain, gene ID |
| Gene Orthologs | 52,684 | Database of evolutionary distances and Ensembl | species, gene symbol, coordinates in other species, percent CDS identity,percent protein identity |
| Alternate Gene Model: MGC Genes | 14,795 | UCSC Golden Path | orientation, exons, CDS |
| Alternate Gene Model: RefSeq Genes | 17,218 | UCSC Golden Path | orientation, exons, CDS |
| Mouse ESTs | 4,561,147 (16,144,465 exons) | UCSC Golden Path | matches, mismatches, ... |
| Mouse mRNAs | 147,463 (859,415 exons) | UCSC Golden Path | matches, mismatches, ... |
| NonMouse ESTs | 24,530,988 (70,554,442 exons) | UCSC Golden Path | matches, mismatches, ... |
| NonMouse mRNAs | 703,408 (3,374,392 exons) | UCSC Golden Path | matches, mismatches, ... |
| Spliced ESTs | 1,583,287 (9,262,777 exons) | UCSC Golden Path | matches, mismatches, ... |
| Multiple alignments | 24,750,372 | UCSC Golden Path and Penn State - Bioinformatics Group scoring using multiz | score |
| Local alignments mouse vs. human | 1,820,537 | UCSC Golden Path and Penn State - Bioinformatics Group | score, lav file sequence and header fields |
| Gap free alignments mouse vs. human | 33,419,379 | 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 | 1,073,162 | UCSC Golden Path | matches, mismatches, ... |
| Chicken net alignments | 702,609 | UCSC Genome Browser | score, level, gaps, repeat bases, N bases, ... |
| Dog net alignments | 5,844,787 | UCSC Genome Browser | score, level, gaps, repeat bases, N bases, ... |
| Human net alignments | 6,264,441 | UCSC Genome Browser | score, level, gaps, repeat bases, N bases, ... |
| Rat net alignments | 7,154,914 | UCSC Genome Browser | score, level, gaps, repeat bases, N bases, ... |
| Regulatory potential score (based on mhr alignments) | 818,124,964 | Penn State - Bioinformatics Group | score |
| Transcription factor binding sites | 209,751,702 | Penn State - Bioinformatics Group and TRANSFAC (free registration required) |
factor, strand, score |
| Conserved Transcription factor binding sites (mm5Hg17Rn3) | 4,704,305 | Penn State - Bioinformatics Group and TRANSFAC (free registration required) |
factor, strand, score |
| Conserved Transcription factor binding sites (mm5Hg17Rn3Canfam1) | 2,893,440 | Penn State - Bioinformatics Group and TRANSFAC (free registration required) |
factor, strand, score |
| CpG islands | 15,601 | UCSC Golden Path | name |
| SNPs | 0 | dbSNP and UCSC Golden Path |
type, allele, frequency |
| Repeats | 4,693,848 | 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 | 131,718 | UCSC Golden Path | percent |
| Isochore | 9,676 | Anton Nekrutenko's Group | percent |
| Restriction sites | 99,236,279 | Penn State - Bioinformatics Group | for 128 different enzymes |