|
Category
|
Number of entries
|
Source
|
Example fields from this category
|
| Genes |
35,146 |
UCSC Genome Browser's track UCSC Known Genes. Click here for restrictions on use |
orientation, exons, CDS |
| Genes with product and function data |
27,576 |
Locus Link |
product, biological process, cellular component, molecular function |
| Expression data |
992,778 |
UniGene at NCBI |
tissue, gene ID |
| Microarray expression data |
13,778 |
GNF |
tissue, expression level |
| Strain with Mutant Allele |
1,716 |
The Jackson Laboratory |
strain, gene ID |
| Gene Orthologs |
human 26,819
rat 9,002 |
Database of evolutionary distances and Ensembl |
species, gene symbol, coordinates in second species, percent CDS identity,percent protein identity |
| Alternate Gene Model: ECgene Genes |
340,368 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Ensembl ESTs |
31,546 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Ensemble Genes |
32,911 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Geneid Genes |
32,453 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Genscan Genes |
42,835 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: MGC Genes |
8,498 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: RefSeq Genes |
13,053 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: SGP Genes |
42,419 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Superfamily Genes |
10,384 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Twinscan Genes |
24,282 |
UCSC Golden Path |
orientation, exons, CDS |
| Mouse ESTs |
2,787,059 (10,649,013 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| Mouse mRNAs |
145,012 (860,792 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| NonMouse ESTs |
22,460,327 (66,543,082 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| NonMouse mRNAs |
674,253 (3,239,375 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| Spliced ESTs |
1,360,653 (7,584,608 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| TIGR Gene Index |
278,497 (1,167,444 exons) |
UCSC Golden Path |
name, score, strand, exon coordinates |
| Multiple alignments |
9,898,671 |
UCSC Golden Path and Penn State - Bioinformatics Group scoring using multiz |
score |
| Local alignments mouse vs. human |
1,584,198 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments mouse vs. human |
34,807,161 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments mouse vs. rat |
1,181,033 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments mouse vs. rat |
26,302,727 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| 3-way conserved |
2,975,616 |
Penn State - Bioinformatics Group |
repetitive element |
| Fugu blat alignments |
354,851 |
UCSC Golden Path |
matches, mismatches, ... |
| Regulatory potential score (based on mh alignments) |
202,845,854 |
Penn State - Bioinformatics Group |
score |
| Human net alignments |
6,049,177 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| Human Conservation score |
212,473,591 |
UCSC Golden Path |
score |
| Transcription factor binding sites |
155,379,374 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score |
| Conserved Transcription factor binding sites (mhr) |
4,081,393 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score |
| CpG islands |
15,587 |
UCSC Golden Path |
name |
| SNPs |
132,652 |
dbSNP
and UCSC Golden Path |
type, allele, frequency |
| Repeats |
4,656,083 |
UCSC Golden Path |
name, class, family |
| Recombination rates |
4,902 |
deCODE Genetics
Marshfield
Genethon
Downloaded from UCSC Golden Path |
recombination rate; sex averaged, F, and M |
| GC percent |
128,875 |
UCSC Golden Path |
percent |
| Isochore |
9,401 |
Anton Nekrutenko's Group |
percent |
| Restriction sites |
96,424,590 |
Penn State - Bioinformatics Group |
for 128 different enzymes |