|
Category
|
Number of entries
|
Source
|
Example fields from this category
|
| Genes |
8,189 |
UCSC Genome Browser's track UCSC Known Genes. Click here for restrictions on use |
orientation, exons, CDS |
| Genes with product and function data |
6,051 |
Locus Link |
product, biological process, cellular component, molecular function |
| Expression data |
48,291 |
UniGene at NCBI |
tissue, gene ID |
| Microarray expression data |
4,450 |
GNF |
tissue, expression level |
| Strain with Mutant Allele |
533 |
Rat Genome Database |
strain, gene ID |
| QTL |
248 |
Rat Genome Database |
qtl, gene ID |
| Gene Orthologs |
human 9,570
mouse 5,513 |
Database of evolutionary distances and Ensembl |
species, gene symbol, coordinates in second species, percent CDS identity,percent protein identity |
| Alternate Gene Model: ECgene Genes |
112,066 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Ensembl Genes |
27,989 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Geneid Genes |
35,750 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Genscan Genes |
44,495 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: RefSeq Genes |
4,539 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: RGD Genes |
3,572 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: SGP Genes |
43,580 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Superfamily Genes |
13,290 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Twinscan Genes |
25,499 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: UCSC Known Genes |
6,366 |
UCSC Golden Path |
orientation, exons, CDS |
| NonRat ESTs |
29,085,214 (90,246,073 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| NonRat mRNAs |
929,622 (5,052,072 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| Rat ESTs |
553,169 (1,558,689 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| Rat mRNAs |
14,499 (118,688 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| Spliced ESTs |
204,159 (951,218 exons) |
UCSC Golden Path |
matches, mismatches, ... |
| TIGR Gene Index |
309,385 (1,185,757 exons) |
UCSC Golden Path |
name, score, strand, exon coordinates |
| Multiple alignments |
9,845,510 |
UCSC Golden Path and Penn State - Bioinformatics Group scoring using multiz |
score |
| Local alignments rat vs. human |
1,579,355 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments rat vs. human |
34,218,863 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments rat vs. mouse |
1,188,862 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments rat vs. mouse |
26,462,610 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| 3-way conserved |
2,847,221 |
Penn State - Bioinformatics Group |
repetitive element |
| Fugu blat alignments |
0 |
UCSC Golden Path |
matches, mismatches, ... |
| Human net alignments |
5,749,354 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| Mouse net alignments |
5,611,024 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| Regulatory potential score (based on rmh alignments) |
167,345,716 |
Penn State - Bioinformatics Group |
score |
| Transcription factor binding sites |
157,656,838 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score |
| Conserved Transcription factor binding sites (rmh) |
4,075,081 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score |
| Micro RNA |
32 |
Sanger Institute |
name |
| CpG islands |
15,314 |
UCSC Golden Path |
name |
| SNPs |
21,856 |
dbSNP
and UCSC Golden Path |
type, allele, frequency |
| Repeats |
4,341,894 |
UCSC Golden Path |
name, class, family |
| Recombination rates |
5,254 |
deCODE Genetics
Marshfield
Genethon
Downloaded from UCSC Golden Path |
recombination rate; sex averaged, F, and M |
| GC percent |
136,009 |
UCSC Golden Path |
percent |
| Isochore |
9,590 |
Anton Nekrutenko's Group |
percent |
| Restriction sites |
99,210,651 |
Penn State - Bioinformatics Group |
for 128 different enzymes |