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1.Nucleotide Sequence Databases
1.1 International Nucleotide Sequence Database Collaboration
Database name
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Full name and/or description
|
URL
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DDBJ-DNA Data Bank of Japan
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All known nucleotide and protein sequences
| |
EMBL-Nucleotide Sequence Database
|
All known nucleotide and protein sequences
| |
GenBank
|
All known nucleotide and protein sequences
|
1.2. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA
Database name
|
Full name and/or description
|
URL
|
ACLAME
|
A classification of genetic mobile elements
| |
CUTG
|
Codon usage tabulated from GenBank
| |
Genetic Codes
|
Genetic codes in various organisms and organelles
| |
Entrez Gene
|
Gene-centered information at NCBI
| |
HERVd
|
Human endogenous retrovirus database
| |
Hoppsigen
|
Human and mouse homologous processed pseudogenes
| |
Imprinted Gene Catalogue
|
Imprinted genes and parent-of-origin effects in animals
| |
Islander
|
Pathogenicity islands and prophages in bacterial genomes
| |
MICdb
|
Prokaryotic microsatellites
| |
NPRD
|
Nucleosome positioning region database
| |
STRBase
|
Short tandem DNA repeats database
| |
TIGR Gene Indices
|
Organism-specific databases of EST and gene sequences
| |
Transterm
|
Codon usage, start and stop signals
| |
UniGene
|
Non-redundant set of eukaryotic gene-oriented clusters
| |
UniVec
|
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
| |
VectorDB
|
Characterization and classification of nucleic acid vectors
| |
Xpro
|
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes
|
1.2.2. Gene structure, introns and exons, splice sites
Database name
|
Full name and/or description
|
URL
|
ASAP
|
Alternative spliced isoforms
| |
ASD
|
Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb
| |
ASDB
|
Alternative splicing database: protein products and expression patterns of alternatively spliced genes
| |
ASHESdb
|
Alternatively spliced human genes by exon skipping database
| |
EASED
|
Extended alternatively spliced EST database
| |
ECgene
|
Genome annotation for alternative splicing
| |
EDAS
|
EST-derived alternative splicing database
| |
ExInt
|
Exon intron structure of eukaryotic genes
| |
HS3D
|
Homo sapiens splice sites dataset
| |
Intronerator
|
Alternative splicing in C.elegans and C.briggsae
| |
SpliceDB
|
Canonical and non-canonical mammalian splice sites
| |
SpliceInfo
|
Modes of alternative splicing in human genome
| |
SpliceNest
|
A tool for visualizing splicing of genes from EST data
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1.2.3. Transcriptional regulator sites and transcription factors
