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Nucleotide Sequence Databases
1.Nucleotide Sequence Databases
1.1 International Nucleotide Sequence Database Collaboration
Database name |
Full name and/or description |
URL |
DDBJ-DNA Data Bank of Japan |
All known nucleotide and protein sequences |
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EMBL-Nucleotide Sequence Database |
All known nucleotide and protein sequences |
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GenBank |
All known nucleotide and protein sequences |
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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 |
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CUTG |
Codon usage tabulated from GenBank |
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Genetic Codes |
Genetic codes in various organisms and organelles |
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Entrez Gene |
Gene-centered information at NCBI |
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HERVd |
Human endogenous retrovirus database |
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Hoppsigen |
Human and mouse homologous processed pseudogenes |
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Imprinted Gene Catalogue |
Imprinted genes and parent-of-origin effects in animals |
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Islander |
Pathogenicity islands and prophages in bacterial genomes |
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MICdb |
Prokaryotic microsatellites |
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NPRD |
Nucleosome positioning region database |
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STRBase |
Short tandem DNA repeats database |
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TIGR Gene Indices |
Organism-specific databases of EST and gene sequences |
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Transterm |
Codon usage, start and stop signals |
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UniGene |
Non-redundant set of eukaryotic gene-oriented clusters |
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UniVec |
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination |
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VectorDB |
Characterization and classification of nucleic acid vectors |
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Xpro |
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes |
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1.2.2. Gene structure, introns and exons, splice sites
Database name |
Full name and/or description |
URL |
ASAP |
Alternative spliced isoforms |
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ASD |
Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb |
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ASDB |
Alternative splicing database: protein products and expression patterns of alternatively spliced genes |
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ASHESdb |
Alternatively spliced human genes by exon skipping database |
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EASED |
Extended alternatively spliced EST database |
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ECgene |
Genome annotation for alternative splicing |
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EDAS |
EST-derived alternative splicing database |
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ExInt |
Exon�intron structure of eukaryotic genes |
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HS3D |
Homo sapiens splice sites dataset |
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Intronerator |
Alternative splicing in C.elegans and C.briggsae |
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SpliceDB |
Canonical and non-canonical mammalian splice sites |
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SpliceInfo |
Modes of alternative splicing in human genome |
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SpliceNest |
A tool for visualizing splicing of genes from EST data |
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1.2.3. Transcriptional regulator sites and transcription factors
Database name |
Full name and/or description |
URL |
ACTIVITY |
Functional DNA/RNA site activity |
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DBTBS |
Bacillus subtilis promoters and transcription factors |
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DoOP |
Database of orthologous promoters: chordates and plants |
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DPInteract |
Binding sites for E.coli DNA-binding proteins |
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EPD |
Eukaryotic promoter database |
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HemoPDB |
Hematopoietic promoter database: transcriptional regulation in hematopoiesis |
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JASPAR |
PSSMs for transcription factor DNA-binding sites |
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MAPPER |
Putative transcription factor binding sites in various genomes |
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PLACE |
Plant cis-acting regulatory DNA elements |
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PlantCARE |
Plant promoters and cis -acting regulatory elements |
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PlantProm |
Plant promoter sequences for RNA polymerase II |
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PRODORIC |
Prokaryotic database of gene regulation networks |
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PromEC |
E . coli promoters with experimentally identified transcriptional start sites |
http://bioinfo.md.huji.ac.il/marg/promec |
SELEX_DB |
DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment |
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TESS |
Transcription element search system |
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TRACTOR db |
Transcription factors in gamma-proteobacteria database |
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TRANSCompel |
Composite regulatory elements affecting gene transcription in eukaryotes |
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TRANSFAC |
Transcription factors and binding sites |
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TRED |
Transcriptional regulatory element database |
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TRRD |
Transcription regulatory regions of eukaryotic genes |
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