Nucleotide Sequence Databases           

International Nucleotide Sequence Databases

Database Name Description

DDBJ-DNA DataBank of Japan

  Nucleotide and Protein Sequences

EMBL-Nucleotide Sequence Database

  Nucleotide and Protein Sequences

GenBank

  Nucleotide and protein Sequences

DNA sequences: genes, motifs and regulatory sites Coding and coding DNA

Database name
 description
 A classification of genetic mobile elements
 Codon usage tabulated from GenBank
 Genetic codes in various organisms and organelles
 Gene-centered information at NCBI
 Human endogenous retrovirus database
 Human and mouse homologous processed pseudogenes
 Imprinted genes and parent-of-origin effects in animals
 Pathogenicity islands and prophages in bacterial genomes
 Prokaryotic microsatellites
 Nucleosome positioning region database
 Short tandem DNA repeats database
 Organism-specific databases of EST and gene sequences
 Codon usage, start and stop signals
 Non-redundant set of eukaryotic gene-oriented clusters

 Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for  vector contamination

 Characterization and classification of nucleic acid vectors

 Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes

Gene structure, introns and exons, splice sites

Database name
Description
 Alternative spliced isoforms

 Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb

 Alternative splicing database: protein products and expression patterns of alternatively spliced genes

 Alternatively spliced human genes by exon skipping database
 Extended alternatively spliced EST database
 Genome annotation for alternative splicing
 EST-derived alternative splicing database
 Exon–intron structure of eukaryotic genes
 Homo sapiens splice sites dataset
 Alternative splicing in C.elegans and C.briggsae
 Canonical and non-canonical mammalian splice sites
 Modes of alternative splicing in human genome
 A tool for visualizing splicing of genes from EST data

Transcriptional regulator sites and transcription factors

Database name
Description
 Functional DNA/RNA site activity
 Bacillus subtilis promoters and transcription factors
 Database of orthologous promoters: chordates and plants
 Binding sites for E.coli DNA-binding proteins
 Eukaryotic promoter database

 Hematopoietic promoter database: transcriptional regulation in hematopoiesis

 PSSMs for transcription factor DNA-binding sites
 Putative transcription factor binding sites in various genomes
 Plant cis-acting regulatory DNA elements
 Plant promoters and cis -acting regulatory elements
 Plant promoter sequences for RNA polymerase II
 Prokaryotic database of gene regulation networks
 E . coli promoters with experimentally identified transcriptional start sites

 DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment

 Transcription element search system
 Transcription factors in gamma-proteobacteria database
 Composite regulatory elements affecting gene transcription in eukaryotes
 Transcription factors and binding sites
 Transcriptional regulatory element database
 Transcription regulatory regions of eukaryotic genes