Database of experimentally defined eukaryotic RNA Polymerase II promoters
Organisms
Eukaryotes
Contact
Research center
Swiss Institute of Bioinformatics
Primary citation
PMID 23193273
Release date
1986
Access
Website
epd.expasy.org
Miscellaneous
License
Free without registration
Curation policy
Yes – manual and automatic
EPD (Eukaryotic Promoter Database) is a biological database and web resource of eukaryotic RNA polymerase II promoters with experimentally defined transcription start sites.[1] Originally, EPD was a manually curated resource relying on transcript mapping experiments (mostly primer extension and nuclease protection assays) targeted at individual genes and published in academic journals. More recently, automatically generated promoter collections derived from electronically distributed high-throughput data produced with the CAGE or TSS-Seq [2][3] protocols were added as part of a special subsection named EPDnew.[4] The EPD web server offers additional services, including an entry viewer which enables users to explore the genomic context of a promoter in a UCSC Genome Browser window, and direct links for uploading EPD-derived promoter subsets to associated web-based promoter analysis tools of the Signal Search Analysis (SSA)[5] and ChIP-Seq servers. EPD also features a collection of position weight matrices (PWMs) for common promoter sequence motifs.
^Cavin Périer, R; Junier, T; Bucher, P (1 January 1998). "The Eukaryotic Promoter Database EPD". Nucleic Acids Research. 26 (1): 353–7. doi:10.1093/nar/26.1.353. PMC 147208. PMID 9399872.
^Tsuchihara, K; Suzuki, Y; Wakaguri, H; Irie, T; Tanimoto, K; Hashimoto, S; Matsushima, K; Mizushima-Sugano, J; Yamashita, R; Nakai, K; Bentley, D; Esumi, H; Sugano, S (April 2009). "Massive transcriptional start site analysis of human genes in hypoxia cells". Nucleic Acids Research. 37 (7): 2249–63. doi:10.1093/nar/gkp066. PMC 2673422. PMID 19237398.
EPD (EukaryoticPromoterDatabase) is a biological database and web resource of eukaryotic RNA polymerase II promoters with experimentally defined transcription...
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on this technology. Curated promoter sequences for eukaryotic organisms are provided by an EPD database; however, promoter activity information at tissue/...
theory is a theory of the origin of introns, long non-coding sequences in eukaryotic genes between the exons. The theory holds that the randomness of primordial...
found in phages as well as eukaryotic chloroplasts and mitochondria, and is related to modern DNA polymerases. Eukaryotic and archaeal RNAPs have more...
contains two small rRNAs and one molecule of large rRNA (~5000 nucleotides). Eukaryotic rRNA has over 70 ribosomal proteins which interact to form larger and...
unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated...
translation. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not. A molecule of eukaryotic mRNA...
genome during development. Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the...
Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. Eukaryotic and archaeal 7S RNAs have very similar secondary structures...
TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding...
systems using multiple eukaryotic cells were developed for applications requiring the proteins be conformed as in, or closer to eukaryotic organisms: cells...
transcript decay. A very important modification of eukaryotic pre-mRNA is RNA splicing. The majority of eukaryotic pre-mRNAs consist of alternating segments called...
manner, as part of the greater process of protein synthesis. Initiation of eukaryotic translation nearly always occurs at and is dependent on the 5' cap of...
ˌnjuːkliˈoʊləs/; pl.: nucleoli /-laɪ/) is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis, which is the...
compaction of the eukaryotic genome by winding DNA around histones to form higher order structures. This compaction makes the gene promoter inaccessible without...
(mtDNA and mDNA) is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate...
basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which...
intermembrane space, inner membrane, cristae, and matrix. Although most of a eukaryotic cell's DNA is contained in the cell nucleus, the mitochondrion has its...
Andorf CM (Apr 2021). "FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences". BMC Bioinformatics...
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