Tag: coding and non-coding dna

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...

The Dfam database is a open collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Dfam represents a collection of multiple sequence alignments, each containing a set of r ...

Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activit ...

PolymiRTS (Polymorphism in microRNAs and their TargetSites) is a database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational ...

UniVec is a database that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination). In addition to vector sequences, UniVec also contains sequences for those adapters, linkers, and pr ...

ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.

NCBI takes great care to ensure that the translation for each coding sequence (CDS) present in GenBank records is correct. Central to this effort is careful checking on the taxonomy of each record and assignment of the correct genetic code for each o ...

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

Gypsy database of mobile genetic elements

Retrotransposons, which comprises LINE, SINE and LTR-containing elements, accounts for almost half of our genome (Fig. 1). They are mobile genetics elements - also known as jumping genes - but only the L1-HS subfamily has retained the ability to jump ...

MethBank stores DNA methylome data across a variety of species. MethBank integrates consensus reference methylomes (CRMs) compiled from healthy human samples at different ages, single-base resolution methylomes (SRMs) of both plant and animal species ...

Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA and contains a variety of tools for their analysis.

Next-generation sequencing single-cytosine-resolution DNA methylation data

R-loop DB is a collection of R-loop forming sequences (RLFS) predicted computationally in the human genome based on quantitative model of RLFS (QmRLFS). The database additionally includes chromosome coordinates and annotation of many hundred thousand ...

InSatDb, unlike many other microsatellite databases that cater largely to the needs of microsatellites as markers, presents an interactive interface to query information regarding microsatellite characteristics of five fully sequenced insect genomes ...

TassDB (TAndem Splice Site DataBase) stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or th ...

OGRDB is a curated database of immunoglobulin and T cell receptor sequences inferred from immune receptor repertoires, together with supporting information describing the repertoires from which they were derived. Researchers can submit sequences and ...

This ontology is about human pseudogenes, extending the existing SO framework to incorporate additional attributes. Relationships between pseudogenes and segmental duplications are defined in this standard. To answer research questions and to annotat ...

Database for dinucleotide properties

CEGA, (Conserved Elements from Genomic Alignments), is a database of conserved vertebrate elements. This database provides acces to precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny.

AU-rich elements in vertebrate mRNA UTR sequences

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5 ...

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains the seed protein sequence alignments from the Pfam-A (curated families) database; nucleotide sequence alignments derived f ...

A database of ultraconserved non-coding elements and gene regulatory blocks

A database of short interspersed elements (SINEs)

Functional annotation and prediction of LINE-1 elements

Group I Intron Sequence and Structure Database

DoriC regions in bacterial and archaeal genomes

DNA methylation data from single molecule, real-time sequencing

3'UTRs and their functional elements in C. elegans

Transposed elements influence on the transcriptome of seven vertebrates and invertebrates

UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes

Repetitive sequences in plant genomes

Data available for download from the SGD site, be aware that data dates from 1997

Macro- and micronuclear genes in spirotrichous ciliates

Nucleosome positioning region database

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and pr ...

The SNPSTR database contains the SNP-STR/microsatellite compound markers in the five model species, where sufficient SNP information exists in both of the NCBI and Ensembl databases. These species are human (Homo sapiens), mouse (Mus musculus), rat ( ...

The Synthetic Gene Database (http://www.evolvingcode.net/codon/sgdb/index.php) is a resource that has collected together sequence information on synthetic genes (i.e. genes that were designed conceptually, rather than built from an initial, physical ...

DNA shape analysis has been established in recent years as an approach that reveals protein-DNA binding specificity determinants beyond nucleotide sequence.GBshape provides DNA shape annotations of entire genomes.The database currently contains annot ...

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a col ...

The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed Sequenc ...

OriDB provides a web-based catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast (S. cerevisiae). Each proposed or confirmed origin site appears as a record in OriDB, with each record comprisin ...

Ultraconserved sequences (UCRs) were first described by Bejerano et al. in 2004. They are highly conserved genome regions that share 100% identity among human, mouse and rat. UCRs are 481 sequences longer than 200 bases. They are frequently located a ...

RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory pro ...

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate clas ...

With the availability of the complete genomic sequence of rice, the identification and annotation of LTR-Retrotransposons has become a necessity as they comprise an important part of plant genomes (1). RetrOryza is a database that aims at providing t ...

The nuclear organization of metaphase and interphase cells has been studied over several decades and increasing evidence supports the concept upon which the eukaryotic chromatin is organized in the form of functional independent loop domains [1; 2]. ...