Tag: gene transcripts

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

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 ...

Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignm ...

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. There are several ways to ...

FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.

Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 5 ...

A database of exosomes, membrane vesicles of endocytic origin released by diverse cell types.

The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is e ...

T-DNA insertions in Arabidopsis and their flanking sequence tags.

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...

The Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including i) Experimentally determined binding sites reported in the li ...

Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides informati ...

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...

Overview The NIH Mammalian Gene Collection (MGC) program is a multi-institutional effort to identify and sequence cDNA clones containing a full-length open reading frame (FL-ORF) for human, mouse, and rat genes. To date, the MGC has produced over 324 ...

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Databas ...

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In t ...

This database includes TSS data from adult and embryonic human tissue. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures.

This ensembl website features the zebrafish whole genome shotgun assembly sequence.

Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.

Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl's comparative genomics resources.

The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.

Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.

AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...

Gene expression and neuroanatomical data.

Long Non-Coding RNA Database

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arab ...

sORFs.org is a database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are pro ...

The Hymenoptera Genome Database (HGD) is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD is divided into three main divisions: BeeBase, which hosts bee genomes and the Bee Pes ...

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information f ...

Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...

PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR ...

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alteratio ...

Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

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 ...

Genome database of the beetle Tribolium castaneum

The ApiDB website (http://eupathdb.org/eupathdb) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center that integrates numerous database resources. The phylum Apicomplexa comprises numerous veterinary and med ...

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tis ...

A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive ann ...

The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.

Gene Signature DataBase

Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.

Gene expression data sorted into two groups: expressed and not expressed genes

Rice transcriptome under natural conditions

Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.

ChimerDB is a database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data and integration with other well known databases. Fusion transcripts with nonoverlapping ali ...

piRBase stores information on piRNAs and piRNA-associated data to support piRNA functional analysis.

Experimentally-determined binding sites of RNA-binding proteins

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarra ...

Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

The Selective Targets database (SelTarbase ) is a curated database of public MNR mutation data in microsatellite unstable human tumors. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is als ...

Cervical cancer gene database

<<<!!!<<< This repository is no longer available >>>!!!>>>

Public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, a ...

Mimotope database, active site-mimicking peptides selected from phage-display libraries

FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...

Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromesome, cytoband, gene and refseq p ...

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multiv ...

Query single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query retur ...

Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon red ...

Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites

HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).

The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous ...

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene e ...

DIGGER is an essential resource for studying the mechanistic consequences of alternative splicing such as isoform-specific interaction and consequence of exon skipping. The database integrates information of domain-domain and protein-protein interact ...

Lnc2Cancer 3.0 includes comprehensive data on experimentally supported long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with human cancers. In addition, web tools for analyzing lncRNA expression by high-throughput RNA sequencing ...

ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms.

The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic prope ...

An integrated database of ncRNA interactions. Noncoding RNAs (ncRNAs) play crucial regulatory roles in a variety of biological circuits. To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database ...

Human lncRNA expression database

Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.

Probe-Level Annotation Database for Affymetrix microarrays

The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one ...

The Dynamic Proteomics database is a compendium of endogenously YFP-tagged human proteins and their time-lapse microscopy movies. These movies show the protein dynamics in space and in time in individual living human cancer cells in response to an an ...

Linking RNA splicing and disease. Database that collects and curates data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent func ...

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, a ...

PmiREN is a comprehensive encyclopedia of plant miRNAs.

Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and trans ...

Coding and non-coding RNA

A database of eukaryotic sequencing projects

miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation for the functional investigation of miRNA. miRGator v2.0 contains information about : 1) Human miRNA expr ...

A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic ...

A database of putative RNA binding protein target sites in the transcriptomes of model species. Dashboard - Overview of the database. Welcome to oRNAment - o RNA motifs enrichment in complete transcriptomes. Here, we developed a computational tool ...

OncoSplicing is a database to systematically study clinically relevant alternative splicing in 33 TCGA cancers and 31 GTEx tissues.

an interactive database of human snoRNA sequences, abundance and interactions. Tool to visualize expression data in heatmaps. Column Options Reset Filters Refresh Table. snoTHAW is a tool to help visualize snoRNA expression data from snoDB

Repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties.

H-DBAS is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. RNA-Seq tag information is correlated to the AS exons and splice junctions. A total of 148,376,598 RNA-Seq tags have been generated from R ...

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionisation equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play ...

"iModulons", groups of independently-modulated genes

Curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, ...

Deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Search by RsID, Gene, Region or Disease:. Links MeT-DB Whistle DRUM DRRMSDB. A database for the disease-associated genetic variants tha ...

Functional annotation of exon skipping event in human. Exon skipping (ES), the most common alternative splicing event, has been reported to contribute to diverse human diseases due to the loss of functional domains sites or frame shifting of open re ...

516 unique variants and 831 patients registered in an updated centralized Variome database | OPA1 (optic atrophy 1 (autosomal dominant)) | Autosomal dominant optic atrophy (DOA, Kjer type, MIM#165500) is characterized by moderate to severe loss of vi ...

Assembled partial genomes for ~250 eukaryotic organisms

Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants.

Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. tRFexplorer is a public database through which users may display the expression profile of tRNA-derived ncRNAs in every cel ...

a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resour ...

An atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids.

RNA Localization in the cell

LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Knowledge of lncRNA spatial expression patterns across tissues is important for identifying their roles in different tissues that provide important insights into disease mechanisms ...

A comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. Welcome to the miRNASNP -v3 database. microRNAs (miRNAs) are endogenous and regulatory non-coding RNAs by targeting mRNAs for cleavage or translational re ...

Projections of protein functional Sites on Exons

PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables user ...

Online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with ...

PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including ...

The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL ...

the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis ...

Dual RNA-seq host-pathogen sequencing

G-quadruplex Ligands Database

Alternative splicing during development in 20 species

EPSD (Eukaryotic Phosphorylation Sites Database) is a well-annotated data resource of protein phosphorylation sites in eukaryotes.

circad is a comprehensive manually curated resource of circular RNA associated with diseases. Circular RNAs (circRNAs) are unique transcript isoforms characterised by back splicing of exon ends to form a covalently closed loop or circular conformatio ...

SyntDB: defining orthologues of human long noncoding RNAs across primates. SyntDB - the database of human long non-coding RNAs conserved across primates. Comprehensive collection of long noncoding RNAs (lncRNAs) and their evolutionary relationships ...

Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing | Tupaia belangeri (Family Tupaia, Genus Tupaia) | Tupaia ( Tupaia belangeri ) is a small mammal belonging to the family Tupaiidae, whic ...

The eQTL Catalogue aims to provide uniformly processed gene expression and splicing QTLs from all available public studies on human. Quantitative trait loci (QTL) are genomic variants that are significantly associated to a measurable phenotype. This ...

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ...

riboCIRC is a comprehensive database of translatable circRNAs. Translation of circular RNAs (circRNAs) now has drawn increasing attention from researchers due to their emerging roles of the functional peptides encoded by circRNAs as new players invol ...

BEable-GPS: Base Editable prediction of Global Pathogenic-related SNVs. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.

FuncPEP is a database of functional peptides encoded by non-coding RNAs.

Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs.

Human IRES Atlas is an integrative platform for studying IRES-driven translational regulation in humans.

dbMTS is a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions. dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotat ...

Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources ...

a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associa ...

Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis

Database of enhancers identified by high-throughput reporter assays.

ConsRM is a collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome.

Database for ncRNA expression in human extracellular vesicles.

CpGDB (Chloroplast Genome Database) is a user friendly, freely available and dynamic relational database which allows search and download of complete chloroplast genome sequences, individual gene sequences and feature records of different plant speci ...

circ2GO is a comprehensive database compiling and analyzing circular RNAs found in lung cancer cell lines providing the data in tables as well as visualizing it in transcript maps and in heatmaps. Importantly, we also provide easy-to-use online tools ...

A database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.

A database for plant circRNAs that act as miRNA decoys. Circular RNAs (circRNAs) are a novel type of RNAs that form covalently closed loop structures with neither 5'- 3' polarities nor polyadenylated tails. GreenCircRNA(v1.0) is the most comprehensi ...

A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database

Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.

PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.

An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma.

A knowledgebase of lncRNA function in human cancer.

TANTIGEN 2.0 (Tumor T-cell Antigen Database) is a knowledge base of tumor T cell antigens and epitopes.

Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.

ctcRbase is agene expression database of circulating tumor cells and microemboli Circulating tumor cells/microemboli (CTCs/CTM) are those cells that depart from cancerous lesions and shed into the bloodstream. Enumeration and analysis of CTCs/CTM may ...

circVAR database is genome-wide archive of genetic variants for human circular RNAs Circular RNAs (circRNAs), the 3' and 5' ends of which are covalently linked, are a kind of widely distributed and abundant RNAs found in eukaryotic organisms in recen ...

Database of fusion transcripts in Arabidopsis thaliana.

A database of experimentally supported protein-coding RNAs and drug associations in human cancer.

An online database for exploring over 2,000 Arabidopsis small RNA libraries.

A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.

Leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease.

FLHdb is database of variants of Familial Hemophagocytic Lymphohistiocytosis from the Clinical and Translational Bioinformatics Research Group at Vall Hebron Institute of Research (VHIR).

Novel disease-associated variants, common sequence variants, and results from newborn screening. The Pompe disease GAA variant database represents an effort to collect all known variants in the GAA gene and is maintained and provide by the Pompe cen ...

scAPAdb provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level in six species based on a large volume of scRNA-seq data. Currently, scAPAdb records APA information in animal speci ...

a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progressi ...

FGviewer is an online visualization tool for functional features of human fusion genes. FGviewer is aiming for the effective visualization of the functional features of fusion genes for better prioritization of therapeutic target selection. FGviewer ...

Fusion gene annotation updates aided by deep learning.

An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers

A comprehensive database of RNAs involved in liquid-liquid phase separation.

Cancer Gene and Pathway Explorer (CGPE) provides a highly integrated bioinformatics webserver for investigating, analyzing, and visualizing the TCGA and GEO gene expression data. CGPE provides key interactive and customizable analysis portal

CRMarker is a manually curated comprehensive resource of both long noncoding and circular cancer RNA markers.

ColorCells is a database of expression, classification and functions of lncRNAs in single cells. Single cell RNA sequencing (scRNA-Seq) technology has revealed significant differences in gene expression levels between different cell groups.

A knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

ExoBCD is a comprehensive database for exosomal biomarker discovery in breast cancer.

CUBAP (Codon Usage Biases Across Populations) is an interactive web portal for analyzing codon usage biases across populations. Although synonymous codon usage does not change the protein primary structure, codon choice significantly impacts translat ...

CONREL is a genome browser that allows for the exploration of consensus regulatory elements at different levels of abstraction. The total binding affinity of transcription factors on whole consensus region sequences is here fully exploited to charact ...

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource. OpenProt is the first database that enforces a polycistronic model of eukaryotic genome annotations. Thus, OpenProt annotates known proteins (called RefProts) but also novel ...

A manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases. ILDGDB is a manually curated database that provides comprehensive experimentally supported associations between genes and inter ...

<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGen ...

The COGEME phytopathogen EST database currently contains expressed sequence tags (ESTs) from eleven species of phytopathogenic fungi and two oomycete species. In order to reduce sequence redundancy, sequence assembly software was used to join togethe ...

Full-length transcripts and conservation of plant circRNAs.

A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.).

ConnecTF is a platform to build gene networks by integrating transcription factor-target gene interactions.

A blood platelets-based gene expression database for disease investigation.

AhNGE is a Database for Arachis hypogaea nodule developmental gene expression.

Barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.

Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.

An automated approach to spectral unmixing of fluorescent biological images.

A Knowledgebase of RAG Regulators.

A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China

A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.

Plant transfer RNA database.

Database and analysis platform for gene expression and alternative splicing of fish species.

T1TAdb is a database of Type I Toxin-Antitoxin systems.

A database of ribozymes.

A database for orchid genomics and molecular biology.

A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data.

A comprehensive database of long inverted repeats in eukaryotic genomes.

An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle.

A database for cancer A-to-I RNA editing with interactive analysis.

An integrated transcriptomic and genomic database for Bombyx mori and related species.

GUIdEStaR (G-quadruplex, uORF, IRES, Epigenetics, Small RNA, Repeats) is the integrated metadatabase in conjunction with neural network methods.

TEx-MST is a novel bioinformatic database for providing the valuable expression information of MANE-select transcripts in normal human tissues.

A centralized datasource for all data relevant for the understanding of viral fusion peptides.

A knowledge database of dense granule proteins of the Apicomplexa.

piRNAdb it's a piwi-interacting RNA sequences storage and search system, providing some others relevant information like alignments, clusters, datasets and targets of these piRNAs.

Buffalo Subclinical Mastitis Methylome–Transcriptome database (BSCM2TDb) is a three-tier architecture-based relational database in Water Buffalo.

A comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis.

AlnC is an extensive database of long non-coding RNAs in Angiosperms.

Mutation update of SERPING1 related to hereditary angioedema in the Chinese population

REVA as a Well-curated Database for Human Expression-modulating Variants.

A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis. MetamORF: A repository of unique short Open Reading Frames identified by both experimental and computatio ...

An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.

A data hub for long genes. Long genes harbor specific genomic and epigenomic features and have been implicated in many human diseases. LongGeneDB is an interactive, visual database containing genomic information of 992 long genes (>200 kb) in 15 spe ...

A unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into eas ...

COGVIC(Catalogue Of Germline Variants In Cancer). A comprehensive database of germline pathogenic variants in East Asian pan-cancer patients.

An ethnic-specific database of Indian germline variants.

A comprehensive database for translatable lncRNAs ( TransLnc) extends immunopeptidome. TransLnc provides both computationally predicted and experimentally supported lncRNA peptides in multiple species.

Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types.

circR2Cancer is a manually curated database of associations between circRNAs and cancers. circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase.

the database of immunologically relevant non-coding RNAs | git clone [email protected]:sschmeier/irndb2.git irndb2 | IRNdb - Database of immunologically relevant non-coding RNAs | // © Massey University 2014-2018 // v1.5.8

An atlas of intronic polyadenylation quantitative trait loci across human tissues.

A comprehensive animal enhancer RNA database.

Here, we have predicted CasRx guide efficiency for all human and mouse RefSeq genes. We have also enabled custom sequence input for CasRx guide design.

database for eukaryotic single-exon coding sequences. Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to det ...

The CerealESTdb, a user-friendly, searchable, and interactive database has been developed with a primary goal to provide information on assembled and annotated ESTs from four major crop plants, namely wheat, rice, maize, and sorghum under multiple en ...

NeuroCirc is an integrative web-based resource of circRNA expression in the human brain, which allows interactive exploration of circRNA expression across multiple datatsets, including circRNA expression in bulk brain tissue, circQTLs, circRNA expres ...

Protein-gene Expression Nexus (PEN), which consolidates an extensive dataset of paired proteomics and genomics studies. PEN present a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy numbe ...

CALR-ETdb is a database of calreticulin variants diversity in essential thrombocythemia

The Chinese Glioma Genome Atlas (CGGA) is a user-friendly web application for data storage and analysis to explore brain tumors datasets. This database includes the whole-exome sequencing, DNA methylation, mRNA sequencing, mRNA microarray and microRN ...

A comprehensive organelle genomes database for algae cpDNA and mtDNA. Algae is the earliest evolutionary biological group on the earth, are thought to have appeared at least 2.6 billion years ago. As the most complex biological group, algae have sho ...

A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Curre ...