Tag: human and other vertebrate genomes

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...

The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

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 ...

Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which ...

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

FlyAtlas 2 is the RNA-Seq successor to the original FlyAtlas (which was based on microarray analysis). Specifically, FlyAtlas 2 now provides access to: transcript information, sex-specific data for adult somatic tissues, and micro-RNA genes. FlyAtlas ...

HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) an ...

neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

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 ...

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

Online GEne Essentiality database

GWIPS-viz is a freely available on-line genome browser which provides pre-populated ribosome profiling (Ribo-seq) and mRNA-seq tracks from published studies.

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.

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.

The European Mouse Mutant Archive (EMMA) is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. The laboratory mouse is the most important m ...

The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of ge ...

AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.

The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.

The objective of this project is to generate the most comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications.

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

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

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.

Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog ...

Human Proteinpedia is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations.

Evola contains ortholog information of all human genes among vertebrates. Orthologs are a pair of genes in different species that evolved from a common ancestral gene by speciation. In Evola, orthologs were detected by comparative genomics and amino ...

A comprehensive online knowledgebase for the monkey research community.

euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, ...

High-throughput screening using the CRISPR/Cas-9 system

Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2

Initiated in 2013, DMDD has the ambitious goal of identifying all embryonic lethal knockout lines made at the Wellcome Trust Sanger institute, through their work as a major centre for creation of individual mouse gene knockouts. DMDD uses a combinati ...

The chicken Variation Database (ChickVD) is an integrated information system for storage, retrieval, visualization and analysis of chicken variation data.

Mutant mouse lines held at MRC Harwell

Integrated database of mammalian genomes, phenotypes, strains and cell lines

The Total Integrated Archive of short-Read and Array (TIARA) accumulates raw-level personal genomic data from whole genome next-generation sequencing (NGS) and comparative genomic hybridization (CGH) arrays. Initially, it contains 36 individual genom ...

MIPS mouse functional genomics database

The MUGEN mouse database (MMdb) is a database of murine models of immune processes and immunological diseases.

The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed ...

3DSNP is a database for comprehensively annotating the regulatory function of human noncoding SNPs by exploring their 3D interactions with genes and genetically associated SNPs mediated by chromatin loops. 3DSNP integrates Hi-C data together with a v ...

A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.

European mutant mice pathology database: histopathology photomicrographs and macroscopic images

The Spirochetes Genome Browser

Unambiguous insertions in the same subgenic regions of annotated mouse genes

A repository for collection and distribution of plasmid clones

Human disease-related phenotypes in model organisms

Full-length pig cDNA libraries and ESTs

The International Protein Index (IPI) provides a top level guide to the main databases that describe the human, mouse and rat proteomes. IPI is built from the protein sequence data taken from the UniProt Knowledgebase, Ensembl and RefSeq databases, w ...

ChIP-Seq and DNase-Seq data in human and mouse

The Spirochetes Genome Browser

Human and mouse homologous processed pseudogenes

Genomic information on chicken and other avian species

Functional network of mouse genes

Nonhuman Primate Reference Transcriptome Resource

Protein-coding exons from completed verterbrate genomes

A database of Translation Initiation Sites

Links from human disease to natural variation data in C. elegans

Sea urchin Strongylocentrotus purpuratus genome database

Embryonic development of the mouse, chicken, zebrafish and human

DataBase of Transcriptome in Mouse Early Embryos

Eukaryotic pseudogenes assigned to different protein families

Database server for cleansed EST libraries

Phylogenetic patterns of genes from the Ensembl database

A curated genome expression database of Oikopleura dioica

Searchable prototype experimental evolutionary database

Conserved syntenies for various animal, plant and bacterial genomes

Gene indices of human, mouse, zebrafish, Arabidopsis, and Drosophila

CRISPR single guide RNAs to zebrafish genes

piggyBac transposon insertions in the mouse genome.

spatio-temporal gene expression patterns indipteran embryos

Public Affymetrix probesets and annotations

Orthologous and Paralogous Transcripts in Clades

Heritability data for various species with trait-associated genomic loci

Annotation and visualization of genome structure for Affymetrix exon array analysis

Databases of predicted human protein sequences

Each LRG is stable genomic DNA sequence for a region of the human genome

University of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data

A phylogeny-based tool for comparative genomics

Cre transgenic mouse lines with links to corresponding publications and to contact information for requests.

The PReMod database describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide/ ...

LIFEdb is a database on the localisation, interaction, functional assays and expression of human proteins. It integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analy ...

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 ( ...

QTL MatchMaker system is designed to integrate and mine QTL information across human, mouse and rat genomes and to annotate functional genomic data. It combines and organizes information from relevant public databases and publications and integrates ...

TRbase is a database relating tandem repeats to gene locations and disease genes in the human genome. This database identifies both perfect and imperfect tandem repeats of 1-2000 bp unit lengths. Tandem repeats can be selected according to a number o ...

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations ...

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databa ...

Tunicates are lower chordates that include among others the two ascidians Ciona intestinalis and Ciona savignyi. This subphylum is particularly interesting because it shares many developmental and physiological characteristics, as well as basic gene ...

ABA (Ascidian Body Atlas) is a digital 3D atlas of ascidian embryo development and gene expression pattern. Our 3D embryo images were reconstructed from more than 3,000 high-resolution real images acquired by a confocal laser microscopy in different ...

TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. ...

Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from more than 1000 organisms representing all the biological kingdoms. We have compiled the known physi ...

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 Mammalia Polymorphism Database (1) is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Mammalia class grouped by name of organism and gene. It allows the search for any polymorphic set accordi ...

GeneLoc unifies gene collections, eliminates redundancies, and assigns each gene a meaningful location-based identifier, which also serves as its GeneCards ID (http://bioinfo.weizmann.ac.il/cards-bin/AboutGCids.cgi). The GeneLoc algorithm (http://bio ...

The GeneAnnot system revises and improves annotation of Affymetrix probe sets. The many-to-many relationship between probe-sets and genes is elucidated by GeneAnnot's direct sequence comparison of probes to Genbank, RefSeq and Ensembl mRNA sequences. ...

The integration of SYSTERS, GeneNest and SpliceNest into one framework facilitates the over-all exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. The SYSTERS protein sequence cluster set provide ...

Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not ye ...

A major challenge following the sequencing of the human genome is to determine the biological functions of the estimated 30,000 genes. This requires the biochemical characterization of expressed proteins in various hosts. To facilitate the protein ex ...