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http://www.genatlas.org/

GENATLAS contains relevant information with respect to gene mapping and genetic diseases. GENATLAS compiles the information relevant to the mapping efforts of the Human Genome Project. This information is collected from more than 48,000 articles in the literature, collected in more than 870 reviews. The articles are daily analyzed by annotators to update the GENATLAS database. Only the objects with a known cytogenetic location are retained. GENATLAS repertories three kinds of objects Genes database ( more than 21.000 entries) Phenotypes database ( 4104 entries , 2000 cloned) References database linked to the two previous ( more than 48000 entries)

Proper citation: GenAtlas (RRID:SCR_007669) Copy   

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http://www.ncrna.org/frnadb

fRNAdb is a database of comprehensive non-coding RNA (ncRNA) sequences including known (or previously reported) ncRNAs, which are acquired from other sequence databases, and ncRNA sequences reported by the joint research groups of the Functional RNA Project. It is funded by the New Energy and Industrial Technology Development Organization.

Proper citation: functional RNAdb (RRID:SCR_007664) Copy   

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http://flysnp.imp.univie.ac.at

This project aims to provide the information and technical resources to support high-throughput positional cloning in Drosophila melanogaster. These resources include a high-density genome-wide map of single nucleotide polymorphisms (SNPs), and inexpensive, high-throughput assays for SNP genotyping. The specific aims were as follows: 1. To establish a map of >2200 SNP marker loci in the Drosophila genome. These SNP markers have been identified in several commonly used genetic strains. The FlySNP project identified SNP markers within the sequenced, euchromatic regions of the X, 2nd and 3rd chromosomes. The average distance between SNPs is about 50 kb. 2. To establish robust, high-throughput assays for SNP genotyping. Assays have been established using PCR, microarray and mass-spectrometry methods. The tag-array mini-sequencing (TAMS) approach has proven to be an especially fast and reliable method for SNP genotyping.

Proper citation: FLYSNP (RRID:SCR_007663) Copy   

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http://www.jncasr.ac.in/cremofac/

CREMOFAC is a database for chromatin remodeling factors has been developed. The database harbors 64 types of remodeling factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways, and phylogenetic relationships has also been covered.

Proper citation: CREMOFAC: A web-database of Chromatin Remodeling Factors (RRID:SCR_007613) Copy   

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http://pgrc.ipk-gatersleben.de/cr-est

The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK. Summarized numbers about genomic data of species are listed in tables. The main database content is original sequence data and cDNA library information from different organisms as well as results from BlastX searches against major protein sequence databases contained in NRPEP. Additionally sequence alignments of stackPACK clustering projects are available. This web application allows to BLAST against CR-EST ESTs and to query and retrieve data from Gene Ontology and metabolic pathway annotations as well as sequence similarities from stored results of BLASTX searches against the NRPEP database. CR-EST also features interactive JAVA-based tools, such as open reading frame visualization and explorative analysis of Gene Ontology mappings to ESTs.

Proper citation: CR-EST - Crop ESTs (RRID:SCR_007612) Copy   

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http://bioinformatics.ramapo.edu/GRSDB2/

GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. Computations were performed with the help of an indigenously developed and previously published software program QGRS Mapper. What is new in GRSDB2: The entire database has been built with a new and much improved version of QGRS Mapper program. It contains data from a large number of eukaryotic genes from several organisms in addition to human and mouse. The data model is different than the first version in that it is centered around Entrez Gene rather than solely GenBank/RefSeq nucleotide entries. The search module has been greatly enhanced. It is possible to search the database with Entrez Gene ID, Gene Name, Gene Symbols, Aliases, relevant Accession numbers and many other parameters like numbers of poly A signals and alternatively spliced products. Complex queries can also be performed. In addition, it is now possible to search the database with Gene Ontology terms. The list of genes matching the query can be sorted. The website also allows to manipulate the list to form sets of genes and perform further computations on these sets through a ''Workbench''. The Gene View, Data View and Graphic View for individual database entries have been significantly enhanced with several additional computational capabilities and links. The data can now be exported into Excel for further analysis. In addition, we have added a Sequence View which displays mapped G-quadruplexes in the context of pre-mRNA sequence. GRSDB2 replaces GRSDB at, http://bioinformatics.ramapo.edu/grsdb/index.php

Proper citation: GRSDB: G-Rich Sequences DataBase (RRID:SCR_007697) Copy   

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http://wheat.pw.usda.gov

Grain Genes is a genome database for Triticeae and Avena. It contains tools that allow users to browse graingenes, search the MySQL database, and view maps, genetic markers, gene expression and sequences.

Proper citation: GrainGenes (RRID:SCR_007696) Copy   

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http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/

The FlyTF database contains information on the manual curation of FlyBase identifiers based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database. FlyBase identifiers are putative site-specific transcription factors. There are currently1052 of them in this database.

Proper citation: FlyTF (RRID:SCR_007611) Copy   

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http://corg.molgen.mpg.de

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements. We use a systematic approach to delineate such conserved non-coding blocks from a collection of vertebrate species. Upstream regions of homologous gene pairs from man, rhesus monkey, mouse, rat, dog, cow, chicken, tetraodon, zebrafish and xenopus are considered for this purpose. Pairwise as well as Multiple alignments based on the pairwise ones are available. 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 provide the CORG-''COmparative Regulatory Genomics''-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service for query and interactive visualization of the conserved blocks and their annotation.

Proper citation: CORG - A database for COmparative Regulatory Genomics (RRID:SCR_007610) Copy   

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https://nar.oxfordjournals.org/content/35/suppl_1/D322.full-text-lowres.pdf

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity. The GO partitions comprise varying numbers of nodes and present relevant information theoretic statistics, so researchers can choose to analyze datasets at arbitrary levels of specificity. The GO Partition Database, featuring GO partition sets for functional analysis of genes from human and ten other commonly-studied organisms with a total of 131,972 genes.

Proper citation: Gene Ontology Partition Database (RRID:SCR_007693) Copy   

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http://gpxmea.gti.ed.ac.uk/

A database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. The objectives of the database are: Provide access to quality assessed gene expression datasets Rapid access to gene expression profile macrophage treated with a variety of conditions Provide datasets for Systems biology

Proper citation: GPX-Macrophage (RRID:SCR_007694) Copy   

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http://www.ebi.ac.uk/GOA

An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website.

Proper citation: GOA (RRID:SCR_007691) Copy   

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http://genolist.pasteur.fr/Colibri/

Database dedicated to the analysis of the genome of Escherichia coli. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The data contained in Colibri originates from two major sources of information, the reference genomic DNA sequence from the E. coli Genome Project and the feature annotations from the EcoGene data collection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Colibri (RRID:SCR_007606) Copy   

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http://comparasite.hgc.jp/

Comparasite is an integrated database of our original full-length cDNA sequence data. It consists of seven sub-databases of apicomplexa protozoa, Plasmodium falciparum, Plasmodium yoelii, Plasmodium vivax, Toxoplasma gondii, Cryptosporidium parvum, Echinococcus multilocularis. Homologous gene groups are clustered and comparative analysis of any combination of these seven species is implemented, such as interspecies comparisons as to cellular localization, motifs or transmembrane regions and so on. For submitted keywords and other search conditions, Comparasite retrieves orthologous gene groups containing a given protein motif/GO term etc in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism.

Proper citation: Comparasite: full length cDNA database (RRID:SCR_007608) Copy   

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http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 11th,2023. The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. It is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters.

Proper citation: Homeobox Genes DataBase (RRID:SCR_007723) Copy   

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http://germsage.nichd.nih.gov

Collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). It includes the three key germ cell stages in spermatogenesis, including mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries and is by far the most comprehensive resource available. Users can choose a global view of germ cell transcriptome data in the UCSC Genome browser. They can also search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.

Proper citation: GermSAGE (RRID:SCR_007689) Copy   

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http://www.jncasr.ac.in/humhot/menuframe.html

HumHot is a collection of human meiotic hot spots obtained from the literature along with interesting information on meiotic recombination and molecular features of meiotic hot spots. It is also updated as more hot spots get discovered in the human genome. The database can be queried by hot spot name or chromosome number.

Proper citation: HumHot (RRID:SCR_007722) Copy   

•   Source: SciCrunch Registry

http://genometrafac.cchmc.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 29,2022. Whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

Proper citation: GenomeTraFaC (RRID:SCR_007686) Copy   

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http://www.ebi.ac.uk/GenomeReviews/

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed.

Proper citation: Genome Reviews (RRID:SCR_007685) Copy   

•   Source: SciCrunch Registry

http://www-alis.tokyo.jst.go.jp/HOWDY/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database system for retrieve human genome information in different data sources that are available to public. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY facilitates obtaining information of human genes by using official symbols and aliases approved by HGNC, GDB and Entrez Gene. It also provides a graphical view of the Human Genome maps for the finished contigs as well as radiation hybrid maps.

Proper citation: Human Organized Whole Genome Database (RRID:SCR_007721) Copy   

•   Source: SciCrunch Registry