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http://genome.imim.es/cgi-bin/u12db/u12db.cgi

This is a searchable database of U12-type introns. U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.Two pathways for the removal of eukaryotic spliceosomal introns exist: a major pathway that is dependent on the main U2 snRNA-containing spliceosome and a minor pathway that is dependent on the low abundance U12 snRNA-containing spliceosome. The two spliceosomes share only one snRNA, U5, but have many of the same protein components in common. They are distinguished mainly by the splice signal sequences in the pre-mRNA to which they bind. U12 consensus sequences for the donor site, RTATCCTTT, and branch point, TTCCTTRAY, are highly conserved and distinct from the U2 consensi. The two spliceosomes also differ in the order of spliceosomal assembly. U11 and U12 form a dimer which then recognizes the donor site and branch point simultaneously, whereas U1 and U2 recognize these sites independently before associating.Computational scans for U12 introns have previously been performed for human (Levine and Durbin, 2001) and Arabidopsis (Zhu and Brendel, 2003). Both scans used similar methodology, essentially predicting introns and confirming them using alignment to expressed sequence. We extended this approach to 20 genomes using spliced alignment of sequence flanking known introns or transcript-confirmed intron predictions to the genomic sequence of orthologous genes. Details can be found in forthcoming article in the Nucleic Acids Research database issue.

Proper citation: U12DB: The U12 Intron Database (RRID:SCR_013410) Copy   

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http://rarge.psc.riken.jp/rartf/

Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available.

Proper citation: RARTF (RRID:SCR_013457) Copy   

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http://www.lamondlab.com/NOPdb/

It archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene its domain structures and relevant protein homologues across species as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints highlighted by visualization means in the NOPdb provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb is searchable by either gene names protein sequences Gene Ontology terms or motifs or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink OMIM and PubMed).

Proper citation: NoPdb: Nucleolar Proteome Database (RRID:SCR_013459) Copy   

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http://www.abrn.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 31,2023.

Proper citation: Australian Prostate Cancer Tissue Bank (RRID:SCR_013221) Copy   

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http://soybeangenome.siu.edu

It provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. It combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. The database is also searchable for listings of these relationships.

Proper citation: The Soybean GBrowse Database (RRID:SCR_013463) Copy   

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http://cdna01.dna.affrc.go.jp/PIPE

A unification tool which dynamically collects and compiles data from scientific databases in National Institute of Agrobiological Sciences (NIAS), and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Oryza sativa into easy to navigate. The mission of Rice PIPELINE is to provide a unique scientific resource of rice that pools publicly available data commonly sought after for any clone sequence, clone name, GenBank accession number, or keyword.

Proper citation: Rice Pipeline (RRID:SCR_013344) Copy   

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http://www.cstl.nist.gov/div831/strbase/

A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.

Proper citation: STRBase (RRID:SCR_013465) Copy   

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http://dorina.mdc-berlin.de/rbp_browser/dorina.html

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.

Proper citation: doRiNA (RRID:SCR_013222) Copy   

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http://www.nccc.com

Provides access to large scale cell culture at reasonable cost. The Cell Culture Center has experience with the production of over 1700 cell lines. Numerous common cell lines, such as HeLa, CHO, 293, BHK, and hybridomas are routinely produced at the Center. We will adapt your cell line or custom protocol to large scale production then deliver the cells in the quantity and frequency you need. Large Scale Production Services: Mammalian cells: Suspension culture (1 to 400 liters per day), Anchorage dependent culture (1 to 200 roller bottles per batch), Purified monoclonal antibodies (10 mg to 100 grams), Non-hybridoma cell secreted proteins, Conditioned media Secreted proteins from suspension cultures can be produced in automated hollow fiber bioreactor systems. These systems may be considered after initial static culture production yields are determined. Upon determining the quantities requested by the investigator, the appropriate automated system will be used. For more information on the automated instrumentation available for the use of secreted protein production, please refer to the Biovest International web page (www.biovest.com). Working with our experienced personnel and quality controlled, state-of-the-art facilities also permits access to large quantities of cells or protein so you aren''t limited by the cell culture capacities of your own laboratory. The Center fulfills the needs of small research laboratories as well as those of larger institutions. Customers from all sectors of the research and industrial community are welcome to inquire about our services. If you''d like to inquire about using our services, use the contact infromation below. Key words: Cell, cells, culture, monoclonal, antibodies, antibody.

Proper citation: National Cell Culture Center (RRID:SCR_013467) Copy   

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http://orygenesdb.cirad.fr/

The Oryza sativa database displays sequence information resulting from the research of the Centre de cooperation internationale en recherche agronomique pour le developpement. It also includes related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc.). Genome Browser (Gbrowse), a Web-based application for displaying genomic annotations and other features, is the core of our database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. We developed a set of tools around GBrowse to retrieve as exhaustively as possible information related to queries with several starting points. These tools allow a molecular geneticist to readily find insertion lines (T-DNA, Tos17, Ds) in genes of interest and to retrieve all the associated annotations related to these sequences.

Proper citation: OryGenesDB (RRID:SCR_013226) Copy   

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http://agem.cnb.csic.es/VisualOmics/aGEM/

Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: aGEM (RRID:SCR_013349) Copy   

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http://sbi.imim.es/cgi-bin/archdb/loops.pl

ArchDB is a compilation of structural classifications of loops extracted from known protein structures.
ArchDB includes 4 classifications:
* ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity.
* ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity.
* ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function
* ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues.
Futhermore, the functional annotation of residues in this database are further classified in four categories:
1. ATP interaction: for residues involved on ATP binding/interaction.
2. Substrate binding: for residues involved in substrate interaction/binding with the exception of ATP
3. Ion interaction: for residues involved in ion interaction/binding of ions needed for the catalytic mechanism
4. Catalytic: involved in reaction, the stabilization of a transition state or the activation of substrates.
Additionally, three different approaches were applied to identify functional residues of the loops of the sub-classes:
1. Residues found within a cut-off distance of 6���� from an heteroatom, ligand, inhibitor, cofactor or complex partner molecule (protein or DNA), with the exception of D2O or crystallization buffer molecules.
2. Residues identified by functional information from ACTSITE and SITE records in the RCSB protein data bank.
3. Residues identified by the functional annotation collected from the literature and assigned to specific motifs of kinases.
Lastly, the multiple ways to browse and query in ArchDB are:
* Search by sequence: Users can search for classified loop(s) with sequence similarity to a query sequence.
* Search by structure: Users can upload protein coordinates in PDB format and its loops will be extracted and compared with those from the classification. First: structural class is assigned comparing loop geometry and, second: the loop conformation is compared among the subclasses within the assigned class.
* Search subclasses and/or Search Loops: A range of options are offered for subclass or loop searches. Users can query ArchDB asking for subclasses or loops with specific flanking secondary structures, length of loops or phi/psi loop conformation. Also, users can retrieve all subclasses or loops with PDB SITE annotations and contacts with co-crystallized ligands. Finally, users can search for subclasses that have SCOP, GO or EC annotations conserved at different percentage levels.
* Search structures: Users can search for classified PDB structures in ArchDB with specific Sprot. Annotation/Keyword, GO annotation, SCOP and EC codes.
* Specific queries for ArchDB-KI: Users can list functional subclasses or loops classified in ArchKI.
:Sponsors: ArchDB is funded by grants from Fundacin Areces (Spain), Ministerio de Ciencia y Tecnologa Spain (MCYT; BIO2002-03609, BIO2001-246 and BIO2001-264), Centre de Referncia en Biotecnologia Generalitat de Catalunya (CERBA), and the Generalitat de Catalunya
:
:Enzyme-specific classification,
:Kinase proteins, ligand, Protein residue, Protein motif, Protein loop,

Proper citation: ArchDB - Biological Database of Protein Loops (RRID:SCR_013472) Copy   

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http://mitodrome.ba.itb.cnr.it/

It has been developed with the aim to annotate the complete set of Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome.

Proper citation: MitoDrome (RRID:SCR_013474) Copy   

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http://www.deathdomain.org/

A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily

Proper citation: Death Domain database (RRID:SCR_013231) Copy   

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http://dsap.cgu.edu.tw/

A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DSAP (RRID:SCR_013352) Copy   

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http://flytrap.med.yale.edu/

The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion.

Proper citation: FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) Copy   

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http://www.collectf.org/browse/home/

A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements.

Proper citation: CollecTF (RRID:SCR_014405) Copy   

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http://www.glycoepitope.jp

A database of carbohydrate antigens and matching antibodies. Epitopes and antibodies are listed within the database. Users may also search for epitopes and antibodies by keyword, epitope ID, tissue, receptor, enzyme, and other fields.

Proper citation: GlycoEpitope (RRID:SCR_014404) Copy   

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http://unicarb-db.biomedicine.gu.se

An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS.

Proper citation: UniCarb-DB (RRID:SCR_014407) Copy   

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http://www.radiometer.dk

Commercial organizations which develops, manufactures, and sells solutions and equipment for blood sampling, blood gas analysis, transcutaneous monitoring, and IT management systems under certain brand names.

Proper citation: Radiometer (RRID:SCR_014772) Copy   

•   Source: SciCrunch Registry