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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences Resource Report Resource Website 1+ mentions |
TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences (RRID:SCR_005538) | data or information resource, database | A collection of amino acid sequences for all the completed genomes and the annotated trans beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. TMBETA-GENOME has the feasibility of selecting the organism from the three kingdoms of life, archaea, bacteria and eukaryote. Further, users have the option to select any of the methods or their combinations, and display the results with/without amino acid sequence information. | has parent organization: Computational Biology Center | nif-0000-03564 | SCR_005538 | TMBETA-GENOME | 2026-08-10 09:32:34 | 1 | ||||||||||
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Sys-BodyFluid Resource Report Resource Website 1+ mentions |
Sys-BodyFluid (RRID:SCR_005335) | data or information resource, database | A database of bodily fluid proteome data. It contains information on proteins from humanplasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Our body fluid protein database, Sys-BodyFluid, contains 11 body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Over 10,000 proteins are included in the Sys-BodyFluid. These body fluid proteome data come from 50 peer-review publications of different laboratories all over the world. Protein annotation are provided including protein description, Gene ontology, Domain information, Protein sequence and involved pathway. User can access the proteome data by protein name, protein accession number, sequence similarity. In addition, user could perform query cross different body fluids to get more comprehensive understanding. The difference and similarity between these 11 body fluids are also analyzed. Thus , the Sys-BodyFluid database could serve as a reference database for body fluid research and disease proteomics. plasm, serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid, protein, proteomics | bronchoalveolar lavage fluid, cerebrospinal fluid, human milk, nipple aspirate fluid, plasm, protein, proteomics, saliva, seminal fluid, serum, synovial fluid, tear fluid, urine | has parent organization: Shandong University; Shandong; China | nif-0000-03526 | SCR_005335 | Sys-BodyFluid | 2026-08-10 09:32:31 | 3 | |||||||||
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Daring Nucleic Adventures - genegeek Resource Report Resource Website |
Daring Nucleic Adventures - genegeek (RRID:SCR_005215) | DNA, DNA - genegeek | data or information resource, blog, narrative resource | Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution. | genetics, molecular biology, dna, science, genome, education |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: LabSpaces |
nlx_144219 | SCR_005215 | Daring Nucleic Adventures | 2026-08-10 09:32:29 | 0 | ||||||||
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International Knockout Mouse Consortium Resource Report Resource Website 50+ mentions |
International Knockout Mouse Consortium (RRID:SCR_005574) | IKMC | data or information resource, database | Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs. | gene, knock out mouse, chromosome, allele, c57bl/6, embryonic stem cell, vector, mutant, es cell, genome, targeting, gene list, FASEB list |
is related to: Texas A and M Institute for Genomic Medicine is related to: European Mouse Mutant Archive is related to: CMMR - Canadian Mouse Mutant Repository is parent organization of: EUCOMMTOOLS is parent organization of: North American Conditional Mouse Mutagenesis Project is parent organization of: European Conditional Mouse Mutagenesis Program is parent organization of: Knockout Mouse Project |
European Union ; NHGRI HG004074 |
PMID:22968824 PMID:21677750 |
nlx_146200 | SCR_005574 | 2026-08-10 09:32:35 | 68 | |||||||
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SwissRegulon Resource Report Resource Website 10+ mentions |
SwissRegulon (RRID:SCR_005333) | SwissRegulon | data or information resource, database | A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format. | genome, binding site, transcription factor, genome-wide annotation, annotation, chip-chip, chip-seq, non-coding region, promoter, motif, transcript, regulatory motif, genome browser, FASEB list |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:23180783 PMID:17130146 |
Acknowledgement requested | nif-0000-03524, OMICS_00543 | SCR_005333 | SwissRegulon Database | 2026-08-10 09:32:31 | 46 | ||||||
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Structure Superposition Database Resource Report Resource Website 1+ mentions |
Structure Superposition Database (RRID:SCR_005236) | data or information resource, database | The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function. We have therefore created the Structure Superposition Database (SSD) for accessing, viewing and understanding large sets of structure superposition data. It contains the results of pairwise, all-by-all superpositions of a representative set of 115 (beta/alpha) barrel structures (TIM barrels). The initial implementation of the SSD contains the results of pairwise, all-by-all superpositions of a representative set of 115 (/alpha)8 barrel structures (TIM barrels). Future plans call for extending the database to include representative structure superpositions for many additional folds. The SSD can be browsed with a user interface module developed as an extension to Chimera, an extensible molecular modeling program. Features of the user interface module facilitate viewing multiple superpositions together. | alpha barrel structure, barrel structure, beta barrel structure, protein, quaternary structure, structure superposition | nif-0000-03504 | SCR_005236 | SSD | 2026-08-10 09:32:30 | 2 | ||||||||||
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neurosphere Resource Report Resource Website 10+ mentions |
neurosphere (RRID:SCR_005478) | Neurosphere | data or information resource, blog, narrative resource | This blog belongs to me, Dave J Hayes PhD, a Neuroscientist at the University of Ottawa''s Institute of Mental Health Research. My research focuses on the neuroscience of motivation and emotion particularly regarding how brains and people respond to aversive and rewarding things in their environment. A neurosphere is a free-floating group of neural stem cells which can multiply, outside of their natural environment, and retain the ability to differentiate into functional brain cells. I don''t work on neurospheres. However, i like the metaphor of a group of people coming together, outside of their natural environment, through their interest in all things neuro which, incidentally, is everything. The sphere of human thought. | neuroscience, brain, environment, motivation, emotion, adverse event, reward | has parent organization: WordPress | nlx_144600 | SCR_005478 | neurosphere - neuroscience in everything | 2026-08-10 09:32:34 | 24 | ||||||||
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TranspoGene Resource Report Resource Website 1+ mentions |
TranspoGene (RRID:SCR_005634) | data or information resource, database | A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. | element, eukaryotic, evolutionary, exon, exonization, family, fruit fly, gene, genome, alternative, chicken, coding, disease, divergence, genomic, hosting, human, human genome databases, intron, location, map, maps, mouse, mrna, nematode, organism, pattern, promoter, protein, sea squirt, sequence, splicing, transcript, transcriptome, transposed, viewers, worm, zebrafish | has parent organization: Tel Aviv University; Ramat Aviv; Israel | nif-0000-03579 | SCR_005634 | TranspoGene | 2026-08-10 09:32:36 | 9 | |||||||||
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Now at NEJM Resource Report Resource Website |
Now at NEJM (RRID:SCR_005239) | Now(at)NEJM | data or information resource, blog, narrative resource | A blog produced by the NEJM publishing communications team about new and innovative content in the New England Journal of Medicine (NEJM.org). Our goal is to inform you about what''s new and provide some additional context to complement the content published in NEJM. Each week we post a piece under Insights about one of the latest research papers in NEJM, discussing its clinical significance, where it may lead us in practice and research, and often giving an editor''s thoughts about why it was important to publish. We pose questions to stimulate your thinking and discussion. The idea is to make it easy for you to give us your views on a particular topic and make the conversation accessible to other doctors and physicians-in-training. Posts contain links to the full article, which will be free to all visitors for a limited time. We also feature two posts from the Resident e-Bulletin each week, with an article summary, Clinical Pearls, and Morning Report Questions teaching points that many of you find so useful in your roles as teachers or trainees. The blog gives us a new way to distribute and store this educational information on the social web, again, inviting comment and discussion. You''ll also hear about new products and applications as we bring them out, such as new Interactive Medical Cases, or iPhone applications, like NEJM This Week and the Image Challenge. We link to videos on the NEJMvideo channel on YouTube, share our Twitter feed, and links to NEJM in the News, too. We''d like this to be an open forum, complementary to the core content of NEJM, engaging you in a new experience beyond the journal page in a more interactive community. | medicine, doctor, physician, resident |
is used by: NIF Data Federation is used by: Integrated Blogs |
Protected by copyright; for your personal noncommercial use. http://www.nejm.org/page/about-nejm/terms-of-use | nlx_144240 | SCR_005239 | NowatNEJM, Now at NEJM - A blog for physicians about NEJM, Now_at_NEJM | 2026-08-10 09:32:30 | 0 | |||||||
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TIGR Plant Transcript Assembly database Resource Report Resource Website 500+ mentions |
TIGR Plant Transcript Assembly database (RRID:SCR_005470) | data or information resource, database | The TIGR database is a collection of plant transcript sequences. Transcript assemblies are searchable using BLAST and accession number. The construction of plant transcript assemblies (TAs) is similar to the TIGR gene indices. The sequences that are used to build the plant TAs are expressed transcripts collected from dbEST (ESTs) and the NCBI GenBank nucleotide database (full length and partial cDNAs). "Virtual" transcript sequences derived from whole genome annotation projects are not included. All plant species for which more than 1,000 ESTs or cDNA sequences are available are included in this project. TAs are clustered and assembled using the TGICL tool (Pertea et al., 2003), Megablast (Zhang et al., 2000) and the CAP3 assembler (Huang and Madan, 1999). TGICL is a wrapper script which invokes Megablast and CAP3. Sequences are initially clustered based on an all-against-all comparisons using Megablast. The initial clusters are assembled to generate consensus sequences using CAP3. Assembly criteria include a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched overhangs. Any EST/cDNA sequences that are not assembled into TAs are included as singletons. All singletons retain their GenBank accession numbers as identifiers. Plant TA identifiers are of the form TAnumber_taxonID, where number is a unique numerical identifier of the transcript assembly and taxonID represents the NCBI taxon id. In order to provide annotation for the TAs, each TA/singleton was aligned to the UniProt Uniref database. For release 1 TAs, a masked version of the Uniref90 database was used. For release 2 and onwards, a masked version of the UniRef100 database is used. Alignments were required to have at least 20% identity and 20% coverage. The annotation for the protein with the best alignment to each TA or singleton was used as the annotation for that sequence. Additionally, the relative orientation of each TA/singleton to the best matching protein sequence was used to determine the orientation of each TA/singleton. Some sequences did not have alignments to the protein database that met our quality criteria, and those sequences have neither annotation nor orientation assignments. The release number for the plant TAs refers to the release version for a particular species. For the initial build, all TA sets are of version 1. Subsequent TA updates for new releases will be carried out when the percentage increase of the EST and cDNA counts exceeds 10% of the previous release and when the increase contains more than 1,000 new sequences. New releases will also include additional plant species with more than 1,000 EST or cDNA sequences that have become publicly available. | FASEB list | has parent organization: J. Craig Venter Institute | nif-0000-03559 | SCR_005470 | TIGR | 2026-08-10 09:32:33 | 828 | |||||||||
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Strepto-DB Resource Report Resource Website |
Strepto-DB (RRID:SCR_005196) | data or information resource, database | A database for comparative genomics of group A and group B streptococci. It is based on OGeR (Open Genome Resource for comparative analysis of prokaryotic genomes) and includes all sequenced GAS and GBS strains and serovars available as EMBL genome review or NCBI GenBank files. Strepto-DB identifies the homologous proteins deduced from the genomes of interest. It allows for the elucidation of the GAS and GBS core- and pan-genomes via genome-wide comparisons. Moreover, an intergenic region analysis tool provides alignments and predictions for transcription factor binding sites in the non-coding sequences. An interactive genome browser visualizes functional annotations. Strepto-DB (http://oger.tu-bs.de/strepto_db) was created by the use of OGeR, the Open Genome Resource for comparative analysis of prokaryotic genomes. OGeR is a newly developed open source database and tool platform for the web-based storage, distribution, visualization and comparison of prokaryotic genome data. The system automatically creates the dedicated relational database and web interface and imports an arbitrary number of genomes derived from standardized genome files. | gas strain, gbs strain, group a streptococci, group b streptococci, serovar, strepcoccus genome, streptococci, streptococci genome, streptococcus | nif-0000-03502 | SCR_005196 | Strepto-DB | 2026-08-10 09:32:29 | 0 | ||||||||||
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Cassandras Tears Resource Report Resource Website |
Cassandras Tears (RRID:SCR_005229) | Cassandras Tears | data or information resource, blog, narrative resource | Science, Technology, Education, Government, and anti-woo. Cassandra had the gift of seeing the future, but the curse of having no one believe her. | science, technology, education, government, astronomy, atheism, biology, chemistry, climate, computer tech, creationism, culture, environment, evolution, medicine, origins of life, paleontology, philosophy, physics, religion, renewable energy, society |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: WordPress |
nlx_144234 | SCR_005229 | Cassandra''s Tears | 2026-08-10 09:32:30 | 0 | ||||||||
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Systems Transcriptional Activity Reconstruction Resource Report Resource Website 5000+ mentions |
Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) | STAR | data or information resource, database, service resource | A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets. | genome browser, genome, next generation sequence, visualization, FASEB list |
is used by: CIRCexplorer is listed by: OMICtools is related to: star-for-criu has parent organization: University of California at San Diego; California; USA |
Account required, Or Guest login | OMICS_00895 | SCR_005622 | Systems Transcriptional Activity Reconstruction Genome Browser, Systems Transcriptional Activity Reconstruction, STAR Genome Browser | 2026-08-10 09:32:36 | 6478 | |||||||
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sfnvideo - YouTube Resource Report Resource Website |
sfnvideo - YouTube (RRID:SCR_005463) | SFNVideo - YouTube | data or information resource, video resource | The Society for Neuroscience (SfN) is a nonprofit membership organization of scientists and physicians who study the brain and nervous system. SFNVideo - YouTube are videos uploaded to YouTube by the Society for Neuroscience (SfN). Since inception in 1969, the Society has grown from 500 members to more than 41,000. Today, SfN is the world''s largest organization of scientists and physicians devoted to advancing understanding of the brain and nervous system. | neuroscience, brain, nervous system | has parent organization: Society for Neuroscience | nlx_144583 | SCR_005463 | Society for Neuroscience Video - YouTube | 2026-08-10 09:32:33 | 0 | ||||||||
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TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac, http://gene-regulation.com/pub/databases.html, https://bio.tools/transfac | SCR_005620 | 2026-08-10 09:32:36 | 266 | |||||
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Plant Repeat Databases Resource Report Resource Website 1+ mentions |
Plant Repeat Databases (RRID:SCR_005460) | data or information resource, database | It assists in the compilation and identification of repeat sequences in plant genomes. All of the repetitive sequences in the database are coded for the convenience of future analyses. In plants, ploidy levels and repetitive sequences contribute significantly to genome size. A number of different repetitive sequences have been reported in the plant genome and these can be classified into super-classes, classes, and subclasses based on structure and sequence composition. The transposable element (TEs) super-class includes retrotransposons, transposons, and miniature inverted-repeat transposable elements (MITEs). Other repetitive sequences are associated the centromere and telomere. Another super-class of repetitive sequences are rDNAs which encode the structural RNA components of ribosomes. | has parent organization: Michigan State University; Michigan; USA | nif-0000-03558 | SCR_005460 | Plant Repeat Databases | 2026-08-10 09:32:33 | 4 | ||||||||||
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Laboratory of Neuro Imaging - YouTube Resource Report Resource Website |
Laboratory of Neuro Imaging - YouTube (RRID:SCR_005462) | loniucla - YouTube | data or information resource, video resource | Videos uploaded to YouTube by the Laboratory of Neuro Imaging (LONI). The Laboratory of Neuro Imaging at UCLA strives to improve our understanding of the brain in health and disease. LONI is a leader in the development of advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function. | human, mouse, brain, health, disease, brain structure, brain function | nlx_144582 | http://www.youtube.com/user/loniucla | SCR_005462 | LONI - YouTube | 2026-08-10 09:32:33 | 0 | ||||||||
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Sciblogs Resource Report Resource Website |
Sciblogs (RRID:SCR_005219) | Sciblogs | data or information resource, blog, narrative resource | Sciblogs brings together the best science bloggers in the country (New Zealand) on one website, creating a hub for scientific analysis and discussion and facilitating reader interaction. The website is for scientists who want to reach out to a general audience to explain their science and how it relates to society. Some Sciblog contributors spend most of their time in the lab or buried in research. Others are authors or entrepreneurs. All of them know what they are talking about and have an interest in engaging in discussion on the big science-related issues facing society. Over time more bloggers will be added to the Sciblogs roster. If you would like to inquire about hosting a blog on Sciblogs contact us. You can easily keep an eye on new Sciblogs posts by subscribing via RSS or email or by following our Twitter feed. Alternatively, there is a Facebook page as well as a Facebook group feel free to join in! Categories: * Science * Agriculture * Technology * Health and Medicine * Environment and Ecology * Science and Society | science, technology, new zealand, clinical health, climate change, clinical, health, agriculture, society, medicine, environment, ecology |
is used by: NIF Data Federation is used by: Integrated Blogs |
Advertising revenue ; AMP Scholarship grant |
Content is property of author and Science Media Centre. Permission for use required or under the terms of fair use of copyright or Creative Commons licensing (indicated prominently on each blog adopting it.) | nlx_144223 | SCR_005219 | SciBlogs.co.nz | 2026-08-10 09:32:29 | 0 | ||||||
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ASH Video Library Resource Report Resource Website |
ASH Video Library (RRID:SCR_005777) | ASH Video Library | data or information resource, video resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. ASH's video library includes a number of films produced on various topics, including ASH''s history and award winners, Society programs such as the Clinical Research Training Institute, and a trailer and clips from the hematology documentary Blood Detectives, which aired on Discovery Health. These videos were created for educational purposes, and we encourage members of the hematology community to share them with others. | hematology, blood | has parent organization: American Society of Hematology | Blood disease, Blood disorder | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149395 | SCR_005777 | American Society of Hematology Video Library | 2026-08-10 09:32:39 | 0 | ||||||
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UCbase & miRfunc: Ultraconserved Sequences and miRNA Funciton Database Resource Report Resource Website |
UCbase & miRfunc: Ultraconserved Sequences and miRNA Funciton Database (RRID:SCR_005771) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. UCbase & miRfunc is a database of (i) human, mouse and rat microRNAs and (ii) Ultraconserved elements providing information about function, expression and correlation between these classes of non-coding RNAs and the disorders related to their aberrant expression. The genomics interface allows the user to explore where whole-genome collections of miRNAs and UCRs are located with respect to annotation sets such as band, disorders and known genes. The Blast interface provides a web tool for matching miRNAs/UCRs elements against any given sequence and providing specific functional information on the results. 481 Ultraconserved sequences (UCRs) longer than 200 bases were discovered in the genomes of human, mouse and rat. These are DNA sequences showing 100 percent identity among the human, mouse and rat genomes. UCRs are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs (miRNAs), the most extensively studied category of non-coding RNAs (ncRNAs). Here we present the first database which links UCRs and miRNAs with the related human disorders and genomic properties. | has parent organization: Ohio State University; Ohio; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03601 | SCR_005771 | UCbase & miRfunc | 2026-08-10 09:32:38 | 0 |
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