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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
RegPrecise
 
Resource Report
Resource Website
50+ mentions
RegPrecise (RRID:SCR_002149) RegPrecise data or information resource, database Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. regulon, genome, transcription factor, gene, operon, transcription factor binding site, taxonomy, rna, effector, pathway, ortholog, function, FASEB list is listed by: OMICtools
has parent organization: Lawrence Berkeley National Laboratory
Department of Energy ;
NSF DBI-0850546
PMID:24175918 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01869 SCR_002149 2026-02-14 02:06:08 80
Primate Orthologous Exon Database
 
Resource Report
Resource Website
1+ mentions
Primate Orthologous Exon Database (RRID:SCR_002065) Primate Orthologous Exon Database data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms. alternative splicing, transcript isoform, ortholog, exon, gene, rna-seq, primate, genome is listed by: OMICtools
has parent organization: University of Chicago; Illinois; USA
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01895 SCR_002065 2026-02-14 02:06:06 1
DBASS
 
Resource Report
Resource Website
1+ mentions
DBASS (RRID:SCR_002107) DBASS data or information resource, database A database of new exon boundaries induced by pathogenic mutations in human disease genes. pathogen, mutation, disease gene, database, splice, mutation pattern, nucleotide structure, exon boundary, aberrant 3' splice site, aberrant 5' splice site is listed by: OMICtools
has parent organization: University of Southampton; Southampton; United Kingdom
PMID:20929868
PMID:16963498
PMID:16141195
PMID:17576681
Free, Freely available OMICS_01883 http://www.dbass.org.uk/ SCR_002107 2026-02-14 02:06:07 2
COSMIC - Catalogue Of Somatic Mutations In Cancer
 
Resource Report
Resource Website
1000+ mentions
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) COSMIC data or information resource, database Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Cancer Wellcome Trust 077012/Z/05/Z PMID:20952405 Free nif-0000-02690, biotools:cosmic, OMICS_00082 http://www.sanger.ac.uk/perl/CGP/cosmic
https://bio.tools/cosmic
SCR_002260 Catalogue Of Somatic Mutations In Cancer 2026-02-14 02:06:06 4486
Autophagy Database
 
Resource Report
Resource Website
10+ mentions
Autophagy Database (RRID:SCR_002671) Autophagy DB, AutophagyDB data or information resource, database Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. autophagy, protein, homolog, ortholog, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Tokyo; Tokyo; Japan
Japanese Ministry of Education Culture Sports Science and Technology MEXT PMID:20972215 Free, Available for download, Freely available OMICS_03306, biotools:the_autophagy_database, r3d100012565 https://bio.tools/the_autophagy_database
https://doi.org/10.17616/R3J786
SCR_002671 2026-02-14 02:05:48 17
Greengenes
 
Resource Report
Resource Website
1000+ mentions
Greengenes (RRID:SCR_002830) data or information resource, database Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. microbiome, rrna, 16s rrna, gene, dna, rna, chimera, alignment, taxonomic classification, taxonomy, FASEB list is listed by: OMICtools
is listed by: re3data.org
is listed by: Human Microbiome Project
has parent organization: Lawrence Berkeley National Laboratory
Department of Energy contract DE-AC02-05CH11231 PMID:16820507 Free, Freely available OMICS_01512, r3d100010549, nif-0000-02927 http://greengenes.lbl.gov
https://doi.org/10.17616/R36C8G
SCR_002830 2026-02-14 02:05:48 3125
DOMINE: Database of Protein Interactions
 
Resource Report
Resource Website
1+ mentions
DOMINE: Database of Protein Interactions (RRID:SCR_002399) DOMINE data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014) domain-domain interaction, prediction, protein domain, interaction, protein domain interaction, protein, domain, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: Pfam
has parent organization: University of Texas at Dallas; Texas; USA
PMID:21113022
PMID:17913741
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01906, nif-0000-02758, biotools:domine https://bio.tools/domine SCR_002399 Database of Protein Domain Interactions 2026-02-14 02:06:07 1
DBTBS
 
Resource Report
Resource Website
10+ mentions
DBTBS (RRID:SCR_002345) DBTBS data or information resource, database Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins. gene, gene regulatory network, transcription factor binding site, transcription factor, regulated operon, motif, promoter, motif conservation is listed by: OMICtools
has parent organization: University of Tokyo; Tokyo; Japan
Japanese Ministry of Education Culture Sports Science and Technology MEXT PMID:17962296
PMID:14681362
PMID:11125112
Acknowledgement requested nif-0000-02736, OMICS_01859 SCR_002345 DBTBS: a database of Bacillus subtilis promoters and transcription factors., DBTBS: a database of Bacillus subtilis promoters and transcription factors 2026-02-14 02:05:39 30
eggNOG
 
Resource Report
Resource Website
1000+ mentions
eggNOG (RRID:SCR_002456) eggNOG data or information resource, database A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014) orthologous gene, ortholog, gene, function, FASEB list is listed by: OMICtools
has parent organization: European Molecular Biology Laboratory
BMBF ;
European Union FP6
PMID:24297252
PMID:22096231
Free, Available for download, Freely available nif-0000-02789, OMICS_01689 SCR_002456 eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups, eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups), evolutionary genealogy of genes: Non-supervised Orthologous Groups 2026-02-14 02:06:10 3564
SuperTarget
 
Resource Report
Resource Website
10+ mentions
SuperTarget (RRID:SCR_002696) SuperTarget data or information resource, database Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. drug metabolism, drug, cytochrome p450, ontology, pathway, target, compound, cytochrome, drug target, protein, side effect, protein-protein interaction is listed by: OMICtools
has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany
BMBF MedSys 0315450A;
DFG RTG Computational Systems Biology GRK1772;
DFG IRTG Systems Biology of Molecular Networks GRK1360;
European Union SynSys ;
NIGMS GM070064
PMID:22067455
PMID:17942422
Free, Freely available r3d100012195, nif-0000-00416, OMICS_01591 http://bioinf-tomcat.charite.de/supertarget/
http://bioinformatics.charite.de/supertarget
https://doi.org/10.17616/R3TM0F
SCR_002696 2026-02-14 02:05:48 28
Binding MOAD
 
Resource Report
Resource Website
10+ mentions
Binding MOAD (RRID:SCR_002294) Binding MOAD data or information resource, database Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. drug, enzymatic, affinity, binding, binding-affinity, biological, chemical, cheminformatic, crystal, crystallography, intermolecular interaction, signaling pathway, ligand, protein, ligand-protein binding, protein crystal structure, protein-ligand, protein-ligand complex is used by: Drug Design Data Resource
is listed by: OMICtools
is listed by: 3DVC
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
has parent organization: University of Michigan; Ann Arbor; USA
MCB 546073 PMID:18055497
PMID:16168689
PMID:15971202
Free, Public, Acknowledgement requested OMICS_01900, nif-0000-21048 SCR_002294 BindingMOAD.org, Binding Mother of All Databases 2026-02-14 02:06:09 18
EDAS - EST-Derived Alternative Splicing Database
 
Resource Report
Resource Website
1+ mentions
EDAS - EST-Derived Alternative Splicing Database (RRID:SCR_002449) EDAS data or information resource, database Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test. alternative splicing, gene, protein, mrna, est, exon, intron, rat, dog is listed by: OMICtools
has parent organization: Moscow State University; Moscow; Russia
PMID:16909834 Free, Freely available nif-0000-02786, OMICS_01885 SCR_002449 EDAS: EST Derived Alternative Splicing Database, EST Derived Alternative Splicing Database 2026-02-14 02:06:07 1
CASBAH
 
Resource Report
Resource Website
1+ mentions
CASBAH (RRID:SCR_002728) CASBAH data or information resource, database Database which contains information pertaining to all currently known caspase substrates. protein, caspase substrate, caspase is listed by: OMICtools
has parent organization: Trinity College Dublin; Dublin; Ireland
PMID:17273173 OMICS_03304 SCR_002728 The CAspase Substrate dataBAse Homepage, The CASBAH, CAspase Substrate dataBAse Homepage 2026-02-14 02:05:48 4
NMR metabolomics database of Linkoping
 
Resource Report
Resource Website
1+ mentions
NMR metabolomics database of Linkoping (RRID:SCR_002758) MDL data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules. nuclear magnetic resonance, metabolomics, mac os x, unix/linux, windows is listed by: OMICtools
has parent organization: Linkoping University; Linkoping; Sweden
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02853 SCR_002758 MDL - The Magnetic Resonance Metabolomics Database, Magnetic Resonance Metabolomics Database 2026-02-14 02:05:48 1
ConsensusPathDB
 
Resource Report
Resource Website
500+ mentions
ConsensusPathDB (RRID:SCR_002231) CPDB data or information resource, database An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered. gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metabolite, FASEB list is listed by: OMICtools
is related to: BIND
is related to: BioCarta Pathways
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: CORUM
is related to: Database of Interacting Proteins (DIP)
is related to: DrugBank
is related to: HPRD - Human Protein Reference Database
is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism
is related to: Integrating Network Objects with Hierarchies
is related to: InnateDB
is related to: IntAct
is related to: KEGG
is related to: MINT
is related to: MIPS Mammalian Protein-Protein Interaction Database
is related to: MatrixDB
is related to: NetPath
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: PDZBase
is related to: Pathway Interaction Database
is related to: PIG - Pathogen Interaction Gateway
is related to: PINdb
is related to: PharmGKB
is related to: PhosphoPOINT
is related to: PhosphoSitePlus: Protein Modification Site
is related to: Reactome
is related to: Small Molecule Pathway Database
is related to: SignaLink
is related to: SPIKE
is related to: Therapeutic Target Database
is related to: WikiPathways
has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany
European Union HEALTH-F4-2007-200767 PMID:23143270
PMID:21071422
PMID:20847220
PMID:18940869
Free, Freely available nif-0000-02684, OMICS_01903, r3d100012822 https://doi.org/10.17616/R3HF8Z SCR_002231 ConsensusPathDB, ConsensusPathDB-human 2026-02-14 02:06:06 667
RefSeq
 
Resource Report
Resource Website
10000+ mentions
RefSeq (RRID:SCR_003496) data or information resource, database Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools is listed by: OMICtools
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: BeetleBase
is related to: EcoGene
is related to: INSDC
is related to: HFV Database
is related to: RefSeqGene
is related to: NCBI Protein Database
is related to: RefSeqGene
is related to: UniParc at the EBI
is related to: NCBI Nucleotide
is related to: UniParc
is related to: ProRepeat
is related to: NCBI Virus
is related to: Codon and Codon-Pair Usage Tables
is related to: RefSeq non-redundant proteins
has parent organization: NCBI
PMID:24316578
PMID:24259432
PMID:22121212
PMID:18927115
PMID:17130148
PMID:15608248
Free, Available for download, Freely available SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 ftp://ftp.ncbi.nlm.nih.gov/refseq
https://bio.tools/refseq
https://doi.org/10.17616/R3HP70
SCR_003496 RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI 2026-02-14 02:05:50 18049
PReMod
 
Resource Report
Resource Website
10+ mentions
PReMod (RRID:SCR_003403) PReMod data or information resource, database Database that 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 / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data. cis-regulatory module, genome, transcription factor binding site, chromosome, module, predict, gene is listed by: OMICtools
has parent organization: McGill University; Montreal; Canada
PMID:17148480 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03334, OMICS_01873 SCR_003403 Predicted Regulatory Modules 2026-02-14 02:06:14 11
mtDB - Human Mitochondrial Genome Database
 
Resource Report
Resource Website
50+ mentions
mtDB - Human Mitochondrial Genome Database (RRID:SCR_002945) mtDB data or information resource, database A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences. human genome, mitochondrial dna, sequence, variant, population genetics, coding region, polymorphic site, population, mitochondrial sequence, mitochondrial polymorphism, FASEB list is listed by: OMICtools
has parent organization: Uppsala University; Uppsala; Sweden
Swedish Research Council PMID:16381973 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02994, OMICS_01642 SCR_002945 Human Mitochondrial Genome Database 2026-02-14 02:06:09 58
miRNAMap
 
Resource Report
Resource Website
100+ mentions
miRNAMap (RRID:SCR_003156) miRNAMap data or information resource, database A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA. microrna, genome, FASEB list is listed by: OMICtools
has parent organization: National Chiao Tung University; Hsinchu; Taiwan
PMID:18029362
PMID:16381831
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03138, OMICS_00408 SCR_003156 2026-02-14 02:06:13 246
ProNIT
 
Resource Report
Resource Website
10+ mentions
ProNIT (RRID:SCR_003431) ProNIT data or information resource, database Database that provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. It contains the properties of the interacting protein and nucleic acid, bibliographic information and several thermodynamic parameters such as the binding constants, changes in free energy, enthalpy and heat capacity. interaction, protein, nucleic acid, protein-nucleic acid interaction, thermodynamic, binding constant, free energy, enthalpy, heat capacity is listed by: OMICtools Japan Society for the Promotion of Science ;
Advanced Technology Institute Inc.
PMID:16381846
PMID:11987161
PMID:11724731
Free, Freely available nif-0000-03347, OMICS_00541 http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html, http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html SCR_003431 2026-02-14 02:05:44 11

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