Pseudogenes are defined as defunct genomic loci with sequence similarity to functional genes but lacking coding potential due to the presence of disruptive mutations such as frame shifts and premature stop codons. The functional paralogs of pseudogenes are often referred to as parent genes.
Gathers information about transcribed pseudogenes (TPGs) and explores the relationships between TPG and its cognate gene with miRNA decoyed mechanisms and TPG-derived eSTIs. PseudoMap furnishes an expression profile for TPGs and their associated cognates as well as miRNA regulators of TPGs and their parental genes. Moreover, it permits TPG-derived esiRNAs detection and allows to build their interactions as well as their interacting gene targets in the human genome.
Provides information about the family structure of pseudogenes. The Pseudofam resource assists users in working about query tools, statistical summaries and sequence alignments. This database offers analyzing pseudogenes from a different perspective and integrates pseudogene families with other related datasets. It aims to better understand the genome remodeling processes.
Gathers information to assist scientists in research of pseudogene annotation. Pseudogene is a searchable repository for all protein-coding derived pseudogenes identified in the literature. This platform contains the following features: (1) integration of different identification methodologies; (2) flexible search capacity; (3) pre-computed search sets; (4) robust interaction with other databases; (5) temporal reconstruct-ability; and (6) simplified accessibility.
Contains genomic information relating to each pseudogene in a consistent manner. psiDR provides a variety of activity information for all the surveyed pseudogenes. It can supply potential targets for further experimental follow-up. It allows users to classify pseudogenes with various attributes, and permits identifying expressed pseudogenes. This database is useful to better understand the regulatory role of pseudogenes, especially in cancer and other developmental processes.
Gathers information about pseudogene annotation in human, worm and fly. psiCube compiles the data resulting from annotation and comparative analysis of pseudogenes using the GENCODE 10 for human pseudogene annotation and curated pseudogene annotation sets extending beyond WormBase WS220 and FlyBase 5.45 for worm and fly. The eight results files can be viewed directly from the web browser.
Provides information about processed pseudogenes location, potential function, base composition and gene structure in human and mouse. HOPPSIGEN is a nucleic acid database that can be useful in comparative and functional genomics. The database allows users to extract complete retroelement sequences or only part of them (5’-FL, CDE, 3’-FL, direct repeats, polyadenylation tracks) as well as processed pseudogenes of different GC-content or similarity percent. HOPPSIGEN also provides alignments and phylogenetic trees.