ORFanBase
Deposit Search Mine

ORFanBase

ORFanBase is a comprehensive database of orphan genes and taxonomically restricted genes (TRGs) for investigators to explore the properties of these exceptional coding sequences in a comparative fashion, not limited to a handful of study groups, but globally across all domains of life and even viruses.

Sequences with limited taxonomic distribution which are also functionally essential to their species, represent a pattern wholly unexplored. We hope that through ORFanBase researchers would be able to find a rigorous analytical mathematical model for essential genes and proteins, so that we can estimate their probability of changing under known evolutionary processes.

ORFanBase Input Pipeline
ORFan gene of the Month

Chromosome 17



TP53 (Tumor Protein P53) is a Protein Coding gene. Diseases associated with TP53 include Li-Fraumeni Syndrome and Osteogenic Sarcoma. Among its related pathways are PI3K/AKT activation and Cell Cycle, Mitotic. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is TP73.
p53 gene
Top ten Genomes mined
Genomes Percentage of Orphans
Features & Highlights
ORfanMine

The ORFan Mine is a pipeline that finds the all ORFan genes for a given Genome. The non redundant database of NCBI is mined using a proprietary algorithm to curate all the ORFans genes of the given species.

ORFanID

ORFanID is a web-based software engine that identifies ORFan genes from the genomes of specified species or from a given list of DNA sequences. The scope of the search for orphan genes can be defined by the selection of the taxonomy level of interest. Detectable homologous sequences are found for candidate gene in the NCBI databases. From these findings the ORFanID engine identifies and depicts orphan genes. Results may be viewed and analyzed graphically for the purpose of scientific research and inquiry

Publications
ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes

Foster thy young: Enhanced prediction of orphan genes in assembled genomes

Rhizomal Reclassification of Living Organisms

Computational Identification of Novel Genes: Current and Future Perspectives

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Open questions: How many genes do we have?

More than just orphans: are taxonomically-restricted genes important in evolution?

Compressive genomics for protein databases

Is everything predetermined? Why physicists are reviving a taboo idea

The dark proteome: translation from noncanonical open reading frames

Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century

Retracing lineage history: time to emphasize genetic turnover

Next generation apomorphy: the ubiquity of taxonomically restricted genes

The ORFanage: an ORFan database