This track represents fixed retrocopies identified and annotated by RCPedia pipeline. Retrocopies are genomic copies generated by reverse transcription and reintegration of processed messenger RNAs (mRNAs). Because they originate from processed transcripts, retrocopies generally lack introns and may retain complete or partial open reading frames from their parental genes.
RCPedia contains more than 219,000 fixed retrocopies across 44 eukaryotic species, providing information on genomic coordinates, parental genes, genomic context, sequence, conservation and expression.
Each feature represents a fixed retrocopy locus in the corresponding reference genome. The track coordinates follow the UCSC Genome Browser 0-based coordinate system.
Fixed retrocopies were identified by aligning RefSeq mRNAs to reference genomes using LAST, followed by filtering based on alignment quality, genomic distance from the parental gene, exon-exon junctions and repetitive sequence content. Candidate loci were further filtered to reduce false positives arising from duplicated genes and large gene families.
For detailed methodology, please refer to the RCPedia FAQ.
RCPedia pipeline was developed by the Galante Lab and collaborators.
For questions or additional information, please visit the RCPedia Contact & Credits page.
Conceição HB, Mercuri RLV, de Castro MPM, Ohara DT, Guardia GDA, Galante PAF. RCPedia: A global resource for studying and exploring retrocopies in diverse species. Bioinformatics. 2024;40(9):btae530. doi:10.1093/bioinformatics/btae530.