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Representative Genomic Sequence

Source: vignettes/articles/representative_sequence.Rmd
representative_sequence.Rmd

In MGI, selecting a representative genome sequence is crucial, as it influences the representative transcript and protein sequences. Priorities for selecting representative genomic sequences include gene model sequences from Ensembl, NCBI, and VISTA annotations. In MGI, gene model sequences define the genomic region using start and end coordinates from providers (source), including regions defined by regulatory feature providers.

MGI representative genomic sequence

For both protein-coding and noncoding RNA genes and pseudogenes, the representative genomic sequence is typically chosen from Ensembl or NCBI gene models. If both providers (source) offer gene models for a feature, the shorter model is selected to avoid extended read-through transcripts. In the absence of gene models, the longest associated GenBank genomic sequence is chosen. For regulatory regions, the gene model from Ensembl, NCBI, or VISTA is selected, with NCBI models preferred for enhancers when available.

Whether a sequence is considered representative is indicated by the variable is_mgi_rep. For example, in the MGI_BioTypeConflict.rpt report, this can be referenced by reviewing the vignette("biotype_conflicts").

MGI representative transcript and protein sequences

Representative transcript and protein sequences are selected algorithmically based on the representative genomic sequence. If the genomic sequence is from Ensembl, the longest Ensembl protein and corresponding transcript are chosen. If it is not from Ensembl, the longest transcript from the genomic gene model provider is selected, and, if coding, the longest associated protein from a provider hierarchy is chosen. If the representative genomic sequence is not a gene model from an annotation provider, both transcript and protein sequences (if coding) are selected from provider (source) hierarchies:

  • Transcript hierarchy: Longest of NM RefSeq > NR RefSeq > GenBank non-EST RNA > XM RefSeq > XR RefSeq > GenBank EST RNA.

  • Protein hierarchy: Longest of SWISS-PROT > RefSeq NP > TrEMBL > RefSeq XP.

References

  • Richard M Baldarelli, Cynthia L Smith, Martin Ringwald, Joel E Richardson, Carol J Bult, Mouse Genome Informatics Group , Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse, Genetics, Volume 227, Issue 1, May 2024, iyae031. doi:10.1093/genetics/iyae031.