Structure-guided isoform identification for the human transcriptome

Folding scores from ColabFold for each transcript from a preliminary new build of the Comprehensive Human Expressed SequenceS (CHESS) database that contained a protein-coding sequence (CDS) that was under 1000aa in length. For transcripts already contained in the released CHESS v3.0 database, the identifier from that database is provided. If the transcript maps to a known gene locus X but is a novel isoform, it is shown with the identifier CHS.X.altY. If a transcript occurs at a novel locus X, the identifier is hypothetical.X.Y, where Y identifies the isoform number. Additional columns show the gene name, the RefSeq ID (release 110), the GENCODE ID (release 40), the predicted local distance difference test (pLDDT) (folding) score, and a flag indicating whether all intron boundaries (for multi-exon genes) are conserved in the mouse genome.

Folding scores and additional data for all Comprehensive Human Expressed SequenceS (CHESS) transcripts that match genes in the MANE v1.0 dataset, limited to protein sequences under 1000aa in length. Transcripts must overlap the annotated CDS of the MANE transcript to be included. Columns include: CHESS_ID_isoform, the CHESS identifier of the alternate isoform transcript; CHESS_ID_MANE, the CHESS identifier of the MANE transcript at the same locus; gene, the gene name; aa_length_isoform, the amino acid length of the alternate isoform’s CDS; aa_length_MANE, the amino acid length of the MANE transcript’s CDS; length_ratio, the ratio of the alternate isoform length to the MANE isoform length; pLDDT_isoform, the predicted folding score of the alternate isoform; pLDDT_MANE, the predicted folding score of the MANE isoform; pLDDT_ratio, the ratio of the alternate isoform folding score to the MANE isoform folding score; GTEx_samples_observed_isoform, the total number of GTEx samples where the alternate isoform was observed at least once; GTEx_samples_observed_MANE, the total number of GTEx samples where the MANE isoform was observed at least once; GTEx_top_tissue_name_isoform, the name of the tissue in which the alternate isoform was observed in the highest number of samples; GTEx_top_tissue_name_MANE, the name of the tissue in which the MANE isoform was observed in the highest number of samples; GTEx_top_tissue_TPM_isoform, the average TPM of the alternate isoform in the named tissue; GTEx_top_tissue_TPM_MANE, the observed transcripts per million (TPM) of the MANE isoform in the named tissue; introns_conserved_in_mouse_isoform, an indicator of whether introns are conserved between the alternate human isoform and any annotated isoform in the GRCm38 mouse reference genome; introns_conserved_in_mouse_MANE, an indicator of whether introns are conserved between the MANE human isoform and any annotated isoform in the GRCm38 mouse reference genome.

A filtered set of Comprehensive Human Expressed SequenceS (CHESS) transcripts compared to MANE according to the criteria detailed in the ‘Filtering MANE comparisons’ section of the Materials and methods. Uses the same column names as Supplementary file 2.