Biotypes

BamQuery biotype classification is based on Ensembl and Repeat_Masker annotations.

  1. Protein-coding Regions: peptide harbored in a transcript containing an open reading frame (ORF)

    In this category the following transcripts types in gencode annotations are considered as Protein-coding Regions:
    Protein_coding, IG genes and TR genes.

    • 5’UTR: peptide harbored into the 5’ UnTranslated Region of the transcript

    • 3’UTR: peptide harbored into the 3’ UnTranslated Region of the transcript

    • In_frame: peptide harbored in the CDS of the transcript, and for which at least 50% of its sequence is In Frame with the protein

    • Frameshift: peptide harbored in the CDS of the transcript, and for which at least 50% of its sequence is Frameshift with the protein

    • CDS: Peptide containing a SNP harbored in the CDS of the transcript. Peptide that is not In_Frame or Frameshift with the protein

    • Junctions: peptide harbored in the junctions (Intron-CDS, CDS-3’UTR, 5’UTR-CDS) of the transcript

    • Other coding regions: peptide harbored in exons into Immunoglobulin gene (IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene) or T cell receptor genes (TR_C_gene, TR_D_gene, TR_J_gene, TR_V_gene)

  2. Non-coding RNAs: peptide harbored in a transcript that doesn’t containing an open reading frame (ORF)

    In this category the following transcripts types in gencode annotations are considered as Non-coding RNAs:
    IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene, IG_pseudogene, Mt_rRNA, Mt_tRNA, TEC, TR_J_pseudogene, TR_V_pseudogene, lncRNA, miRNA, misc_RNA, non_stop_decay, nonsense_mediated_decay, polymorphic_pseudogene, processed_pseudogene, processed_transcript, pseudogene, rRNA, rRNA_pseudogene, retained_intron, ribozyme, sRNA, scRNA, scaRNA, snRNA, snoRNA, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, translated_processed_pseudogene, translated_unprocessed_pseudogene, unitary_pseudogene, unprocessed_pseudogene, vault_RNA.

    • Non_coding Exons: peptide harbored in the exons of the transcript

    • Non_coding Junctions: peptide harbored in the junctions (Exon-Intron, Intron-Exon) of the transcript

  3. Intergenic Regions: peptide harbored in a non-annotated region

    • Intergenic Regions: peptide harbored in a non-annotated region either in Ensembl or in Repeat Masker

  4. Intronic Regions: peptide harbored in a intronic region of any type transcripts

    • Intronic Regions: peptide harbored in an intronic region of any type of transcript, whether protein-coding or non-coding RNA

  5. EREs: peptide harbored in a ERE (based on Repeat Masker annotations)

    • LINE: peptide harbored in a ERE class LINE

    • LTR: peptide harbored in a ERE class LTR

    • SINE: peptide harbored in a ERE class SINE

    • Antisense_EREs: peptide harbored in the antisense of a ERE of any class

    • Other EREs: peptide harbored in a ERE of other class (DNA, RC, RNA, Satellite, Simple_repeat, Unknown, Retroposon, Low_complexity, rRNA, scRNA, snRNA, srpRNA, tRNA)