Gene annotations for antibody genes

We use gene annotations (Ensembl GRCh37) to extract antibody genes. We extracted gene annotationsof BCR and TCR loci:

  • constant genes (labeled as IG_C_gene, Ensembl GRCh37)
  •  variable genes (labeled as IG_V_gene, Ensembl GRCh37)
  • diversity genes (labeled as IG_D_gene, Ensembl GRCh37)
  • joining genes (labeled as IG_J_gene, Ensembl GRCh37)

We exclude the BCR and TCR pseudogene (labeled as IG_C_pseudogene, IG_V_pseudogene, IG_D_pseudogene, IG_J_pseudogene, TR_C_pseudogene, TR_V_pseudogene, TR_D_pseudogene, and TR_J_pseudogene). In addition, we exclude the patch contigs HG1592_PATCH and HG7_PATCH as they are not part of Ensembl hg19 reference, and reads are not mapped on the patch contigs by the high throughput aligners .  After following the filtering steps described above, we extracted a total of 386 immune genes: 207 BCR genes and 179 TCR genes.  The gene annotations for antibody genes (GTF formatted file) are available here

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