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Fig. 4 | BMC Genomics

Fig. 4

From: Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

Fig. 4

a The genomic organization and sequence surrounding the deletion. A comparison of canine genome assembly (CanFam3.1), the allele without the deletion (NoDel) and with deletion (Del). The deletion (chr11: 40,854,701 - 40,863,575) is indicated as a grey area and starts in a genomic gap (NNN1, location chr11: 40,853,967 - 40,855,084) and ends around a region of IFNA7 (RefSeq annotation, location chr11: 40,862,587 - 40,863,150) and another genomic gap (NNN3, location chr11: 40,863,280 - 40,863,289). The correct location of IFNA7 was determined based on alignment of human IFNA7 gene to the improved canine sequence produced using Oxford Nanopore MinION sequencing. The grey dashed lines between NoDel and Del alleles indicate high sequence similarities in the deletion 5’and 3′ breakpoints. The deletion creates a fusion gene between an unannotated IFNA gene (IFNA?) and IFNA7, with an intact coding sequence encoding a protein identical to IFNA7 and being regulated by regulatory elements upstream IFNA?. The arrows indicate the transcriptional direction of the genes. b, c Multiple sequence alignments of 5′ and 3′ deletion breakpoints for the CanFam3.1 genome assembly and alleles with deletion (Del) and without deletion (NoDel). The 5′ deletion breakpoint is located in the gap on CanFam3.1 assembly, indicated with ‘n’s. d Protein alignments of IFNA?, IFNA7 and IFNA?/IFNA7 fusion proteins

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