single locus complement [GENO_0000516]

A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism. A ‘complement’ refers to an exhaustive collection of all objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a ‘single locus complement’ is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. The fact that we are counting how many copies of the same sequence exist in a genome, as opposed to how many of the same feature, is what sets feature-level concepts like ‘single locus complement’. apart from sequence-level concepts like ‘copy number complement’. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The ‘copy number complement’ for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the ‘single locus complement’ at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.

Open single locus complement in VFB

VFB Term Json

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            "short_form": "GENO_0000516",
            "label": "single locus complement"
        },
        "description": [
            "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism."
        ],
        "comment": [
            "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets  feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene.  The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome.  But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus."
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