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Genomic orientation

The 'genomic orientation' concept is a set of concepts that define the orientation of genomic instances (chromosome, locus and gene).

There are three concepts of 'genomic orientation', when each genomic instance is considered by itself, respectively:

The concept of orientation for genomic instances allows to characterize the orientation of:

two genomic instances relative to each other:

For a cluster outside the main locus (orphons), the genomic orientation of the cluster is only given on a chromosome, the orientation in a locus being irrelevant.

clone sequence (experimental data) or a contig relative to genomic instances:

A clone sequence results from experimental data and, theoretically, both DNA strands can be sequenced. By convention, the sequence of a DNA strand is given from 5' to 3'. It can correspond, depending on the sequenced DNA strand, to either the FWD or REV orientation on a chromosome, or to either the direct or opposite orientation on a locus.

The 'genomic orientation' concept is part of the 'ORIENTATION' axiom of IMGT-ONTOLOGY [1].

Reference:
[1] Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999) PMID: 10745995, LIGM:221 pdf