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 'chromosome orientation' concept have two exclusive instances:
- forward (or 'Watson') (FWD) orientation: from pter (short arm telomeric end) to qter (long arm telomeric end),
- reverse (REV) orientation: from qter to pter.
- The 'locus orientation' concept has a unique instance: 5' → 3', characterized by the orientation of transcription of the C-GENE(s) and/or the orientation of transcription of the majority of the genes in the locus.
- The 'gene orientation' concept has a unique instance: 5' → 3'. It is by convention the orientation of transcription of the gene.
The concept of orientation for genomic instances allows to characterize the orientation of:
two genomic instances relative to each other:
- a locus or a gene (included an orphon) on a chromosome. A locus, or a gene, (including an orphon) can be in:
- forward (FWD) orientation on a chromosome (locus or gene orientation 5' → 3' in same orientation as FWD),
- reverse (REV) orientation on a chromosome. This orientation is shown by arrows in Chromosomal localizations.
- a gene or a cluster (set of genes, except for orphons) in a locus. A gene or a cluster can be in:
- direct orientation (same orientation as the locus),
- opposite orientation (opposite orientation indicated by an horizontal arrow in Locus representations).
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.