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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].

IMGT locus map orientation

An IMGT locus representation is shown from 5' to 3'.
When centromeres are precisely chatacterized, the orientation of an IMGT locus on the chromosome is defined by the centromeric and telomeric ends.
If the locus has a FWD orientation on the chromosome, the map goes from Telomeric to Centromeric (locus on the short arm) or from Centromeric to Telomeric (locus on the long arm).
If the locus has a REV orientation on the chromosome, the map goes from Centromeric to Telomeric (locus on the short arm) or from Telomeric to Centromeric (locus on the long arm).

When centromeres are not precisely characterized, the orientation of an IMGT locus on the chromosome is defined by the telomeric ends:
Telomeric (FWD 5') : Telomeric end corresponding on the forward strand to the 5' end of the locus.
Telomeric (FWD 3') : Telomeric end corresponding on the forward strand to the 3' end of the locus.
If the locus has a FWD orientation on the chromosome, the map goes from Telomeric (FWD 5') to Telomeric (FWD 3').
If the locus has a REV orientation on the chromosome, the map goes from Telomeric (FWD 3') to Telomeric (FWD 5').

More information:

Chromosomal localizations http://www.imgt.org/IMGTrepertoire/LocusGenes/#h1_0 (IMGT Repertoire (IG) and (TR)).
Locus representations http://www.imgt.org/IMGTrepertoire/LocusGenes/#B (IMGT Repertoire (IG) and (TR)).

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