IMGT®, the international ImMunoGeneTics information system®

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 '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.
  Examples of forward (FWD) and reverse (REV) locus
• 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).
  Example of Human IGK locus with genes in both direct or opposite orientation.

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.

• a clone sequence or a contig on a chromosome. Depending on the sequenced DNA strand, a clone sequence or a contig can be in:
  • forward (FWD) orientation on the chromosome (sequence in the same orientation as FWD),
  • reverse (REV) orientation on a chromosome (sequence in same orientation as REV).
• a clone sequence or a contig on a locus. Depending on the sequenced DNA strand, a clone sequence or a contig can be in:
  • direct orientation (clone sequence in same orientation as the locus),
  • opposite orientation (clone sequence in opposite orientation relative to the locus).
  For the orientation of a clone or a contig on a locus it is necessary to know, either the orientation of at least one gene (of that clone or contig) in the locus, or the respective positions of two genes (of that clone or contig) in the 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)).