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IMGT annotation rules

IMGT annotation rules provide information on practical questions raised in the process of annotation and which may be useful to the IMGT/LIGM-DB users.

Annotation level in IMGT/LIGM-DB

Annotation level is indicated on the ID line at the top of the flat file.
To retrieve sequences according to the annotation level, go to the "Catalogue" module of IMGT/LIGM-DB.

Gene and allele names in IMGT/LIGM-DB

Limits of labels

Germline sequences

Rearranged sequences not yet annotated with IMGT/JunctionAnalysis

C-REGION in genomic DNA and cDNAs

CH3 (or CH4) exon and domain, and CHS

Hinge

Functionality

Functionality is shown between:

In IMGT Gene tables:

Partial sequences

Insertion in a sequence alignment

In case of an unusual insertion in a sequence alignment or display (Alignments of alleles, Protein displays, etc.), the 5' part of the sequence with the insertion is preferentially moved to the left to allow the insertion (if not possible, the 3' part of the sequence is moved to the right to allow the insertion). In both cases, the sequences with no insertion have a blank at that position.

Symbols for description of genes and alleles in IMGT Repertoire

#: rearranged
#c: rearranged cDNA
#g: rearranged genomic DNA
c: cDNA sequence
°: genomic DNA, but not known as being germline or rearranged.
~: genomic DNA rearranged in a cassette (for example in the IGH locus of chondrichthyes)
~VD,DJ: VD,DJ genomic DNA rearranged in the cassette.
~VD: VD genomic DNA rearranged in the cassette.
~VDJ: VDJ genomic DNA rearranged in the cassette.

(m): transcript of a membrane chain.
(s) : transcript of a secreted chain.
(st): sterile transcript.

MAP: Mapped reference sequences: "mapped" refers to sequences which have been obtained from clones (phages, cosmids, YACs...) either by subcloning or PCR, and does not apply to sequences obtained directly from genomic DNA.

Other symbols

(nd): not defined.

Rules for description of genes and alleles in IMGT Repertoire

In Alignments of alleles, when several alleles are shown, the nucleotide mutations and amino acid changes for a given codon are indicated in red letters. Nucleotides and amino acids at the 3' end of V-REGION, 5' end of J-REGION, or on either end of D-REGION, which may belong to the N-REGION, are shown in italics and in black. This representation also applies for sequencing errors.

Translation

Bibliographical references format

In IMGT Repertoire, the format for bibliographical references is the following:

Created:
26/06/2001
Last updated:
Friday, 27-May-2016 21:00:51 CEST
Authors:
Christèle Martinez-Jean and Marie-Paule Lefran
Editor:
Chantal Ginestoux
Scientific officer:
Marie-Paule Lefranc