Citing IMGT/GeneInfo: T-P. Baum(1), N. Pasqual(2), F. Thuderoz(1), V. Hierle(2), D. Chaume(3), M-P. Lefranc(3), E. Jouvin-Marche(2), P-N. Marche(2), J. Demongeot(1) IMGT/GeneInfo : enhancing V(D)J recombination database accessibility Nucleic Acids Research, 2004, Vol. 32, Database issue D51-D54.

Introduction

IMGT/GeneInfo provides information on data resulting from the mechanisms of V-J and V-D-J gene rearrangements in the T cell receptor (TR) loci of Homo sapiens and Mus musculus.

IMGT/GeneInfo query

IMGT/GeneInfo query is made in 2 steps through 2 pages:

1. IMGT/GeneInfo query page

In the first screen, select the species (Homo sapiens or Mus musculus), the locus (TRA or TRB), and the gene combination (V-V, V-J or V-D-J).

You can either choose combinations corresponding to existing rearrangements, or "virtual" non-existing combinations given for informational purposes, (e.g. V-V combinations).

Once the desired combination is selected, click on the "submit" button.

Submit

2. IMGT/GeneInfo gene choice page

Depending on your preceding choice, you can select the genes (V,D,J) for which information is queried, according to the gene name (official IMGT nomenclature or previous ones), or the relative position of the gene within the locus (number prefixing each gene name).

Once your selection is made, click on the submit button.

result

IMGT/GeneInfo results

The IMGT/GeneInfo results page is divided in seven parts.

Part one (your query) is a reminder of what you asked for (species, locus, genes).

Part two (info sources) is the source from which information was collected (e.g. AE000658 for the human TRA/TRD locus).

Part three (schematic drawing of the locus) is an image that corresponds to the selected combination of genes and that explains visually which gene types are concerned, how the genes and the RS are oriented, and how distances between genes were computed.

Part four (synthethic view of all TCR parameters) is a table that contains, for each gene, a summary with the gene name, the functionality (functional, pseudogene, open reading frame) and the nucleotide sequences for each RS part (heptamer, spacer, nonamer). It also contains the corresponding consensus sequence when it exists; the position relative to the first base of: TRAC for the TRA/TRD loci and TRBC2 for the TRB loci; and the genomic distance in base pairs between the genes of the selected combination, in their germline configuration (from V-last base to J-first base).

Part five (DNA sequences) corresponds to the sequences of the gene and, for a V gene, to its various parts (L-PART1, V-INTRON, V-EXON), sequences can be selected for copy and paste. A color code is associated to all information originating from the same gene to make it easier to see and remember.

Part six (Spliced V-(D)-J rearranged sequence) is the complete rearranged and spliced sequence.

Part seven (Link) is a link towards additional and complementary information in the IMGT site.

Synthetic view

For enquiries concerning IMGT/GeneInfo, please contact Thierry-Pascal BAUM

More information:
See also: