IMGT overview: the mouse Im T cell receptor alpha TRA genes Muno ene G Information N. Bosc, D. Scaviner, G. Folch, C. Ginestoux, V. Giudicelli and M.-P. Lefranc Tics system®
IMGT the international ImMunoGeneTics information system®, LIGM, UM2, CNRS UPR1142, IGH http://imgt.cines.fr 141 rue de la Cardonille, 34396 Montpellier Cedex 05, France - [email protected]
How are TRA genes How many functional How many TRA genes? organized? TRA genes?
Chromosome 14 C1 TRA locus Potential repertoire
The total number of T cell receptor Locus representation: Mouse (Mus musculus) TRA The potential TRA repertoire per haploid alpha TRA genes per haploid genome in on chromosome 14 C1 genome comprises 112-123 functional Mus musculus laboratory mice is 159 Centromeric genes (including 10 TRAV/DV): 73-84 1 (including 10 TRAV/DV: 8 rearranged 5' 200 TRAV (10 TRAV/DV), 38 TRAJ and 1 D-3
6 2 4-1 6-2 7D-2 7D-3 3-1 5-1 6-1 7-1 either to TRAJ or to TRDD, 2 assigned 4D-2 TRAC. 400 by homology).
7D-4 5D-3 5D-3 12D-3 6D-4 8D-1 9D-1 6D -5 10D 6D-6 11D 7D-5 12D-1 13D-1 14D-1 15D-1/DV6D-1 3D-2 9D-2 4D-3 5D-2 12D-2 13D-2 9D-3 Overview A1 The mouse (Mus musculus) 600 A2 Number of genes Functional genes A3 TRA locus is located on chromosome 14 C1 at 19.7 TRAV 98 73-84 B cM. 14D-2 15D-2/DV6D-2 3D-3 9D-4 4D-4 5D-4 6D-7 7D-6 13D-3 8D-2 16D/DV11 13D-4 14D-3/DV8 15D-3 7-2 4-2 6-3 7-3 800 TRAJ 60 38 5' TRAC 1 1 6-4 7-4 8-1 9-1 6-5 10 6-6 11 7-5 12-1 13-1 14-1 15-1/DV6-1 3-2 9-2 4-3 1000 C1 TRAV: 98 Total 159 112-123 TRAJ: 60 2 C2 TRAC: 1 5-2 12-2 9-3 5-3 12-3 13-2 14-2 15-2/DV6- 3-3 9-4 4-4/DV10 5-4 6-7/DV9 7-6 13-3 8-2 16 13-4/DV7 14-3 15-3 3-4 12-4 C3 1200 1,650 kb D1 The definitive IMGT nomenclature of the 3' (159 genes) 20 D2 13-5 17 18 19 21/DV12 TRDV1 22 TRDV2-1 TRDV2-2 23 1400 mouse TRAV genes and the correspondence with the provisional D3 60 TRAJ (on 64 kb) 61.... 35 15 ....5 4 3 21 nomenclature have been established. E1 The mouse TRA locus spans Telomeric E2.1 TRDJ TRDV4 1,650 kb and comprises, TRDV3 1 2 The mouse TRA genes and alleles and E2.2 3'
from 5' to 3', 98 TRAV genes 1700 kb the corresponding IMGT reference TRAC E2.3 TRDC TRDV5 E3 organized in 2 clusters TRDD1 TRDD2 sequences were provided to Mouse E4 upstream of 60 TRAJ genes Genome Informatics MGD in July 2002 0 50 100 150 200 kb E5 and of a single TRAC gene. and are available in IMGT/GENE-DB. 14
Lefranc, M.-P. et al., In Silico Biology, 5, 45-60 (2005) Bosc, N. et al., Dev. Comp. Immunol., 27, 465-497 (2003) Giudicelli, V. et al., Nucl. Acids Res., 33, D256-D261 (2005)
IMGT tools to analyse expressed variable genes
IMGT/V-QUEST IMGT Colliers de Perles IMGT/3Dstructure-DB IMGT/JunctionAnalysis IMGT/StructuralQuery Sequence analysis 2D representations 3D structures
Analysis of the TRAV genes (germline or Mus musculus (Mouse) TRAV_1 V-DOMAIN from Three-dimensional structures of 17 V- 2C (1g6r_A) rearranged) can be performed by CDR-IMGT lengths [6.7.10] ALPHA domains encoded by rearranged IMGT/V-QUEST and analysis of the V-J TRAV-TRAJ genes are available in CDR1-IMGT junctions by IMGT/JunctionAnalysis. IMGT/3D-structure-DB. Seven TR- CDR3-IMGT CDR2-IMGT ALPHA-BETA have been crystallised. Results of IMGT/V-QUEST
TR
1g6r
MHC-I
IMGT Colliers de Perles are according to the IMGT unique numbering for V- Jmol DOMAIN. Hydrogen bonds are shown The ALPHA chain is in spacefill (the BETA as green lines. chain and MHC-I are in wireframe). Lefranc, M.-P. et al., Dev. Comp. Immunol., 25, 55-77 (2003) Kaas, Q. et al., Nucl. Acids Res., 32, D208-210 (2004) Giudicelli, V. et al., Nucl. Acids Res., 32, W435-W440 (2004) Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005) Kaas, Q. and Lefranc, M.-P., In Silico Biol., 5, 0046 (2005)
IMGT initiator and coordinator: Marie-Paule Lefranc ([email protected]) Bioinformatics manager: Véronique Giudicelli ([email protected]) Computer manager: Denys Chaume ([email protected]) Interface design: Chantal Ginestoux ([email protected]) © Copyright 1995-2005 IMGT, the international ImMunoGeneTics information system® ©2005 C. Ginestoux and M.-P. Lefranc