IMGT overview: the mouse Im delta TRD Muno ene G Information N. Bosc, 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 TRD genes How many How many TRD genes? organized? TRD functional genes?

Chromosome 14 C1 TRD locus Potential repertoire

The total number of T cell receptor Locus representation: Mouse (Mus musculus) TRA The potential TRD repertoire per haploid on chromosome 14 C1 delta TRD genes per haploid genome in genome comprises 10 functional genes

Mus musculus laboratory mice is 11 (21 Centromeric (19-20 with the TRAV/DV): 5 TRDV 1 including 10 upstream TRAV/DV). 5' 200 (14-15 with the TRAV/DV), 2 TRDD, 2 D-3

TRDJ and 1 TRDC. 6 2 4-1 6-2 7D-2 7D-3 3-1 5-1 6-1 7-1 4D-2 400 The mouse (Mus musculus)

A1

A2 TRD locus is located on Overview 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 A3 chromosome 14 C1 at 19.7 9D-3 600 Number of genes Functional genes cM. B TRDV 6 5

TRAV/DV: 10 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 TRAV/DV 10 9-10 TRDV: 5 TRDD 2 2 C1

TRDD: 2 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 5' 1000 TRDJ 2 2 C2 TRDJ: 2 3' 2 1 1 C3 TRDC: 1 TRDC

TRDV: 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 Total 21 19-20 D1 1200 275 kb D2 (21 genes) The definitive IMGT nomenclature of the 20 D3 13-5 17 18 19 21/DV12 TRDV1 22 TRDV2-1 TRDV2-2 23 1400 The mouse TRD spans 275 mouse TRDV genes and the E1 60 TRAJ (on 64 kb) correspondence with the provisional kb, nestled in the TRA locus. 61.... 35 15 ....5 4 3 21 E2.1 nomenclature have been established. E2.2 It comprises 6 TRDV (16 Telomeric TRDJ TRDV4 E2.3 including 10 upstream TRDV3 1 2 3' E3 The mouse TRD genes and alleles and TRAV/DV), 2 TRDD, 2 TRDJ, 1700 kb TRAC TRDC TRDV5 E4 1 TRDC. One TRDV is in TRDD1 TRDD2 the corresponding IMGT reference E5 inverted orientation in 3' of sequences were provided to Mouse 14 TRDC. 0 50 100 150 200 kb Genome Informatics MGD in July 2002 and are available in IMGT/-DB.

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/Collier de perles tool

Sequence analysis 2D representations Towards 3D structures

Analysis of the TRDV genes (germline Mus musculus (Mouse) TRDV-TRDD-TRDJ There is no known three dimensional or rearranged) can be performed by CDR-IMGT lengths [8.6.12] X13315 structure of V-DELTA domains or TR- CDR1-IMGT DELTA chain, but IMGT Colliers de IMGT/V-QUEST and analysis of the V-D- CDR2-IMGT CDR3-IMGT J junctions by IMGT/JunctionAnalysis. Perles can be constructed with the tool available at the IMGT/3Dstructure-DB Results of IMGT/V-QUEST home page. CDR1-IMGT CDR3-IMGT CDR2-IMGT

IMGT Colliers de Perles are according to the IMGT unique numbering for V- DOMAIN.

Giudicelli, V. et al., Nucl. Acids Res., 32, W435-W440 (2004) Lefranc, M.-P. et al., Dev. Comp. Immunol., 25, 55-77 (2003) Kaas, Q. et al., Nucl. Acids Res., 32, D208-210 (2004) Yousfi Monod, M. et al., Bioinformatics, 20, I379-I385 (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