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IMGT Overview: the Mouse T Cell Receptor Gamma TRG Genes

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IMGT Overview: the Mouse T Cell Receptor Gamma TRG Genes IMGT overview: the mouse Im T cell receptor gamma TRG genes Muno ene G Information G. Folch, D. Scaviner, 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 TRG genes How many functional How many TRG genes? organized? TRG genes? Chromosome 13 A3.1 TRG locus Potential repertoire The total number of T cell receptor The mouse TRG locus spans 200 kb and The potential TRG repertoire per haploid gamma TRG genes per haploid genome comprises 7 TRGV genes belonging to 5 genome comprises 14 functional genes: in Mus musculus laboratory mice is 15. subgroups, 4 TRGJ and 4 TRGC. The 7 TRGV, 4 TRGJ and 3 TRGC. TRG locus is organized in four clusters for the first one: 4 TRGV, 1TRGJ TRGV: 4 and 1 TRGC Overview A1 TRGJ: 1 for the others: 1 TRGV, 1 TRGJ and TRGC: 1 Number of genes Functional genes A2 5' 1 TRGC. A3.1 TRGV: 1 TRGV 7 7 TRGJ: 1 The third cluster is in inverted A3.2 3' 4 4 A3.3 TRGC: 1 orientation. TRGJ A4 4 3 TRGC: 1 Centromeric Telomeric TRGC A5 TRGJ: 1 V7 V4V6 V5 J1 C1 V3 J3 C3 C2 J2 V2 V1 C4 5' 3' Total 15 14 TRGV: 1 Enhancer Enhancer Enhancer J4 205 kb B1 TRGV: 1 41 kb 29 kb 36 kb 13 kb 0 50 100 150 200 kb B2 TRGJ: 1 The definitive IMGT nomenclature of the TRGC: 1 B3 mouse TRGV genes and the 205 kb C1 (15 genes) Gene exon/intron organization of the correspondence with the provisional C2 mouse TRGC genes nomenclature have been established. C3 EX1 EX2 EX3 TRGC1 5' 3' 3 kb The mouse (Mus musculus) 330 45 141 The mouse TRG genes and alleles and 1431 521 the corresponding IMGT reference TRG locus is located on polyA EX1 EX2 EX3 D1 TRGC2 5' 3' 3 kb sequences were provided to Mouse chromosome 13 A3.1 at 10.0 330 30 141 6 1423 564 387 D2.1 cM. Genome Informatics MGD in July 2002 EX1 EX2 EX3 polyA D2.2 TRGC3 5' 3' and are available in IMGT/GENE-DB. D2.3 330 45 141 3 391 387 13 EX1 EX2AEX2B EX3 TRGC4 5' 3' 9 kb 330 5445 140 4648 740 1825 Lefranc, M.-P. et al., In Silico Biology, 5, 45-60 (2005) Lefranc, M.-P. et al., Nucl. Acids Res., 33, D593-D597 (2005) 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 TRGV genes (germline Mus musculus (Mouse) TRGV2-TRGJ2 There is no known three dimensional CDR-IMGT lengths [8.6.12] M34971 structure of V-GAMMA domain or TR or rearranged) can be performed by CDR3-IMGT CDR1-IMGT GAMMA chain, but IMGT Colliers de IMGT/V-QUEST and analysis of the V-J CDR2-IMGT junctions by IMGT/JunctionAnalysis. Perles can be constructed with the tool available at the IMGT/3Dstructure-DB home page. Results of IMGT/V-QUEST CDR1-IMGT CDR2-IMGT CDR3-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.
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