IMGT, the international I ImMunoGeneTics information ... · The T cell receptor FactsBook, Academic...
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©2006 C. Ginestoux and M.-P. Lefranc IMGT founder and director: Marie-Paule Lefranc ([email protected]) Bioinformatics manager: Véronique Giudicelli ([email protected]) Computer manager: Patrice Duroux ([email protected]) Interface design: Chantal Ginestoux ([email protected]) © Copyright 1995-2006 IMGT, the international ImMunoGeneTics information system® IMGT Index IMGT Scientific chart IMGT Education IMGT Medical page IMGT Veterinary page IMGT Bloc-notes Lefranc, M.-P., Nucl. Acids Res., 33, D593-D597 (2005) IMGT Other Web resources IMGT Repertoire 2D Colliers de Perles 3D representations FR-IMGT and CDR-IMGT lengths... E V Q L Q E S G T C T V S G G S I S S G D Y Y W S W Y R G W I G Y I Y Y S G S T Y Y N P S M S V D T S K N H F W L N Y C A R S . . . . . _____________CDR2- 53 54 55 56 57 58 59 60 L V S F Y N N E CTG GTT TCC TTT TAT AAT AAT GAA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Description of mutations |c334 | t30 |t270 |c334 | |c334>t| (if IGKV1-12*02) t30>c|t270>c|c334>t| (if IGKV1D-12*02) a123 ,*41 |a326 ,N109 | a123>g,*41>W|a326>g,N109>S| |a326 ,N109 | QVQLVQSGA.EVKKPGASVKVSCKAS GYTFTSYD.... INWVRQA QVQLVQSGA.EVKKPGASVKVSCKAS GYTFTSYG.... ISWVRQA QVQLVQSGA.EVKKPGASVKVSCKVS GYTLTELS.... MHWVRQA QMQLVQSGA.EVKKTGSSVKVSCKAS GYTFTYRY.... LHWVRQA QVQLVQSGA.EVKKPGASVKVSCKAS GYTFTSYY.... MHWVRQA QMQLVQSGP.EVKKPGTSVKVSCKAS GFTFTSSA.... VQWVRQA QVQLVQSGA.EVKKPGSSVKVSCKAS GGTFSSYA.... ISWVRQA KSGASVKVSCSFS GFTITSYG.... IHWVQQS EVQLVQSGA.EVKKPGATVKISCKVS GYTFTDYY.... MHWVQQA QITLKESGP.TLVKPTQTLTLTCTFS GFSLSTSGVG.. VGWIRQP QVTLKESGP.VLVKPTETLTLTCTVS GFSLSNARMG.. VSWIRQP QVTLRESGP.ALVKPTQTLTLTCTFS GFSLSTSGMC.. VSWIRQP EVQLVESGG.GLVQPGGSLRLSCAAS GFTFSSYW.... MSWVRQA Pommié, C. et al., J. Mol. Recognit., 17, 17-32 (2004) TRGV TRGV Reference subgroup gene name Fct R T P sequences 1 TRGV1 ORF(11) - - - V1 TRGV2 F + + + V2 (F) + + + Vgamma1.9 TRGV3 F + + + V3 F + + + Vgamma1.1 TRGV4 F + + + V4 F + + + V4 TRGV5 F + + + V5 TRGV5P P(2) - - - V5P Lefranc, M.-P., Nucl. Acids Res., 33, D593-D597 (2005) Sequences Genome 2D and 3D structures Alignments of alleles Tables of alleles Protein displays Allotypes, Isotypes... Lefranc, M.-P. et al., In Silico Biology, 4, 17-29 (2004) Lefranc, M.-P. et al., In Silico Biology, 5, 45-60, Epub 2005, 5, 0006 (2004) Lefranc, M.-P., Molecular Immunol., 40, 647-660 (2004) Chromosomal localizations Locus representations Gene tables... Gm 5*;3;.. Gm 5,10,11,13,14,26,27;3;.. Gm 5*;3;23 Gm 5,10,11,13,14, 26,27;3;23 Gm 21*;1,17;.. Gm 21,26,27,28;1,17;.. Gm 21*;1,2,17;.. Gm 21,26,27,28;1,2,17;.. Gm 5*;1,17;.. Gm 5,10,11,13,14,26,27;1,17;.. Gm 6,24*;1,17;.. Gm 5,6,11,24,26;1,17;.. Gm 6*;1,17;.. Gm 5,6,10,11,14,26,27;1,17;.. IMGT/LIGM-DB Other accesses SRS: EBI (UK), Institut Pasteur (France), CEINGE (Italy), CU (USA), DDBJ (Japan), DIC (India), IUBio (USA) FTP: weekly releases: CINES (Montpellier, France) and EBI (UK) BLAST: CINES (France), EBI (UK), Institut Pasteur (France) LinkOut (nucleotides) at NCBI (USA) IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) created in 1989 by Marie-Paule Lefranc (Université Montpellier II, CNRS), a European project since 1992 provides a common access to all Immunogenetics data is the international reference in Immunogenetics and Immunoinformatics based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules consists of databases, interactive tools and Web resources IMGT, the international ImMunoGeneTics information system ® F. Ehrenmann, V. Giudicelli, C. Ginestoux, G. Folch, J. Jabado-Michaloud, Q. Kaas, P. Duroux, M.-P. Lefranc Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142, Montpellier (France) I m Muno Gene Tics Information system® http://imgt.cines.fr Books Lefranc, M.-P. and Lefranc, G., The Immunoglobulin FactsBook, Academic Press, 458 pages (2001) Lefranc, M.-P. and Lefranc, G., The T cell receptor FactsBook, Academic Press, 398 pages (2001) IMGT databases IMGT/LIGM-DB IG and TR from human and 150 other vertebrate species LIGM Lefranc, M.-P., Nucl. Acids Res., 33, D781-D784 (2006) IMGT/PRIMER-DB IG and TR oligonucleotides LIGM and EUROGENTEC Lefranc, M.-P., Nucl. Acids Res., 33, D593-D597 (2005) IMGT/MHC-DB HLA and MHC/NHP ANRI, BPRC and EBI Robinson, J. et al., Nucl. Acids Res., 31, 311-314 (2003) IMGT/GENE-DB IMGT/LIGM-DB IMGT/MHC IMGT/GENE-DB The international reference for IG and TR gene and allele nomenclature LIGM Lefranc, M.-P., Nucl. Acids Res., 33, D256-D261 (2005) Lefranc, M.-P. In: Antibody engineering: methods and protocols (Lo B.K.C. ed), 248, 27-49 (2003) Lefranc, M.-P. and Lefranc, G. In: Molecular Biology of B cells (Honjo, T., Alt F.W. and Neuberger M.S., eds) pp. 37-59 (2004) IMGT/3Dstructure-DB IG, TR, MHC and RPI structures LIGM Kaas, Q. et al., Nucl. Acids Res., 32, D208-D210 (2004) 2D and 3D structures Sequences Genome IMGT tools IMGT/ JunctionAnalysis IMGT/V-QUEST Sequence analysis Genome analysis 3D structure analysis IMGT/DomainGapAlign IMGT/Collier-de-Perles IMGT/StructuralQuery LIGM Kaas, Q. and Lefranc, M.-P., In Silico Biology, 5, 505-528, Epub 2005, 5 0046 (2005) IMGT/LocusView... LIGM Lefranc, M.-P., Molecular Immunology, 40, 647-660 (2004) IMGT/GeneInfo TIMC and ICH (Grenoble) Baum, P. et al., BMC Bioinformatics, 7, 224 (2006) IMGT/GeneFrequency LIGM Lefranc, M.-P. et al., In Silico Biology, 5, 45-60, Epub 2005, 5, 0006 (2004) IMGT/V-QUEST LIGM Giudicelli, V. et al., Nucl. Acids Res., 32, W435-W440 (2004) IMGT/JunctionAnalysis LIGM Yousfi Monod, M. et al., Bioinformatics 20 Supplement, 1, I379-I385 (2004) IMGT/Allele-Align LIGM Lefranc, M.-P., Molecular Immunology, 40, 647-660 (2004) IMGT/PhyloGene LIGM Elemento, O. and Lefranc, M.-P., Dev. Comp. Immunol., 27, 763-779 (2003)
Transcript of IMGT, the international I ImMunoGeneTics information ... · The T cell receptor FactsBook, Academic...
©2006 C. Ginestoux and M.-P. Lefranc
IMGT founder and director: Marie-Paule Lefranc ([email protected])Bioinformatics manager: Véronique Giudicelli ([email protected])Computer manager: Patrice Duroux ([email protected])Interface design: Chantal Ginestoux ([email protected])© Copyright 1995-2006 IMGT, the international ImMunoGeneTics information system®
IMGT IndexIMGT Scientific chartIMGT EducationIMGT Medical pageIMGT Veterinary pageIMGT Bloc-notes
Lefranc, M.-P., Nucl. Acids Res., 33, D593-D597 (2005)
IMGT Other Web resources
IMGT Repertoire
2D Colliers de Perles3D representationsFR-IMGT and CDR-IMGT lengths...
1 EVQLQESG T
23 CTV
26 SGGSIS
S GDYY
39 WS
41 WYR G
WIG
55 YIYYS
G ST
66 YYNPS M
S
80 VDT
SK 85N
HFW
89 LN Y
104 CARS
.
.
.
.
.
_____________CDR2- 53 54 55 56 57 58 59 60 L V S F Y N N E
CTG GTT TCC TTT TAT AAT AAT GAA
--- --- --- --- --- --- --- ---
--- --- --- --- --- --- --- ---
Description of mutations |c334 |t30 |t270 |c334 | |c334>t| (if IGKV1-12*02)
t30>c|t270>c|c334>t| (if IGKV1D-12*02)a123 ,*41 |a326 ,N109 |a123>g,*41>W|a326>g,N109>S| |a326 ,N109 |
QVQLVQSGA.EVKKPGASVKVSCKAS GYTFTSYD.... INWVRQAQVQLVQSGA.EVKKPGASVKVSCKAS GYTFTSYG.... ISWVRQAQVQLVQSGA.EVKKPGASVKVSCKVS GYTLTELS.... MHWVRQAQMQLVQSGA.EVKKTGSSVKVSCKAS GYTFTYRY.... LHWVRQAQVQLVQSGA.EVKKPGASVKVSCKAS GYTFTSYY.... MHWVRQAQMQLVQSGP.EVKKPGTSVKVSCKAS GFTFTSSA.... VQWVRQAQVQLVQSGA.EVKKPGSSVKVSCKAS GGTFSSYA.... ISWVRQA KSGASVKVSCSFS GFTITSYG.... IHWVQQSEVQLVQSGA.EVKKPGATVKISCKVS GYTFTDYY.... MHWVQQAQITLKESGP.TLVKPTQTLTLTCTFS GFSLSTSGVG.. VGWIRQPQVTLKESGP.VLVKPTETLTLTCTVS GFSLSNARMG.. VSWIRQPQVTLRESGP.ALVKPTQTLTLTCTFS GFSLSTSGMC.. VSWIRQPEVQLVESGG.GLVQPGGSLRLSCAAS GFTFSSYW.... MSWVRQA
Pommié, C. et al., J. Mol. Recognit., 17, 17-32 (2004)
TRGV TRGV Referencesubgroup gene name Fct R TP sequences
1 TRGV1 ORF(11) - - - V1 TRGV2 F + ++ V2 (F) + ++ Vgamma1.9 TRGV3 F + ++ V3 F + ++Vgamma1.1 TRGV4 F + ++ V4 F + ++ V4 TRGV5 F + ++ V5 TRGV5P P(2) - - - V5P
Lefranc, M.-P., Nucl. Acids Res., 33, D593-D597 (2005)
Sequences
Genome
2D and 3D structures
Alignments of alleles
Tables of alleles
Protein displays
Allotypes, Isotypes...
Lefranc, M.-P. et al., In Silico Biology, 4, 17-29 (2004)
Lefranc, M.-P. et al., In Silico Biology, 5, 45-60, Epub 2005, 5, 0006 (2004)
Lefranc, M.-P., Molecular Immunol., 40, 647-660 (2004)
Chromosomal localizations
Locus representations
Gene tables...
Gm 5*;3;.. Gm 5,10,11,13,14,26,27;3;..
Gm 5*;3;23 Gm 5,10,11,13,14, 26,27;3;23
Gm 21*;1,17;.. Gm 21,26,27,28;1,17;..
Gm 21*;1,2,17;.. Gm 21,26,27,28;1,2,17;..
Gm 5*;1,17;.. Gm 5,10,11,13,14,26,27;1,17;..
Gm 6,24*;1,17;.. Gm 5,6,11,24,26;1,17;..
Gm 6*;1,17;.. Gm 5,6,10,11,14,26,27;1,17;..
IMGT/LIGM-DB Other accesses
SRS: EBI (UK), Institut Pasteur (France), CEINGE (Italy), CU (USA), DDBJ (Japan), DIC (India), IUBio (USA)
FTP: weekly releases: CINES (Montpellier, France) and EBI (UK)
BLAST: CINES (France), EBI (UK), Institut Pasteur (France)
LinkOut (nucleotides) at NCBI (USA)
IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI)
created in 1989 by Marie-Paule Lefranc (Université Montpellier II, CNRS), a European project since 1992
provides a common access to all Immunogenetics data
is the international reference in Immunogenetics and Immunoinformatics
based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules
consists of databases, interactive tools and Web resources
IMGT, the international ImMunoGeneTics information system®
F. Ehrenmann, V. Giudicelli, C. Ginestoux, G. Folch, J. Jabado-Michaloud, Q. Kaas, P. Duroux, M.-P. Lefranc
Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142, Montpellier (France)
ImMunoGeneTics
Informationsystem®
http://imgt.cines.fr
Books
Lefranc, M.-P. and Lefranc, G.,The Immunoglobulin FactsBook, Academic Press, 458 pages (2001)
Lefranc, M.-P. and Lefranc, G.,The T cell receptor FactsBook, Academic Press, 398 pages (2001)
IMGT databases
IMGT/LIGM-DBIG and TR from human and 150 other vertebrate speciesLIGMLefranc, M.-P., Nucl. Acids Res., 33, D781-D784 (2006)
IMGT/PRIMER-DBIG and TR oligonucleotidesLIGM and EUROGENTECLefranc, M.-P., Nucl. Acids Res., 33, D593-D597 (2005)
IMGT/MHC-DBHLA and MHC/NHPANRI, BPRC and EBIRobinson, J. et al., Nucl. Acids Res.,31, 311-314 (2003)
IMGT/GENE-DB
IMGT/LIGM-DB
IMGT/MHC
IMGT/GENE-DBThe international reference for IG and TR gene and allele nomenclatureLIGMLefranc, M.-P., Nucl. Acids Res., 33, D256-D261 (2005)
Lefranc, M.-P. In: Antibody engineering: methods and protocols (Lo B.K.C. ed), 248, 27-49 (2003)
Lefranc, M.-P. and Lefranc, G. In: Molecular Biology of B cells (Honjo, T., Alt F.W. and Neuberger M.S., eds) pp. 37-59 (2004)
IMGT/3Dstructure-DBIG, TR, MHC and RPI structuresLIGMKaas, Q. et al., Nucl. Acids Res., 32, D208-D210 (2004)
2D and 3D structures
Sequences
Genome
IMGT tools
IMGT/JunctionAnalysis
IMGT/V-QUEST
Sequence analysis
Genome analysis
3D structure analysis
IMGT/DomainGapAlignIMGT/Collier-de-PerlesIMGT/StructuralQueryLIGMKaas, Q. and Lefranc, M.-P., In Silico Biology, 5, 505-528, Epub 2005, 5 0046 (2005)
IMGT/LocusView...LIGMLefranc, M.-P., Molecular Immunology, 40, 647-660 (2004)
IMGT/GeneInfoTIMC and ICH (Grenoble)Baum, P. et al., BMC Bioinformatics, 7, 224 (2006)
IMGT/GeneFrequencyLIGMLefranc, M.-P. et al., In Silico Biology, 5, 45-60, Epub 2005, 5, 0006 (2004)
IMGT/V-QUESTLIGMGiudicelli, V. et al., Nucl. Acids Res., 32, W435-W440 (2004)
IMGT/JunctionAnalysisLIGMYousfi Monod, M. et al., Bioinformatics20 Supplement, 1, I379-I385 (2004)
IMGT/Allele-AlignLIGMLefranc, M.-P., Molecular Immunology,40, 647-660 (2004)
IMGT/PhyloGeneLIGMElemento, O. and Lefranc, M.-P.,Dev. Comp. Immunol., 27, 763-779 (2003)
