imgc_igk
TRANSCRIPT
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7/29/2019 IMGC_IGK
1/12005 C. Ginestoux and M.-P. Lefranc
IMGT initiator and coordinator: Marie-Paule Lefranc ([email protected])
Bioinformatics manager: Vronique Giudicelli ([email protected])
Computer manager: Denys Chaume ([email protected])
Interface design: Chantal Ginestoux ([email protected])
Copyright 1995-2005 IMGT, the international ImMunoGeneTics information system
IMGT tools to analyse expressed variable genes
IMGT/3Dstructure-DBIMGT/StructuralQuery
Three-dimensional structures of 396 V-
KAPPA domains encoded by rearrangedIGKV-IGKJ genes are available inIMGT/3D-structure-DB. Only twocomplete IG with KAPPA chains (1 igt, 1igy) have been crystallised.
The IG kappa chains (pink and blue) arein spacefill (heavy chains are inwireframe with carbohydrates in whitespacefill).
3D structures
Kaas, Q. et al., Nucl. Acids Res., 32, D208-210 (2004)
Jmol
1igt
IMGT Colliers de Perles are according to
the IMGT unique numbering for V-DOMAIN and C-DOMAIN. Hydrogenbonds are shown as green lines.
IMGT Colliers de Perles
2D representations
Mus musculus (Mouse) IGKV_1 V-DOMAIN from
231 (1igt_A)CDR-IMGT lengths [6.3.9]
CDR3-IMGT
CDR1-IMGT
CDR2-IMGT
Lefranc, M.-P. et al., Dev. Comp. Immunol., 25, 55-77 (2003)Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005)
IMGT/V-QUESTIMGT/JunctionAnalysis
Analysis of the IGKV genes (germline or
rearranged) can be performed byIMGT/V-QUEST and analysis of the V-Jjunctions by IMGT/JunctionAnalysis.
Sequence analysis
Results of IMGT/V-QUEST
Giudicelli, V. et al., Nucl. Acids Res., 32, W435-W440 (2004)Yousfi Monod, M. et al., Bioinformatics, 20, I379-I385 (2004)
How many functionalIGK genes?
Potential repertoire
The potential IGK repertoire per haploidgenome comprises 99-101 functionalgenes: 94-96 IGKV, 4 IGKJ, and 1IGKC.
The definitive IMGT nomenclature of themouse IGKV genes and thecorrespondence with the provisionalnomenclature have been established.
The mouse IGK genes and alleles andthe corresponding IMGT referencesequences were provided to Mouse
Genome Informatics MGD in July 2002and are available in IMGT/GENE-DB.
Number of genes
1745
1
180
Overview
Functional genes
94-964
1
99-101
IGKVIGKJ
IGKC
Total
Giudicelli, V. et al., Nucl. Acids Res., 33, D256-D261 (2005)
How are IGK genesorganized?
IGK locus
Martinez-Jean, C. et al., Exp. Clin. Immuno., 18, 255-279 (2001)
0 50 100 150 200 kb
5-43
12-4
2
12-41
5-3
9
12-40
8-3
0
8-31
6-3
2
7-33
8-34
1-35
18-3
6
5-3
7
12-38
6-29
8-2
8
8-2
1
8-2
2
6-2
3
8-24
6-2
5
8-26
8-2
7
8-1
9
6-2
0
6-1
5
6-1
4
8-16
6-1
7
8-1
8
3'
CJ1to5
3-1
3-2
3-3
3-4
3-5
3-6
3-7
3-8
3-9
3-1
0
3-11
3-12
6-13
E n h a n ce rs
12-4
4
4-5
5
4-54
4-5
3
4-5
2
4-5
1
4-5
0
12-49
L10
RS
sa
d
13-5
4-1
13-5
5-1
5-40-1
5-4
5
12-4
6
12-4
7
5-48
2200
2400
2600
2800
3000
3200
4-5
6
?
5'
14-1
00
15-1
01
15-1
02
15-1
03
16-1
04
2-1
05
11-1
06
2-1
07
1-1
08
2-1
09
1-110
14-1
11
2-1
12
2-1
13
11-1
14
1-1
15
2-1
16
9-1
19
9-1
20
17-1
21
1-122
9-1
28
17-1
27
14-126
9-1
24
9-1
23
14-1
30
1-131
1-1
32
9-1
29
2-1
37
1-1
36
1-1
35
1-1
33
17-134
tub
15-1
01-1
14-1
18-1
14-1
18-2
14-126-1
14-134-1
11-1
25
1-1
17
11-1
18
200
400
600
800
1000
D6Bhm9
probe
4-5
9
4-5
8
4-5
7
4-6
0
4-6
2
4-6
3
13-6
4
4-6
5
12-6
6
12-6
7
4-6
8
4-6
9
4-7
0
4-7
1
4-7
2
4-7
3
4-7
4
4-7
5
13-7
6
4-7
7
4-7
8
4-7
9
4-8
0
4-8
1
13-8
2
4-8
3
13-8
4
13-8
5
4-8
6
13-8
7
1-8
8
12-8
9
4-9
0
4-9
1
4-9
2
19-9
3
10-9
5
10-9
6
15-9
7
12-9
8
10-9
4
4-6
1
13-5
6-1
13-5
7-1
13-6
2-1
13-6
1-1
13-7
1-1
13-7
3-1
13-7
4-1
13-7
8-1
13-8
0-1
2-9
3-1
13-8
9-1
2-9
5-1
2-9
5-2
1200
1400
1600
1800
2000
1-9
9
?
D6Mit72
probe
E5' E3'
kb
Locus representation: Mouse (Mus musculus) IGKon chromosome 6 C2
How many IGK genes?
Chromosome 6 C2
The total number of immunoglobulinkappa IGK genes per haploid genomein Mus musculus laboratory mice is 180(190, if the 10 IGKV orphons areincluded).
Lefranc, M.-P. et al., In Silico Biology, 5, 45-60 (2005)
IGKV: 174
IGKJ: 5
IGKC: 1
3,200 kb
(180 genes)
5'
3'
A1
A2
A3
B1
B2
B3
C1
C2
C3
D1
D2D3
E1
E2
E3
F1
F2
F3
G1
G2G3
6
The mouse IGK locus islocated on chromosome 6 C2at 30.0 cM.
The mouse IGK locus spans3,200 kb and comprises, from5' to 3", 174 IGKV genes thatbelong to 19 subgroups and
to three clans, 5 IGKJ genesand 1 IGKC.
ImMunoGeneTics
Information
system
http://imgt.cines.fr
IMGT overview: the mouse
immunoglobulin kappa IGK genesG. Folch, C. Jean, C. Ginestoux, V. Giudicelli and M.-P. Lefranc
IMGT the international ImMunoGeneTics information system, LIGM, UM2, CNRS UPR 1142, IGH141 rue de la Cardonille, 34396 Montpellier Cedex 05, France - [email protected]