Nomenclature and Overview of the Mouse ( Mus musculus and ... · and (8) ‘Complete list of the...

IMGT Locus in Focus

Exp Clin Immunogenet 2001;18:255–279

Nomenclature and Overview of theMouse (Mus musculus and Mus sp.)Immunoglobulin Kappa (IGK) Genes

Christèle Martinez-Jean Géraldine Folch Marie-Paule Lefranc

IMGT Nomenclature Committee, CNRS, Université Montpellier II, Montpellier, France

Received: June 29, 2001

Prof. Marie-Paule Lefranc, IMGT Laboratoired’ImmunoGénétique Moléculaire, LIGM, UPR CNRS 1142, IGH141, rue de la Cardonille, F–34396 Montpellier Cedex 5 (France)Tel. +33 4 99 61 99 65, Fax +33 4 99 61 99 01E-Mail [email protected], IMGT: http://imgt.cines.fr

ABCFax + 41 61 306 12 34E-Mail [email protected]

© 2001 S. Karger AG, Basel0254–9670/01/0184–0255$17.50/0

Accessible online at:www.karger.com/journals/eci

Key WordsMouse W IMGT W Immunoglobulin W

Kappa chain genes W Orphons

Abstract‘Nomenclature and overview of the mouse(Mus musculus and Mus sp.) immunoglobu-lin kappa (IGK) Genes’, the 19th report of the‘IMGT Locus in Focus’ section, provides thefirst complete list of all the mouse (M. muscu-lus) IGK genes. The mouse (M. musculus)locus spans 3,200 kb. The total number ofmouse (M. musculus) IGK genes per haploidgenome is 164 (174 if the orphons are in-cluded). The functional genomic repertoirecomprises 93 IGKV belonging to 18 sub-groups, 5 IGKJ and 1 IGKC gene. IMGT genenames and definitions of the mouse (M. mus-culus) IGK genes on chromosome 6 and IGKorphons are provided with the gene function-ality and the number of alleles, according tothe concepts of IMGT-ONTOLOGY and torules of the IMGT Scientific chart, with theaccession numbers of the IMGT reference

sequences. These tables and figures areavailable at the IMGT Marie-Paule page ofIMGT, the international ImMunoGeneTicsdatabase (http://imgt.cines.fr) created byMarie-Paule Lefranc, Université MontpellierII, CNRS, France.

Copyright © 2001 S. Karger AG, Basel

Introduction

‘Nomenclature and overview of the mouse(Mus musculus and Mus sp.) immunoglobulinkappa (IGK) Genes’ is the 19th report of the‘IMGT Locus in Focus’ section launched inthe April 1998 issue of Experimental andClinical Immunogenetics [1–19]. This reportcomprises two figures: (1) ‘Representation ofthe mouse (Mus musculus) IGK locus onchromosome 6’ (2) ‘The classification conceptof IMGT-ONTOLOGY exemplified for themouse (Mus musculus) IGKV genes’ andeight tables entitled: (1) ‘Mouse (Mus mus-culus) germline IGKV genes and alleles’;(2) ‘Mouse (Mus musculus) IGKV orphons’;

256 Exp Clin Immunogenet 2001;18:255–279 Martinez-Jean/Folch/Lefranc

Fig. 1. Representation of themouse (M. musculus) IGK locuson chromosome 6. Horizontal ar-rows indicate inverse orientation oftranscription of the IGKV genescompared to that of the IGKJgenes. A question mark belowIGKV4-52 and IGKV4-60 indi-cates that the orientation of tran-scription of these genes is un-known. Two enhancers have beenidentified: E5) between the IGKJgenes and the IGKC gene [28–30],and E3) located 8.5 kb downstreamof the IGKC gene [31]. The mouseIGKV representation has been setup with data from [20–24] and up-dated with ‘The immunoglobulin Îgenes and the Î locus of the mouse’(http://www.med.uni-muenchen.de/biochemie/zachau/kappa.htm) –July 2000 version. These updates,compared to the publications [20–24], include: suppression of thegaps between IGKV14-111 andIGKV2-112, and between IGKV2-116 and IGKV1-117; suppressionof the gaps between IGKV1-122and IGKV9-123, and betweenIGKV9-124 and IGKV11-125, andchange of orientation and positionof the IGKV9-123 and IGKV9-124genes; suppression of gw1, ca9and cc9, now considered as or-phons on the same chromosome 6(IGKV1/OR6-1, IGKV14/OR6-2and IGKV14/OR6-3, respective-ly). The IGKV4-52 gene is locatedbetween IGKV4-51 and IGKV4-53, but the exact distance to one orthe other gene is not known. TheD6Bhm9 probe (EMBL Acces-sion number Z72363) is describedin Schupp IW, et al: Immuno-genetics 1997;95:180–187. Tub =a-tubulin like (EMBL AccessionNo. AJ235970). Sad = S-adeno-syl methionine decarboxylase like(EMBL Accession No. AJ132684).

Mouse IGK Gene Nomenclature Exp Clin Immunogenet 2001;18:255–279 257

(3) ‘Correspondence between mouse (Musmusculus) IGKV nomenclatures’; (4) ‘Num-ber of mouse (Mus musculus) germline IGKVgenes on chromosome 6 and potential reper-toire’; (5) ‘Mouse (Mus musculus) germlineIGKJ genes’; (6) ‘Mouse (Mus musculus)IGKJ alleles’; (7) ‘Mouse (Mus musculus, Mussaxicola, Mus pahari, Mus minutoides, Muscookii, Mus spretus) IGKC genes and alleles’and (8) ‘Complete list of the mouse (Mus mus-culus) IGK genes on chromosome 6’.

The mouse (M. musculus) IGK locus,located on chromosome 6, spans 3,200 kb.It consists of 158 IGKV genes [20–24],belonging to 19 subgroups, localized on3,100 kb, 5 IGKJ genes [25–26] and 1 IGKCgene [27]. The potential genomic M. musculusIGK repertoire comprises 93 functionalIGKV genes belonging to 18 subgroups, 5IGKJ and 1 IGKC gene. The total number ofmouse (M. musculus) IGK genes per haploidgenome is 164 (174 if the orphons are in-cluded), of which 99 are functional. Eighty-one IGKV genes are in opposite orientation oftranscription, 59 of them are functional andmust rearrange by a mechanism of inversion.IMGT gene names and definitions of themouse (M. musculus) IGK genes on chro-mosome 6 and IGK orphons are providedwith the gene functionality and the numberof alleles, according to the concepts of IMGT-ONTOLOGY [32] and to rules of the IMGTScientific chart, with the accession numbersof the IMGT reference sequences. These ta-bles and figures are available at the IMGTMarie-Paule page of IMGT, the internation-al ImMunoGeneTics database (http://imgt.cines.fr) created by Marie-Paule Lefranc,Université Montpellier II, CNRS, France[33–35]. Description of functionality (FUNC-TIONAL, ORF, PSEUDOGENE) and de-scription of mutations are according to theIMGT scientific chart available at the IMGTMarie-Paule page.

IGK Gene Nomenclature and IMGTScientific Chart

Gene NamesGene names (tables 1, 2, 5, 7, 8) are accord-

ing to the IMGT gene name nomenclaturefor IG and TR of all vertebrates based onthe ‘CLASSIFICATION’ concept of IMGT-ONTOLOGY [32] (Appendix), and accordingto rules of the IMGT Scientific chart [1] avail-able at http://imgt.cines.fr.

FunctionalityCriteria of functionality (F: functional, P:

pseudogene, ORF: open reading frame) (tables1, 2, 5–8) are described in the IMGT Scientificchart [1]. The definition of functionality isbased on sequence analysis. As examples, theinstances functional (for germline V, D, J, andfor C genes) mean that the coding regions havean open reading frame without a stop codon,and that there is no described defect in thesplicing sites, and/or recombination signals,and/or regulatory elements. According to thegravity of the identified defects, the functional-ity can be defined as ORF, pseudogene or ves-tigial (for germline V, D, J, and for C genes) [1].Complete definitions are available in theIMGT Scientific chart at the IMGT Marie-Paule page. Information on gene rearrange-ment, DNA transcription into mRNA, andRNA translation into a polypeptide chain isprovided in the IMGT ‘Germline gene tables’in the IMGT Repertoire (columns designatedas R, T, and Pr, respectively). This informationis extracted from the literature and throughIMGT/LIGM-DB sequence database search[33–35]. The IMGT/V-QUEST tool, availableat the IMGT Home page at http://imgt.cines.fr,allows the identification of the germline IGKVand IGKJ genes from IGKV-J genomic rear-rangements and transcripts, and providestranslation and 2D representation (Collier dePerles) of the variable regions [33–36].


Tab

le 1

. Mou

se (M

us m

uscu

lus)

ger

mlin

e IG

KV

gen

es a

nd a

llele

sFc

t: FU

NC

TIO

NA

LIT

Y; F

: Fun

ctio

nal;

P: P

seud

ogen

e; O

RF:

Ope

n R

eadi

ng F

ram

e; v

g: V

esti

gial

; R: R

earr

ange

d; T

: Tra

nscr

ibed

; Pr:

Tra

nsla

ted

into

pro

tein

. ‘+’

or ‘

–’ in

dica

tes

if th

e ge

ne se

quen

ces h

ave

been

foun

d (+

) or n

ot b

een

foun

d (–

) rea

rran

ged,

tran

scri

bed,

and

/or t

rans

late

d in

to p

rote

in. A

rbit

rari

ly th

at in

form

atio

n is

show

n th

at o

n th

e fi

rst l

ine

of e

ach

gene

whe

n th

e da

ta h

ave

been

con

firm

ed b

y se

vera

l stu

dies

.Fu

ncti

onal

ity

is s

how

n be

twee

n pa

rent

hese

s w

hen

the

acce

ssio

n nu

mbe

r re

fers

to

rear

rang

ed g

enom

ic D

NA

or

cDN

A a

nd t

he c

orre

spon

ding

ger

mlin

e ge

ne h

as n

ot y

et b

een

isol

ated

.R

efer

ence

sequ

ence

s in

bold

hav

e be

en m

appe

d: ‘m

appe

d’ re

fers

to se

quen

ces w

hich

hav

e be

en o

btai

ned

from

clo

nes (

phag

es, c

osm

ids,

YA

Cs.

..) e

ithe

r by

subc

loni

ng o

r PC

R, a

nddo

es n

ot a

pply

to se

quen

ces o

btai

ned

dire

ctly

from

gen

omic

DN

A.

In th

e ‘S

eque

nces

from

the

liter

atur

e’ c

olum

n, n

ames

of t

he se

quen

ces a

re p

rece

ded

by th

e de

sign

atio

n of

the

mou

se st

rain

.T

he o

rien

tati

on o

f tra

nscr

ipti

on o

f IG

KV

gen

es, c

ompa

red

to th

at o

f the

IGK

J ge

nes,

is in

dica

ted

in a

col

umn

on th

e ri

ght o

f the

IGK

V g

ene

nam

e:+

indi

cate

s a IG

KV

gen

e w

hich

is in

the

sam

e or

ient

atio

n as

the

IGK

J ge

nes.

– in

dica

tes a

IGK

V g

ene

whi

ch is

in th

e op

posi

te o

rien

tati

on o

f tra

nscr

ipti

on a

nd m

ust r

earr

ange

by

a m

echa

nism

of i

nver

sion

.?

indi

cate

s a IG

KV

gen

es fo

r whi

ch th

e or

ient

atio

n is

unk

now

n.o

indi

cate

s a IG

KV

gen

e w

hich

is u

nmap

ped.

IGK

Vsu

bgro

upIG

KV

gene

nam

eIG

KV

alle

le n

ame

(46)

Fct

RT

Pr

Stra

ins

Ref

eren

cese

quen

ces

Acc

essi

on n

umbe

rsSe

quen

ces f

rom

the

liter

atur

e

11-

35–

1-35

*01

OR

F(18

)C

3Hcu

2A

J231

200

[31–

34]

1-88

–1-

88*0

1F

++

C57

BL

/6cs

1A

J231

206

[31–

34]

1-99

+1-

99*0

1F

++

C3H

cv1

AJ2

3120

7 [3

1–34

]1-

108

+1-

108*

01P

(1)

C3H

cq1

AJ2

3120

4 [3

1–34

]1-

110

+1-

110*

01F

++

+B

AL

B/c

K5.1

D00

080/

M15

566

[14]

BA

LB

/c, V

-1A

[M28

131]

[19]

,C

57B

L/6

, bb1

[AJ2

3120

1][3

1–34

]1-

110*

02 (4

7)F

++

+N

ZB

/BIN

JV

-1B

M28

132

[19]

1-11

5+

1-11

5*01

P(2

)C

3Hcz

1A

J231

208

[31–

34]

1-11

7–

1-11

7*01

F+

++

BA

LB

/cK

1A

5D

0008

1 [1

4]B

AL

B/c

, [M

1556

7][1

4],

BA

LB

/c, V

-1C

[M28

133]

[19]

,C

3H, c

r1 [A

J231

205]

[31–

34]

1-11

7*02

F+

+C

E/J

V-1

Cf

M28

134

[19]

1-12

2+

1-12

2*01

F+

++

BA

LB

/cK

18.1

D00

082

[14]

BA

LB

/c, [

M15

568]

[14]

,C

57B

L/6

, bl1

[AJ2

3120

3][3

1–34

]1-

131

–1-

131*

01O

RF(

17)

C57

BL

/6bh2

AJ2

3119

7 [3

1–34

]1-

132

+1-

132*

01F

++

C57

BL

/6bi2

AJ2

3119

8 [3

1–34

]1-

133

+1-

133*

01F

++

+12

9/Sv

70/1

Z72

382

[27]

C57

BL

/6, b

j2 [A

J231

199]

[31–

34]

1-13

5+

1-13

5*01

F+

++

129/

Sv70/3

Z72

384

[27]

C57

BL

/6, b

d2 [A

J231

196]

[31–

34]

1-13

6+

1-13

6*01

P(3

)C

57B

L/6

bc1

rA

J231

202

[31–

34]

22-

93-1

–2-

93-1

*01

P(v

g)–

––

C3H

hh24r

AJ2

3126

5 [3

4]2-

95-1

+2-

95-1

*01

P(v

g)–

––

C57

BL

/6hb24r

AJ2

3126

1 [3

4]2-

95-2

–2-

95-2

*01

P(v

g)–

––

C57

BL

/6hi2

4r

AJ2

3126

6 [3

4]2-

105

+2-

105*

01P

(4)

C3H

hd24

AJ2

3126

2 [3

1–34

]2-

107

+2-

107*

01P

(5)

C3H

hc2

4A

J132

682

[31–

34]

2-10

9+

2-10

9*01

F+

++

C3H

he2

4A

J132

683

[31–

34]

2-10

9*02

(48)

F+

+B

AL

B/c

24B

K02

418

[8]


2-11

2+

2-11

2*01

F+

+B

AL

B/c

167

J005

62 [6

]B

AL

B/c

, 24

[K02

415]

[9],

C3H

, hg2

4 [A

J231

264]

[31–

34]

2-11

3+

2-11

3*01

P(6

)C

57B

L/6

ha2

4A

J231

260

[31–

34]

2-11

6+

2-11

6*01

P(7

)C

57B

L/6

hk24

AJ2

7784

3 [3

1–34

]2-

137

+2-

137*

01F

++

+C

3Hhf2

4A

J231

263

[31–

34]

2-a

(49)

o2-

a*01

F+

+B

AL

B/c

24A

K02

417

[9]

33-

1+

3-1*

01F

++

BA

LB

/c21

GX

1695

5 [1

8]3-

2+

3-2*

01F

++

BA

LB

/c21

AX

1695

4 [1

8]3-

3+

3-3*

01F

++

BA

LB

/c18

kbK

0216

2 [1

0]3-

4+

3-4*

01F

++

+C

57B

L/6

21-4

Y15

968

[29]

3-5

+3-

5*01

F+

++

BA

LB

/c21

CK

0216

1 [1

0]3-

6+

3-6*

01P

(8)

C57

BL

/621-6

Y15

969

[29]

3-7

+3-

7*01

F+

++

BA

LB

/c1.

6kb

K02

158

[10]

3-8

+3-

8*01

P(9

)C

57B

L/6

21-8

Y15

971

[29]

3-9

+3-

9*01

FC

57B

L/6

21-9

Y15

972

[29]

3-10

+3-

10*0

1F

++

+B

AL

B/c

21B

K02

160

[10]

3-11

+3-

11*0

1P

(10)

C57

BL

/621-1

1Y

1597

3 [2

9]3-

12+

3-12

*01

F+

+B

AL

B/c

21E

K02

159

[10]

44-

50–

4-50

*01

FC

57B

L/6

4-5

0A

J235

938

[31–

34]

R13

[11]

4-51

–4-

51*0

1F

L8J0

0575

/V01

565

[7]

C3H

, 4-5

1 [A

J235

939]

[31–

34]

4-52

(60)

?4-

52*0

1F

C57

BL

/6ko4

AJ2

3919

8 [3

1–34

]4-

53–

4-53

*01

F+

++

C57

BL

/6kh4

AJ2

3123

1 [3

1–34

]4-

54 (6

0)–

4-54

*01

FC

57B

L/6

ar4

AJ2

3122

3 [3

1–34

]4-

55–

4-55

*01

F+

++

C57

BL

/6at

4A

J231

225

[31–

34]

4-56

–4-

56*0

1P

(11)

C57

BL

/6ao

4A

J231

220

[31–

34]

4-57

–4-

57*0

1F

++

C57

BL

/6ap

4A

J231

221

[31–

34]

4-58

–4-

58*0

1F

++

+B

AL

B/c

S107b

K00

884

[4]

R1

[11]

,C

57B

L/6

, kj4

[AJ2

3123

3][3

1–34

]4-

59+

4-59

*01

F+

+B

AL

B/c

VO

x1S3

7664

[11]

H3

[11]

,C

57B

L/6

, kk4

[AJ2

3123

4][3

1–34

]

4-60

?4-

60*0

1P

(12)

C57

BL

/6kl4

AJ2

3594

1 [3

1–34

]4-

61–

4-61

*01

F+

++

C57

BL

/6aa

4A

J231

209

[31–

34]

H4

[11]

4-62

–4-

62*0

1O

RF(

13)

C57

BL

/6ab

4A

J231

210

[31–

34]

4-63

–4-

63*0

1F

++

+C

57B

L/6

ac4

AJ2

3121

1 [3

1–34

]4-

65–

4-65

*01

P(1

4)C

57B

L/6

ki4

AJ2

3123

2 [3

1–34

]4-

68–

4-68

*01

F+

+C

57B

L/6

aq4

AJ2

3122

2 [3

1–34

]H

13 [1

1]4-

69–

4-69

*01

F+

++

C57

BL

/6km

4A

J235

942

[31–

34]

H9

[11]

4-70

–4-

70*0

1F

++

+C

57B

L/6

kn4

AJ2

3594

3 [3

1–34

]R

9 [1

1]4-

71–

4-71

*01

FC

57B

L/6

al4

AJ2

3121

8 [3

1–34

]4-

72–

4-72

*01

F+

+C

57B

L/6

am4

AJ2

3121

9 [3

1–34

]4-

73–

4-73

*01

FC

57B

L/6

ah4

AJ2

3121

6 [3

1–34

]

+


Tab

le 1

(con

tinu

ed)

IGK

Vsu

bgro

upIG

KV

gene

nam

eIG

KV

alle

le n

ame

(46)

Fct

RT

Pr

Stra

ins

Ref

eren

cese

quen

ces

Acc

essi

on n

umbe

rsSe

quen

ces f

rom

the

liter

atur

e

4-74

–4-

74*0

1F

++

+C

57B

L/6

ai4

AJ2

3121

7 [3

1–34

]4-

75–

4-75

*01

P(1

5)C

57B

L/6

ka4

AJ2

3122

7 [3

1–34

]4-

77–

4-77

*01

P(5

9)C

57B

L/6

aj4

AJ2

3594

0 [3

1–34

]H

8 [1

1]4-

78–

4-78

*01

FC

57B

L/6

ad4

AJ2

3121

2 [3

1–34

]H

1 [1

1]4-

79–

4-79

*01

F+

++

C57

BL

/6ae

4A

J231

214

[31–

34]

4-80

–4-

80*0

1F

++

+C

57B

L/6

af4

AJ2

3121

3 [3

1–34

]4-

81–

4-81

*01

FC

57B

L/6

ag4

AJ2

3121

5 [3

1–34

]R

11 [1

1]4-

83–

4-83

*01

P(1

6)C

57B

L/6

kg4

AJ2

3123

0 [3

1–34

]H

2 [1

1]4-

86–

4-86

*01

F+

+B

AL

B/c

X24

X05

555

[15]

H6

[11]

,C

57B

L/6

, kb4

[AJ2

3122

8][3

1–34

]4-

90–

4-90

*01

F+

+C

57B

L/6

an4

AJ2

3122

4 [3

1–34

]R

2 [1

1]4-

91–

4-91

*01

F+

+C

57B

L/6

kf4

AJ2

3122

9 [3

1–34

]4-

92–

4-92

*01

FC

57B

L/6

ay4

AJ2

3122

6 [3

1–34

]

55-

37–

5-37

*01

F+

+C

57B

L/6

23-3

7A

J235

963

[31–

34]

5-39

–5-

39*0

1F(

24)

++

+C

57B

L/6

23-3

9A

J235

964

[31–

34]

5-40

-1–

5-40

-1*0

1P

(vg)

––

–C

57B

L/6

fp23r

AJ2

3597

6 [3

4]5-

43–

5-43

*01

F+

++

C3H

23-4

3A

J235

973

[31–

34]

5-45

–5-

45*0

1F

++

+C

57B

L/6

23-4

5A

J235

974

[31–

34]

5-48

–5-

48*0

1F

++

BA

LB

/cL7

V01

564

[5]

C57

BL

/6, 2

3-4

8 [A

J235

975]

[31–

34](

44)

66-

13–

6-13

*01

(F)

++

Vtn

pJ0

0569

[8]#

g6-

14–

6-14

*01

F+

+C

57B

L/6

19-1

4Y

1597

5 [2

9]6-

15–

6-15

*01

F+

+C

57B

L/6

19-1

5Y

1597

6 [2

9]6-

17+

6-17

*01

F+

++

C57

BL

/619-1

7Y

1597

8 [2

9]6-

20–

6-20

*01

F+

+C

57B

L/6

19-2

0Y

1598

1 [2

9]6-

23–

6-23

*01

F+

++

C57

BL

/619-2

3A

J235

961

[31–

34]

6-25

+6-

25*0

1F

++

+C

57B

L/6

19-2

5A

J235

962

[31–

34]

6-29

–6-

29*0

1F

C57

BL

/619-2

9A

J235

967

[31–

34]

6-32

–6-

32*0

1F

++

+C

57B

L/6

19-3

2A

J235

968

[31–

34]

6-32

*02

(50)

FB

AL

B/c

V-S

era

M14

360

[13]

6-b

o6-

b*01

(51)

F+

+C

58V

-Ser

bM

1436

1 [1

3]6-

co

6-c*

01 (5

1)F

++

SKSK

/Cam

RK

M24

937

[20]

6-d

o6-

d*01

(51)

F+

+P

ER

AP

ER

A/E

iL

3624

9 [2

0]

77-

33–

7-33

*01

F+

+B

AL

B/c

22G

AF0

4419

8 [3

0]C

57B

L/6

, 22-3

3 [A

J235

965]

[31–

34]


88-

16–

8-16

*01

F+

+C

57B

L/6

8-1

6Y

1597

7 [2

9]8-

18+

8-18

*01

OR

F(20

)C

57B

L/6

8-1

8Y

1597

9 [2

9]8-

19–

8-19

*01

F+

+C

57B

L/6

8-1

9Y

1598

0 [2

9]8-

21–

8-21

*01

F+

+C

57B

L/6

8-2

1Y

1598

2 [2

9]8-

22–

8-22

*01

P(1

9)C

57B

L/6

8-2

2Y

1598

3 [2

9]8-

24–

8-24

*01

F+

++

C57

BL

/68-2

4A

J235

944

[31–

34]

8-26

+8-

26*0

1O

RF(

20)

C57

BL

/68-2

6A

J235

945

[31–

34]

8-27

–8-

27*0

1F

++

+C

57B

L/6

8-2

7A

J235

946

[31–

34]

8-28

–8-

28*0

1F

++

+C

57B

L/6

8-2

8A

J235

947

[31–

34]

8-28

*02

(52)

FM

RL

GL

vk50

L17

135

[24]

8-30

–8-

30*0

1F

++

C3H

8-3

0A

J235

948

[31–

34]

8-31

–8-

31*0

1P

(21)

C3H

8-3

1A

J235

957

[31–

34]

8-34

–8-

34*0

1F

129/

Sv8-3

4A

J235

958

[31–

34]

99-

119

+9-

119*

01P

(22)

C57

BL

/6bp9

AJ2

3123

6 [3

1–34

]9-

120

+9-

120*

01F

++

C57

BL

/6V

K41

V00

804/

J005

66 [1

][A

F003

293]

[26]

,C

3H, b

v9 [A

J242

670]

[31–

34]

9-12

3–

9-12

3*01

F+

++

VK

9bA

F003

295

[26]

C3H

, cy9

[AJ2

3125

0][3

1–34

]9-

124

–9-

124*

01F

++

VK

9aA

F003

294

[26]

C3H

, cw

9 [A

J231

248]

[31–

34]

9-12

8+

9-12

8*01

P(2

3)C

3Hcl

9A

J231

245

[31–

34]

9-12

9+

9-12

9*01

F+

+B

AL

B/c

M17

3bK

0088

0 [2

]C

3H, c

j9 [A

J231

244]

[31–

34]

1010

-94

–10

-94*

01F

+

++

A/J

AJ2

M54

906

[23]

C3H

, cp9 [A

J231

247]

[31–

34]

10-9

4*02

FP

ER

UP

ER

U2

M54

908

[23]

10-9

4*03

F+

AK

RA

KR

2M

5490

4 [2

3]M

RL

, MR

LB [A

F346

760]

[36]

10-9

5+

10-9

5*01

F(24

)+

+B

AL

B/c

VK

10c

AF0

2926

1 [2

8]C

57B

L/6

, by9

[AJ2

3123

9][3

1–34

]10

-96

–10

-96*

01F

++

+A

/J91

A3

M15

520

[16]

Id(C

R) [

X05

795]

[17]

,A

/J, A

J1 [M

5490

5][2

3],

129/

Sv, c

e9 [A

J239

197]

[31–

34]

10-9

6*02

F+

PE

RU

PER

U1

M54

907

[23]

10-9

6*03

FA

KR

AK

R1

M54

903

[23]

MR

L, M

RLA

[AF3

4676

1][3

6]

1111

-106

+11

-106

*01

P(2

5)C

3Hia

11

AJ2

3125

2 [3

1–34

]11

-114

+11

-114

*01

P(2

6)C

3Hic

11

AJ2

3125

3 [3

1–34

]11

-118

+11

-118

*01

P(2

7)C

3Hie

11

AJ2

3125

5 [3

1–34

]11

-125

+11

-125

*01

F+

++

129/

Svif

11

AJ2

3125

6 [3

1–34

]

1212

-38

–12

-38*

01F

++

+C

57B

L/6

12-3

8A

J235

951

[31–

34]

12-4

0–

12-4

0*01

P(2

8)C

57B

L/6

12-4

0A

J235

952

[31–

34]

12-4

1–

12-4

1*01

F+

++

C57

BL

/612-4

1A

J235

953

[31–

34]

12-4

1*02

(53)

F+

+B

AL

B/c

k2

J005

45 /V

0077

8 [3

]12

-42

–12

-42*

01P

(29)

C3H

12-4

2A

J235

954

[31–

34]

12-4

4–

12-4

4*01

F+

+C

3H12-4

4A

J235

955

[31–

34]

12-4

6–

12-4

6*01

F+

+C

57B

L/6

12-4

6A

J235

956

[31–

34]

12-4

7–

12-4

7*01

P(3

0)C

57B

L/6

12-4

7A

J235

959

[31–

34]

+


Tab

le 1

(con

tinu

ed)

IGK

Vsu

bgro

upIG

KV

gene

nam

eIG

KV

alle

le n

ame

(46)

Fct

RT

Pr

Stra

ins

Ref

eren

cese

quen

ces

Acc

essi

on n

umbe

rsSe

quen

ces f

rom

the

liter

atur

e

12-4

9–

12-4

9*01

P(3

1)C

57B

L/6

12-4

9A

J235

960

[31–

34]

12-6

6–

12-6

6*01

P(3

2)C

57B

L/6

fr12

AJ2

3593

4 [3

1–34

]12

-67

–12

-67*

01P

(33)

C57

BL

/6fg

12

AJ2

3593

3 [3

1–34

]12

-89

–12

-89*

01F

++

+C

57B

L/6

fl12

AJ2

3595

0[31

–34]

12-9

8+

12-9

8*01

F+

++

C3H

ci12

AJ2

3594

9 [3

1–34

]12

-eo

12-e

*01

FB

AL

B/c

k3

J005

46 [3

]

1313

-54-

1+

13-5

4-1*

01P

(vg)

––

–C

57B

L/6

gy3

3r

AJ1

3268

0 [3

4]13

-55-

1+

13-5

5-1*

01P

(vg)

––

–C

57B

L/6

gx3

3r

AJ1

3267

9 [3

4]13

-56-

1+

13-5

6-1*

01P

(vg)

––

–C

57B

L/6

gg33r

AJ1

3267

5 [3

4]13

-57-

1+

13-5

7-1*

01P

(vg)

––

–C

57B

L/6

gz3

3r

AJ1

3268

1 [3

4]13

-61-

1+

13-6

1-1*

01P

(vg)

––

–C

57B

L/6

gh33r

AJ1

3267

6 [3

4]13

-62-

1+

13-6

2-1*

01P

(vg)

––

–C

57B

L/6

gc3

3r

AJ1

3267

2 [3

4]13

-64

+13

-64*

01P

(34)

C57

BL

/6gu33

AJ2

3596

9 [3

1–34

]13

-71-

1+

13-7

1-1*

01P

(vg)

––

–C

57B

L/6

gd33r

AJ1

3267

3 [3

4]13

-73-

1+

13-7

3-1*

01P

(vg)

––

–C

57B

L/6

go33r

AJ1

3267

7 [3

4]13

-74-

1+

13-7

4-1*

01P

(vg)

––

–C

57B

L/6

gv3

3r

AJ1

3267

8 [3

4]13

-76

+13

-76*

01P

(35)

C57

BL

/6ga3

3A

J231

271

[31–

34]

13-7

8-1

+13

-78-

1*01

P(v

g)–

––

C57

BL

/6gb33r

AJ1

3267

1 [3

4]13

-80-

1+

13-8

0-1*

01P

(vg)

––

–C

57B

L/6

ge3

3r

AJ1

3267

4 [3

4]13

-82

+13

-82*

01P

(36)

C57

BL

/6gq33

AJ2

3127

6 [3

1–34

]13

-84

+13

-84*

01F

++

C57

BL

/6gm

33

AJ2

3127

3 [3

1–34

]B

AL

B/c

, Vk3

4C [M

3515

6 [2

1](4

5)13

-85

–13

-85*

01F

++

C57

BL

/6gn33

AJ2

3127

4 [3

1–34

]13

-85*

02 (5

4)F

BA

LB

/cV

k34B

M35

154

[21]

(45)

13-8

5*03

(54)

FA

KR

Vk3

4AM

3515

5 [2

1](4

5)13

-87

+13

-87*

01P

(37)

C57

BL

/6gp33

AJ2

3127

5 [3

1–34

]13

-89-

1+

13-8

9-1*

01P

(vg)

––

–C

57B

L/6

gf3

3r

AJ2

3127

2 [3

4]

1414

-100

+14

-100

*01

F+

+C

3Hcf

9A

J231

243

[31–

34]

14-1

11+

14-1

11*0

1F

++

BA

LB

/cL6

V01

563

[5]

VT

1 [V

0152

2][3

5],

9M [M

7471

3][2

2], C

57B

L/6

,ba

9 [A

J231

235]

[31–

34]

14-1

18-1

+14

-118

-1*0

1P

(vg)

––

–C

57B

L/6

bz9

AJ2

7784

4 [3

4]14

-118

-2+

14-1

18-2

*01

P(v

g)–

––

C57

BL

/6bq9

AJ2

3123

7 [3

4]14

-126

+14

-126

*01

P(3

8)C

3Hbr9

AJ2

3123

8 [3

1–34

]14

-126

-1+

14-1

26-1

*01

P(v

g)–

––

C57

BL

/6co

9A

J231

246

[34]

14-1

30+

14-1

30*0

1F

++

+C

57B

L/6

cb9

AJ2

3124

1 [3

1–34

]14

-134

-1+

14-1

34-1

*01

P(v

g)–

––

C3H

cx9

AJ2

3124

9 [3

4]12

9/Sv

, 294

A9

[Z72

385

][27

]


1515

-97

+15

-97*

01P

(39)

C3H

gk32

AJ2

3126

7 [3

1–34

]15

-101

–15

-101

*01

P(4

0)C

3Hgl3

2A

J231

268

[31–

34]

15-1

01-1

+15

-101

-1*0

1P

(vg)

––

–C

3Hgt3

2r

AJ2

3125

1 [3

4]15

-102

–15

-102

*01

P(4

1)C

3Hgs3

2A

J231

270

[31–

34]

15-1

03+

15-1

03*0

1O

RF(

42)

++

C3H

gr3

2A

J231

269

[31–

34]

1616

-104

+16

-104

*01

F+

+C

3HR

FA

J235

936

[31–

34]

1717

-121

+17

-121

*01

F+

+C

57B

L/6

bt2

0A

J231

258

[31–

34]

17-1

27+

17-1

27*0

1F

++

C57

BL

/6bw

20

AJ2

3125

9 [3

1–34

]17

-134

–17

-134

*01

P(4

3)12

9/Sv

294A

9Z

7238

6 [2

7]C

57B

L/6

,bk20 [A

J231

257]

[31–

34]

1818

-36

–18

-36*

01F

C3H

dv-

36

AJ2

3596

6 [3

1–34

]

1919

-93

–19

-93*

01F

++

C57

BL

/6gj3

8c

AJ2

3593

5 [3

1–34

]

#g: R

earr

ange

d ge

nom

ic D

NA

.

Mou

se (M

us m

uscu

lus

cast

aneu

s) IG

KV

IGK

Vsu

bgro

upIG

KV

gene

nam

eIG

KV

alle

le n

ame

Fct

RT

Pr

Stra

ins

Ref

eren

cese

quen

ces

Acc

essi

on n

umbe

rs

22S

4F

CaV

24

M80

407

[25]

2S5

P(5

5)C

aV24A

M80

408

[25]

2S6

FC

aV24B

–1M

8040

9 [2

5]2S

7F

CaV

24B

–2M

8041

0 [2

5]2S

8P

(56)

CaV

24D

–1M

8041

1 [2

5]2S

9P

(57)

CaV

24D

–2M

8041

2 [2

5]2S

10P

(58)

CaV

24D

–3M

8041

3 [2

5]

+


Tab

le 1

(con

tinu

ed)

MG

T n

ote

s:(1

)A lo

t of m

utat

ions

, DE

LE

TIO

Ns i

n th

e L

-PA

RT

2 an

d in

the

FR1-

IMG

T a

nd a

n IN

SER

TIO

N o

f 1 n

ucle

otid

e (t

at p

osit

ion

1101

) in

the

FR2-

IMG

T.

(2)I

n fr

ame

STO

P-C

OD

ON

at c

odon

10

in L

-PA

RT

1.(3

)A lo

t of m

utat

ions

, DE

LE

TIO

Ns a

nd IN

SER

TIO

Ns i

n th

e V

-RE

GIO

N.

(4)I

NSE

RT

ION

of 1

nuc

leot

ide

(a a

t pos

itio

n 67

2) in

the

CD

R1-

IMG

T a

nd IN

SER

TIO

N o

f 1 n

ucle

otid

e (a

at p

osit

ion

833)

in th

e FR

3-IM

GT

.(5

)A lo

t of m

utat

ions

, DE

LE

TIO

Ns a

nd IN

SER

TIO

Ns i

n th

e V

-RE

GIO

N a

nd n

on c

anon

ical

V-H

EP

TA

ME

R: C

GC

AG

TG

inst

ead

of C

AC

AG

TG

.(6

)IN

SER

TIO

N o

f 1 n

ucle

otid

e (a

at p

osit

ion

852)

in th

e FR

3-IM

GT

.(7

)DE

LE

TIO

N o

f 1 n

ucle

otid

e (b

etw

een

posi

tion

s 720

/721

) in

FR1-

IMG

T a

nd D

EL

ET

ION

of 2

2 nu

cleo

tide

s (be

twee

n po

siti

ons 7

81/7

82) b

etw

een

the

FR1-

IMG

T a

nd th

eC

DR

1-IM

GT

.(8

)IN

SER

TIO

N o

f 566

nuc

leot

ides

(pos

itio

ns 7

06–1

271)

in C

DR

3-IM

GT

.(9

)In

fram

e ST

OP

-CO

DO

N (p

osit

ions

332

–334

) at c

odon

17

in F

R1-

IMG

T.

(10)

INSE

RT

ION

of 5

66 n

ucle

otid

es (p

osit

ions

713

–127

8) in

CD

R3-

IMG

T.

(11)

DE

LE

TIO

N o

f 3 n

ucle

otid

es (b

etw

een

posi

tion

s 178

/179

) in

the

L-P

AR

T1.

(12)

No

INIT

-CO

DO

N a

nd p

arti

al F

R3-

IMG

T.

(13)

Non

can

onic

al V

-NO

NA

ME

R: A

CC

CT

CT

AA

inst

ead

of A

CA

AA

AA

CC

.(1

4)ST

OP

-CO

DO

N in

the

FR2-

IMG

T, D

EL

ET

ION

of 1

nuc

leot

ide

(bet

wee

n po

siti

ons 5

94/5

95),

and

non

cano

nica

l OC

TA

ME

R, V

-HE

PT

AM

ER

and

V-N

ON

AM

ER

.(1

5)IN

SER

TIO

N o

f 1 n

ucle

otid

e (p

osit

ion

162)

in th

e L

-PA

RT

1 an

d ST

OP

-CO

DO

Ns i

n th

e FR

2-IM

GT

.(1

6)N

o IN

IT-C

OD

ON

, in

fram

e ST

OP

-CO

DO

N (p

osit

ion

686–

688)

at c

odon

53

in th

e FR

2-IM

GT

and

non

can

onic

al O

CT

AM

ER

.(1

7)N

on c

anon

ical

V-H

EP

TA

ME

R: C

AC

AG

AC

inst

ead

of C

AC

AG

TG

and

DE

LE

TIO

N in

the

V-S

PA

CE

R (o

nly

4 nu

cleo

tide

s ins

tead

12

nucl

eoti

des)

.(1

8)N

on c

anon

ical

V-N

ON

AM

ER

: AA

AA

AA

AA

A in

stea

d of

AC

AA

AA

AT

A.

(19)

STO

P–C

OD

ON

(pos

itio

ns 5

61–5

63) i

n FR

2-IM

GT

, IN

SER

TIO

N o

f 1 n

ucle

otid

e (g

at p

osit

ion

600)

and

IN

SER

TIO

N o

f 4 n

ucle

otid

es (p

osit

ions

606

–609

) in

FR3-

IMG

T, a

nd D

EL

ET

ION

of 3

nuc

leot

ides

(bet

wee

n po

siti

ons 7

15/7

16) i

n C

DR

3-IM

GT

.(2

0)N

on c

anon

ical

V-H

EP

TA

ME

R: C

AC

AG

AG

inst

ead

of C

AC

AG

TG

.(2

1)IN

SER

TIO

N o

f 5 n

ucle

otid

es (p

osit

ions

698

–702

) in

FR3-

IMG

T a

nd n

on c

anon

ical

OC

TA

ME

R: A

TT

CT

CA

C in

stea

d of

NT

TT

GC

AT

.(2

2)In

fram

e ST

OP

-CO

DO

N (5

71–5

73) i

nste

ad o

f the

con

serv

ed 1

st-C

YS

in th

e FR

1-IM

GT

.(2

3)In

fram

e ST

OP

-CO

DO

N (p

osit

ions

490

–492

) at c

odon

74

in th

e FR

3-IM

GT

.(2

4)N

on c

anon

ical

V-H

EP

TA

ME

R: C

AC

AA

TG

inst

ead

of C

AC

AG

TG

.(2

5)N

on c

anon

ical

DO

NO

R-S

PL

ICE

: NG

G in

stea

d of

NG

T in

the

L-P

AR

T1

and

DE

LE

TIO

N o

f 2 n

ucle

otid

es (b

etw

een

posi

tion

s 360

/361

) in

the

CD

R1-

IMG

T.

(26)

DE

LE

TIO

N o

f 2

nucl

eoti

des

(bet

wee

n po

siti

ons

338/

339)

in

the

FR1-

IMG

T a

nd D

EL

ET

ION

of

1 nu

cleo

tide

(be

twee

n po

siti

ons

408/

409)

, an

d no

n ca

noni

cal

V-H

EP

TA

ME

R: C

AC

AA

TG

inst

ead

of C

AC

AG

TG

.(2

7)IN

SER

TIO

N o

f 4 n

ucle

otid

es (p

osit

ions

455

–458

) and

DE

LE

TIO

N o

f 1 n

ucle

otid

e (b

etw

een

posi

tion

s 462

/463

) in

the

FR1-

IMG

T, a

nd n

on c

anon

ical

V-H

EP

TA

ME

R:

CA

GA

GT

G in

stea

d of

CA

CA

GT

G, n

on c

anon

ical

V-N

ON

AM

ER

: AC

AT

AA

GC

C.

(28)

In fr

ame

STO

P-C

OD

ON

(pos

itio

ns 4

51–4

53) a

t cod

on 4

3 in

the

FR2-

IMG

T.

(29)

DE

LE

TIO

N o

f 16

nuc

leot

ides

(be

twee

n po

siti

ons

467/

468)

in t

he F

R3-

IMG

T, n

on c

anon

ical

V-H

EP

TA

ME

R: C

AA

GT

G in

stea

d of

CA

CA

GT

G a

nd n

on c

anon

ical

V-N

ON

AM

ER

: AT

AT

AA

GC

A in

stea

d of

AC

AT

AA

AC

C.

(30)

DE

LE

TIO

N in

the

CD

R3-

IMG

T a

nd n

on c

anon

ical

V-H

EP

TA

ME

R: C

AA

GT

G in

stea

d of

CA

CA

GT

G, p

arti

al F

R3-

IMG

T.

(31)

DE

LE

TIO

N o

f 1 n

ucle

otid

e in

L-P

AR

T1,

IN

SER

TIO

N o

f 1 n

ucle

otid

e (p

osit

ion

474)

, DE

LE

TIO

N o

f 1 n

ucle

otid

e (b

etw

een

posi

tion

s 49

5/49

6) a

nd m

utat

ions

in th

eFR

3-IM

GT

.(3

2)IN

SER

TIO

N o

f 1 n

ucle

otid

e (t

at p

osit

ion

322)

in th

e FR

1-IM

GT

.(3

3)IN

SER

TIO

N o

f 1 n

ucle

otid

e (c

at p

osit

ion

434)

in th

e FR

1-IM

GT

.


(34)

DE

LE

TIO

N o

f 1 n

ucle

otid

e (b

etw

een

posi

tion

s 33

4/33

5) in

the

FR1-

IMG

T, D

EL

ET

ION

of 1

nuc

leot

ide

(bet

wee

n po

siti

ons

416/

417)

and

non

can

onic

al V

-HE

PT

A-

ME

R: C

AC

AA

TG

inst

ead

of C

AC

AG

TG

.(3

5)In

fram

e ST

OP

-CO

DO

N a

t cod

on 6

in th

e FR

1-IM

GT

and

in fr

ame

STO

P-C

OD

ON

at c

odon

39

in th

e FR

2-IM

GT

.(3

6)ST

OP

-CO

DO

Ns

in t

he L

-PA

RT

1 an

d ST

OP

-CO

DO

Ns

in t

he F

R1-

IMG

T a

nd i

n th

e FR

2-IM

GT

and

non

can

onic

al V

-HE

PT

AM

ER

: C

AC

AA

TG

ins

tead

of

CA

CA

GT

G.

(37)

STO

P-C

OD

ON

s in

the

L-P

AR

T1

and

STO

P-C

OD

ON

in

the

FR2-

IMG

T,

DE

LE

TIO

N o

f 1

nucl

eoti

de (

betw

een

posi

tion

s 52

6/52

7) i

n th

e FR

3-IM

GT

, an

d no

nca

noni

cal O

CT

AM

ER

and

V-H

EP

TA

ME

R.

(38)

INSE

RT

ION

of 1

nuc

leot

ide

(pos

itio

n 41

8) in

the

FR1-

IMG

T a

nd n

on c

anon

ical

V-H

EP

TA

ME

R: C

AC

GT

TG

inst

ead

of C

AC

AG

TG

.(3

9)D

EL

ET

ION

of 1

2 nu

cleo

tide

s (be

twee

n po

siti

ons 4

59/4

60) i

n th

e FR

3-IM

GT

and

non

can

onic

al V

-HE

PT

AM

ER

: CA

CA

TG

T in

stea

d of

CA

CA

GT

G.

(40)

STO

P-C

OD

ON

s in

the

FR1-

IMG

T a

nd th

e FR

3-IM

GT

and

non

can

onic

al V

-HE

PT

AM

ER

: TA

CA

GT

G in

stea

d of

CA

CA

GT

G.

(41)

A lo

t of I

NSE

RT

ION

s in

the

L-P

AR

T1,

in fr

ame

STO

P-C

OD

ON

s at

cod

ons

3 an

d 18

in th

e FR

1-IM

GT

and

in fr

ame

STO

P-C

OD

ON

at c

odon

44

in th

e FR

2-IM

GT

,an

d no

n ca

noni

cal O

CT

AM

ER

.(4

2)N

on c

anon

ical

DO

NO

R-S

PL

ICE

: NG

C in

stea

d of

NG

T.

(43)

DE

LE

TIO

N o

f 4 n

ucle

otid

es (b

etw

een

posi

tion

s 497

/498

) in

the

FR1-

IMG

T.

(44)

Par

tial

V-R

EG

ION

: onl

y A

A66

to 7

1 ar

e pr

esen

t (pa

rtia

l FR

3-IM

GT

).(4

5)P

arti

al V

-RE

GIO

N: A

A10

2 to

104

are

mis

sing

(par

tial

FR

3-IM

GT

).(4

6)Se

quen

ces

diff

erin

g by

8 n

ucle

otid

es o

r le

ss t

han

8 nu

cleo

tide

s fr

om g

erm

line

map

ped

refe

renc

e se

quen

ces

are

tem

pora

rily

con

side

red

as a

llele

s of

the

se s

eque

nces

.Se

quen

ces

diff

erin

g by

mor

e th

an 8

nuc

leot

ides

fro

m g

erm

line

map

ped

refe

renc

e se

quen

ces

are

cons

ider

ed a

s ne

w u

nmap

ped

gene

s an

d ar

e de

sign

ated

by

a nu

mbe

r fo

r th

esu

bgro

up, f

ollo

wed

by

a hy

phen

and

a sm

all l

ette

r, fo

r exa

mpl

e IG

KV

2-a.

The

se d

ata

need

to b

e co

nfir

med

by

gene

tic

data

.(4

7)T

his s

eque

nce,

whi

ch d

iffe

rs fr

om th

e ge

rmlin

e m

appe

d re

fere

nce

sequ

ence

by

5 nu

cleo

tide

s, c

an b

e co

nsid

ered

tem

pora

rily

as

an a

llele

.(4

8)T

his s

eque

nce,

whi

ch d

iffe

rs fr

om th

e ge

rmlin

e m

appe

d re

fere

nce

sequ

ence

by

2 nu

cleo

tide

s, c

an b

e co

nsid

ered

tem

pora

rily

as

an a

llele

.(4

9)T

his s

eque

nce,

whi

ch d

iffe

rs fr

om th

e ne

ares

t map

ped

germ

line

gene

(AJ1

3268

3) b

y 21

nuc

leot

ides

, can

be

cons

ider

ed a

s a n

ew u

nmap

ped

gene

.(5

0)T

his s

eque

nce,

whi

ch d

iffe

rs fr

om th

e ge

rmlin

e m

appe

d re

fere

nce

sequ

ence

by

1 nu

cleo

tide

, can

be

cons

ider

ed te

mpo

rari

ly a

s an

alle

le.

(51)

The

se s

eque

nces

, whi

ch d

iffe

r fr

om t

he n

eare

st m

appe

d ge

rmlin

e ge

ne (

AJ2

3596

8) b

y re

spec

tive

ly 1

1, 9

and

15

nucl

eoti

des,

can

be

cons

ider

ed a

s ne

w u

nmap

ped

gene

s. (52)

Thi

s seq

uenc

e, w

hich

dif

fers

from

the

germ

line

map

ped

refe

renc

e se

quen

ce b

y 8

nucl

eoti

des,

can

be

cons

ider

ed te

mpo

rari

ly a

s an

alle

le.

(53)

Thi

s seq

uenc

e, w

hich

dif

fers

from

the

germ

line

map

ped

refe

renc

e se

quen

ce b

y 1

nucl

eoti

de, c

an b

e co

nsid

ered

tem

pora

rily

as

an a

llele

.(5

4)T

hese

sequ

ence

s, w

hich

dif

fer f

rom

the

germ

line

map

ped

refe

renc

e se

quen

ce b

y re

spec

tive

ly 3

and

7 n

ucle

otid

es, c

an b

e co

nsid

ered

tem

pora

rily

as a

llele

s.(5

5)D

EL

ET

ION

of 5

nuc

leot

ides

(bet

wee

n po

siti

ons 2

1/22

) in

the

FR1-

IMG

T le

adin

g to

a fr

ames

hift

and

mut

atio

ns in

the

V-R

EG

ION

.(5

6)IN

SER

TIO

N o

f 1 n

ucle

otid

e (p

osit

ion

879)

in F

R3-

IMG

T le

adin

g to

a fr

ames

hift

.(5

7)IN

SER

TIO

N o

f 1 n

ucle

otid

e (p

osit

ion

828)

in F

R3-

IMG

T le

adin

g to

a fr

ames

hift

.(5

8)ST

OP

-CO

DO

Ns i

n FR

2-IM

GT

and

INSE

RT

ION

of 1

nuc

leot

ide

(pos

itio

n 78

0) in

FR

3-IM

GT

.(5

9)In

fram

e ST

OP

-CO

DO

N (p

osit

ions

540

–542

) at c

odon

40

in F

R2-

IMG

T .

(60)

The

IG

KV

4-52

*01

(AJ2

3919

8) a

nd th

e IG

KV

4-54

*01

(AJ2

3122

3) V

-RE

GIO

N n

ucle

otid

e se

quen

ces

are

100%

iden

tica

l. T

hese

two

gene

s di

ffer

by

one

nucl

eoti

de in

thei

r L-P

AR

T2

(at p

osit

ion

12 a

ccor

ding

to th

e IM

GT

num

beri

ng).

+


Tab

le 1

(con

tinu

ed)

Ref

eren

ces:

[1]S

eidm

an, J

.G. e

t al.,

Pro

c. N

atl.

Aca

d. S

ci. U

.S.A

., 75

, 388

1–38

85 (1

978)

.[2

]Max

, E.E

. et a

l., C

ell,

21, 7

93–7

99 (1

980)

.[3

]Nis

hiok

a, Y

. et a

l., J

. Bio

l. C

hem

., 25

5, 3

691–

3694

(198

0).

[4]K

wan

, S.P

et a

l., C

ell,

26, 5

7–66

(198

1).

[5]P

ech,

M. e

t al.,

Nat

ure,

291

, 668

–670

(198

1).

[6]S

elsi

ng, E

. et a

l., C

ell,

25, 4

7–58

(198

1).

[7]H

oech

tl, J

. et a

l., P

roc.

Nat

l. A

cad.

Sci

. U.S

.A.,

79, 1

383–

1387

(198

2).

[8]H

awle

y, R

.G. e

t al.,

Pro

c. N

atl.

Aca

d. S

ci. U

.S.A

., 79

, 742

5–74

29 (1

982)

.[9

]Joh

o, R

. et a

l., E

MB

O J

., 3,

185

–191

(198

4).

[10]

Hei

nric

h, G

. et a

l., J

. Exp

. Med

., 15

9, 4

17–4

35 (1

984)

.[1

1]E

ven,

J. e

t al.,

EM

BO

J.,

4, 3

439–

3445

(198

5) a

nd M

ilste

in, C

. et a

l., E

ur. J

. Im

mun

ol.,

22, 1

627–

1634

(199

2).

[12]

Kel

ley,

D.E

. et a

l., M

ol. C

ell.

Bio

l., 5

, 166

0–16

75 (1

985)

.[1

3]B

oyd,

R. T

. et a

l., P

roc.

Nat

l. A

cad.

Sci

. U.S

.A.,

83, 9

134–

9138

(198

6).

[14]

Cor

bet,

S. e

t al.,

J. I

mm

unol

., 13

8, 9

32–9

39 (1

987)

.[1

5]H

elle

r, M

. et a

l., J

. Exp

. Med

., 16

6, 6

37–6

46 (1

987)

.[1

6]Sa

nz, I

. et a

l., P

roc.

Nat

l. A

cad.

Sci

. U.S

.A.,

84, 1

085–

1089

(198

7).

[17]

Wys

ocki

, L.J

. et a

l., J

. Exp

. Med

., 16

6, 1

–11

(198

7).

[18]

Ala

nen,

A. e

t al.,

Eur

. J. I

mm

unol

., 19

, 196

1–19

63 (1

989)

.[1

9]N

g, K

.H. e

t al.,

J. I

mm

unol

., 14

3, 6

38–6

48 (1

989)

.[2

0]P

onat

h, P

.D. e

t al.,

Imm

unog

enet

ics,

29,

249

–257

(198

9).

[21]

Val

iant

e, N

.M. a

nd C

aton

, A.J

., Im

mun

ogen

etic

s, 3

2, 3

45–3

50 (1

990)

.[2

2]D

udle

y, J

.P. e

t al.,

J. V

irol

., 65

, 391

1–39

14 (1

991)

.[2

3]K

im, S

.O. e

t al.,

Imm

unog

enet

ics,

34,

231

–241

(199

1).

[24]

Fost

er, M

.H. e

t al.,

J. I

mm

unol

., 15

1, 8

14–8

24 (1

993)

.[2

5]H

ende

rson

, T.J

. et a

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Table 2. Mouse (Mus musculus) IGKV orphonsFct: FUNCTIONALITY; P: Pseudogene; ORF: Open Reading FrameReference sequences in bold have been mapped: ‘mapped‘ refers to sequences which have been obtained from clones (phages,cosmids, YACs...) either by subcloning or PCR, and does not apply to sequences obtained directly from genomic DNA.In the ‘Sequences from the literature‘ column, names of the sequences are preceded by the designation of the mouse strain.

IGKVsubgroup

IGKVgene name

Fct Strain Referencesequences

Accessionnumbers

Sequences fromthe literature

1/OR6-1 P (1) C57BL/6 gw1 AJ235937 [3] BALB/c, Psi 1.7 [X58991][1]1/OR16-1 P (2) 129/Sv 68 Z72381 [2] C57BL/6, be2 [AJ235971][3]1/OR19-1 P (3) 129/Sv 70/2 Z72383 [2] C57BL/6, bn2 [AJ235972][3]

14 14/OR6-2 P (4) C57BL/6 ca9 AJ231240 [3] BALB/c, 9B.8 [X58992][1]14/OR6-3 P (5) C57BL/6 cc9 AJ231242 [3]14/OR16-2 P (6) C57BL/6 bg9 AJ235977 [3]

17 17/OR16-3 P C57BL/6 bf20part1 AJ235930 [3]17/OR16-4 ORF C57BL/6 bf20part2 AJ235929 [3]17/OR19-2 P C57BL/6 bu20part1 AJ235931 [3]17/OR19-3 ORF (7) C57BL/6 bu20part2 AJ235932 [3]

IMGT notes:(1) A lot of mutations, DELETIONs and INSERTIONs.(2) INSERTION of 1 nucleotide (position 645) in CDR1-IMGT and DELETION of 1 nucleotide (between positions 796/797)

in FR3-IMGT.(3) DELETION of 2 nucleotides (between positions 518/519) in FR1-IMGT and DELETION of 1 nucleotide (between posi-

tions 742/743) in FR3-IMGT.(4) INSERTION of 2 nucleotides (positions 560-561) in FR3-IMGT.(5) INSERTION of 1 nucleotide (positions 385) in CDR1-IMGT and DELETION of 3 nucleotides (between positions 427/

428) in FR2-IMGT.(6) DELETION or INSERTION leading a frameshift in the CDR3-IMGT.(7) CONSERVED-TRP (codon 41 in FR2-IMGT) is replaced by a Gly and 2nd-CYS (codon 104 in FR3-IMGT) is replaced by

a Tyr.

References:[1] Lawler, A.M. et al., Mol. Immunol. 29, 295–301 (1992).[2] Schupp, I. W. et al., Immunogenetics, 45, 180–187 (1997).[3] Schäble, K.F. et al., Eur. J. Immunol., 29, 2082–2086 (1999).

Mouse (Mus musculus) IGKV orphons by chromosome

Chromosome IGKV subgroup IGKV gene name

6 IGKV1 IGKV1/OR6-1IGKV14 IGKV14/OR6-2

IGKV14/OR6-3

16 IGKV1 IGKV1/OR16-1IGKV14 IGKV14/OR16-2IGKV17 IGKV17/OR16-3

IGKV17/OR16-4

19 IGKV1 IGKV1/OR19-1IGKV17 IGKV17/OR19-2

IGKV17/OR19-3

IGKV1


Table 3. Correspondence betweenmouse (Mus musculus) IGKVnomenclatures

A Correspondence between mouse IGKV subgroup designations

Information on the related human IGKV subgroups is shown in the right column.

IMGT mouseIGKV subgroups

Previous mouse IGKV subgroupdesignations

Ref. [1] Ref. [2–6]

IMGT related humanIGKV subgroups

VK1 and VK2 VK1 and VK2 IGKV2IGKV2 VK24/25 VK24/25 IGKV2IGKV3 VK21 VK21 IGKV7IGKV4 VK4/5 VK4/5 IGKV1, IGKV2, IGKV3IGKV5 VK23 VK23 IGKV6IGKV6 VK19/28 VK19/28 IGKV4IGKV7 VK22 VK22 IGKV4IGKV8 VK8 VK8 IGKV4IGKV9 VK9A IGKV9/10 IGKV1IGKV10 VK10 IGKV9/10 IGKV1IGKV11 VK11 VK11 IGKV1IGKV12 VK12/13 VK12/13 IGKV1IGKV13 VK33/34 VK33/34 IGKV1IGKV14 VK9B IGKV9/10 IGKV1IGKV15 VK32 VK32 IGKV1IGKV16 VKRF VKRF IGKV1IGKV17 VK20 VK20 IGKV5IGKV18 dv IGKV3IGKV19 38c IGKV1

References:[1] Almagro, J. C. et al., Immunogenetics, 47, 355–363 (1998).[2] Kirschbaum, T. et al., Eur. J. Immunol., 28, 1458–1466 (1998).[3] Kirschbaum, T. et al., Eur. J. Immunol., 29, 2057–2064 (1999).[4] Röschenthaler, F. et al., Eur. J. Immunol., 29, 2065–2071 (1999).[5] Thiebe, R. et al., Eur. J. Immunol., 29, 2072–2081 (1999).[6] Schäble, K.F. et al., Eur. J. Immunol., 29, 2082–2086 (1999).

Reference SequencesFor each gene, an IMGT reference se-

quence accession number is given (tables 1, 2,5–8). For the functional or ORF genes, theIMGT reference sequence accession numberis that corresponding to the allele *01. Notethat the number *01 does not necessarilymean that other alleles are already known, butit signifies that any new polymorphic se-quence will be described by comparison tothat allele *01. Although the IMGT accessionnumbers are the same as those from theEMBL/GenBank/DDBJ generalist databases,the content of the IMGT/LIGM-DB flat files

differs by the expertized annotations, addedby IMGT.

AllelesThe number of alleles of the IGKV, IGKJ

and IGKC genes (tables 1, 6–8) is accordingto ‘Tables of alleles and Alignments of alleles,in the IMGT Repertoire. Alignments of allknown germline functional and ORF se-quences assigned to the different alleles, bycomparison to the allele *01, are displayed athttp://imgt.cines.fr. A dash (–) indicates thatallele polymorphism of the pseudogenes hasnot been studied.


B Correspondence with the previous provisory mouse (Mus musculus) IMGT IGKV gene names

Only mouse (Mus musculus) gene names quoted in [4] are shown in this table.

IGKVsubgroup

IMGT mouseIGKV gene andallele name

Previous provisoryIMGT mouse genename [4]

IGKVsubgroup

IMGT mouseIGKV gene andallele name

Previous provisoryIMGT mouse genename [4]

1 1-110*01 1S11-110*02 1S41-117*01 1S21-117*02 1S51-122*01 1S31-133*01 1S71-135*01 1S6

2 2-109*02 2S32-112*01 2S12-a*01 2S2

3 3-1*01 3S73-2*01 3S63-3*01 3S53-4*01 3S83-5*01 3S43-6*01 3S93-7*01 3S33-8*01 3S103-9*01 3S113-10*01 3S23-11*01 3S123-12*01 3S1

4 4-50*01 4S104-51*01 4S14-58*01 4S24-59*01 4S44-61*01 4S84-68*01 4S64-69*01 4S74-70*01 4S54-77*01 4S94-78*01 4S134-81*01 4S144-83*01 4S124-86*01 4S34-90*01 4S11

5 5-48*01 5S1

6 6-14*01 6S56-15*01 6S66-17*01 6S76-20*01 6S86-32*02 6S16-b*01 6S26-c*01 6S36-d*01 6S4

7 7-33*01 7S1

8 8-16*01 8S28-18*01 8S38-19*01 8S48-21*01 8S58-28*02 8S1

9 9-120*01 9S19-123*01 9S49-124*01 9S39-129*01 9S2

10 10-94*01 10S410-94*02 10S610-94*03 10S310-95*01 10S710-96*01 10S110-96*02 10S510-96*03 10S2

12 12-41*02 12S112-e*01 12S2

13 13-84*01 13S313-85*02 13S113-85*03 13S2

14 14-111*01 14S114-134-1*01 14S4

17 17-134*01 17S1


Table 4. Number of mouse (Mus musculus) germline IGKV genes on chromosome 6 andpotential repertoire


Table 5. Mouse (Mus musculus) germline IGKJ genes


Table 6. Mouse (Mus musculus) IGKJ alleles

Table 7. Mouse (Mus musculus, Mus saxicola, Mus pahari, Mus minutoides, Mus cookii, Mus spretus) IGKCgenes and alleles


Table 7 (continued)


Table 8. Complete list of the mouse (Mus musculus) IGK genes on chromosome 6


Table 8 (continued)

+


Table 8 (continued)


Fig. 2. The ‘CLASSIFICATION’concept of IMGT-ONTOLOGY,exemplified for the mouse IGKVgenes.

Correspondences betweenNomenclatures and Numberings

Correspondence between the mouse IGKVgroup and gene nomenclatures is reported intable 3.

In order to easily compare sequences ofimmunoglobulins and T cell receptors, aunique numbering has been defined for thevariable regions [36, 37]. Correspondence be-tween the IMGT unique numbering and othernumberings for the IGKV genes is availablefrom the IMGT Scientific chart. The IMGTunique numbering relies on the high conser-vation of the structure of the variable region.This numbering takes into account and com-bines the definition of the framework (FR)and complementarity determining regions(CDR) [38], structural data from X-ray dif-fraction studies [39], and the characterizationof the hypervariable loops [40]. The uniquenumbering has allowed the redefinition of thelimits of the FR and CDR [36]. The FR-IMGT and CDR-IMGT lengths themselves

become crucial information characterizingthe variable regions belonging to a group, asubgroup, and/or a gene. For example, for agermline gene of the mouse (M. musculus)IGKV1 subgroup, the lengths of the 3 CDR-IMGT, in number of amino acids is designat-ed as [11.3.7] (IMGT Repertoire12D and 3Dstructures) [36]. The unique numbering isused as the output of the IMGT/V-QUESTalignment tool, and in the ‘Alignments ofalleles (IMGT Repertoire1Proteins and al-leles).

Acknowledgements

I am grateful to Valérie Contet for the editorialwork and to Sandrine Béranger for the figures. IMGTis funded by the European Union’s 5th PCRDT(QLG2-2000-01287) program, the Centre National dela Recherche Scientifique, the Ministère de la Re-cherche and the Ministère de l’Education Nationale.Subventions have been received from Associationpour la Recherche sur le Cancer and the Région Lan-guedoc-Roussillon.


Appendix

The ‘CLASSIFICATION’ concept ofIMGT-ONTOLOGYThe ‘CLASSIFICATION’ concept of IMGT-ON-

TOLOGY (fig. 2) organizes the immunogeneticsknowledge useful to name and classify the immuno-globulin genes [32].

‘Locus’: A locus is a group of immunoglobulingenes that are ordered and are localized in the samechromosomal location in a given species. The ‘locus’IGK on chromosome 6 is one of the three main immu-noglobulin loci in the mouse genome. Immunoglobulingenes have also been identified in other chromosomallocations outside the main loci which represent newinstances of the concept locus. However, the genes theycontain, designated as orphons, are not functional.

‘Group’: A group is a set of genes which share thesame ‘gene type’ (V, D, J or C) and participate poten-tially in the synthesis of a polypeptide of the same‘chain type’. By extension, a group includes the relatedpseudogenes and orphons. A 4-letter root designatesthe ‘group’: for example, IGKV, IGKJ, and IGKC forthe immunoglobulin kappa genes.

‘Subgroup’: A subgroup is a set of genes whichbelong to the same group, in a given species, and whichshare at least 75% identity at the nucleotide level (in

the germline configuration for V, D, and J). For exam-ple, the mouse (M. musculus) IGKV genes belong to 19subgroups.

‘Gene’: A gene is defined as a DNA sequence thatcan be potentially transcribed and/or translated (thisdefinition includes the regulatory elements in 5) and 3),and the introns, if present). Instances of the ‘gene’ con-cept are gene names. By extension, orphons and pseu-dogenes are also instances of the ‘gene’ concept. Foreach gene, IMGT has defined a reference sequence.For the V, D, and J genes, the reference sequence cor-responds to a germline entity. The rules for the choiceof the reference sequences are described at http://imgt.cines.fr in the IMGT Scientific chart.

‘Allele’: An allele is a polymorphic variant of agene. Alleles are described, exhaustively and in a stan-dardized way, for the four ‘core’ coding regions, that isthe germline V-REGIONs, D-REGIONs, and J-RE-GIONs, and for the C-REGIONs, from immunoglobu-lin genes. These alleles refer to sequence polymor-phisms, with mutations described at the sequence level[1]. Their sequences are compared to the referencesequence designated as *01 (see IMGT Scientific chartat http://imgt.cines.fr for IMGT description of muta-tions, and IMGT allele nomenclature for sequencepolymorphisms).

References

1 Lefranc MP: IMGT (ImMunoGe-neTics) Locus on Focus. A new sec-tion of Experimental and ClinicalImmunogenetics. Exp Clin Immu-nogenet 1998;15:1–7.

2 Pallarès N, Frippiat JP, GiudicelliV, Lefranc MP: The human immu-noglobulin lambda variable (IGLV)genes and joining (IGLJ) segments.Exp Clin Immunogenet 1998;15:8–18.

3 Barbié V, Lefranc MP: The humanimmunoglobulin kappa variable(IGKV) genes and joining (IGKJ)segments. Exp Clin Immunogenet1998;15:171–183.

4 Martinez C, Lefranc MP: Themouse (Mus musculus) immuno-globulin kappa variable (IGKV)genes and joining (IGKJ) segments.Exp Clin Immunogenet 1998;15:184–193.

5 Pallarès N, Lefebvre S, Contet V,Matsuda F, Lefranc MP: The hu-man immunoglobulin heavy vari-able (IGHV) genes. Exp Clin Immu-nogenet 1999;16:36–60.

6 Ruiz M, Pallarès N, Contet V, Bar-bié V, Lefranc MP: The humanimmunoglobulin heavy diversity(IGHD) and joining (IGHJ) seg-ments. Exp Clin Immunogenet1999;16:173–184.

7 Scaviner D, Barbié V, Ruiz M,Lefranc MP: Protein displays ofthe human immunoglobulin heavy,kappa and lambda variable andjoining regions. Exp Clin Immuno-genet 1999;16:234–240.

8 Folch G, Lefranc MP: The human Tcell receptor beta variable (TRBV)genes. Exp Clin Immunogenet 2000;17:42–54.

9 Scaviner D, Lefranc MP: The hu-man T cell receptor alpha variable(TRAV) genes. Exp Clin Immuno-genet 2000;17:83–96.

10 Scaviner D, Lefranc MP: The hu-man T cell receptor alpha joining(TRAJ) genes. Exp Clin Immuno-genet 2000;17:97–106.

11 Folch G, Lefranc MP: The human Tcell receptor beta diversity (TRBD)and beta joining (TRBJ) genes. ExpClin Immunogenet 2000;17:107–114.

12 Artero S, Lefranc MP: The Teleosteiimmunoglobulin heavy IGH genes.Exp Clin Immunogenet 2000;17:148–161.

13 Artero S, Lefranc MP: The Teleosteiimmunoglobulin light IGL1 andIGL2 V, J and C genes. Exp ClinImmunogenet, 2000;17:162–172.


14 Folch G, Scaviner D, Contet V, Le-franc MP: Protein displays of thehuman T cell receptor alpha, beta,gamma and delta variable and join-ing regions. Exp Clin Immunogenet2000;17:205–215.

15 Bosc N, Lefranc MP: The Mouse(Mus musculus) T cell receptor betavariable (TRBV), diversity (TRBD),and joining (TRBJ) genes. Exp ClinImmunogenet 2000;17:216–228.

16 Bosc N, Contet V, Lefranc MP: Themouse (Mus musculus) T cell recep-tor delta variable (TRDV), diversity(TRDD), and joining (TRDJ) genes.Exp Clin Immunogenet 2001;18:51–58.

17 Lefranc MP: Nomenclature ofthe human immunoglobulin heavy(IGH) genes. Exp Clin Immunoge-net 2001;18:100–116.

18 Lefranc MP: Nomenclature of thehuman immunoglobulin kappa(IGK) genes. Exp Clin Immunoge-net 2001;18:161–174.

19 Lefranc MP: Nomenclature of thehuman immunoglobulin lambda(IGL) genes. Exp Clin Immunogenet2001;18:242–254.

20 Kirschbaum T, Pourrajabi S, Zo-cher I, Schwendinger J, Heim V, Ro-schenthaler F, Kirschbaum V, Za-chau HG: The 3) part of the immu-noglobulin kappa locus of themouse. Eur J Immunol 1998;28:1458–1466.

21 Kirschbaum T, Roschenthaler F,Bensch A, Holscher B, Lautner-Rieske A, Ohnrich M, Pourrajabi S,Schwendinger J, Zocher I, ZachauHG: The central part of the mouseimmunoglobulin kappa locus. Eur JImmunol 1999;29:2057–2064.

22 Röschenthaler F, Kirschbaum T,Heim V, Kirschbaum V, SchableKF, Schwendinger J, Zocher I, Za-chau HG: The 5) part of the mouseimmunoglobulin kappa locus. Eur JImmunol 1999;29:2065–2071.

23 Thiebe R, Schable KF, BenschA, Brensing-Kuppers J, Heim V,Kirschbaum T, Mitlohner H, Ohn-rich M, Pourrajabi S, RoschenthalerF, Schwendinger J, Wichelhaus D,Zocher I, Zachau HG: The variablegenes and gene families of the mouseimmunoglobulin kappa locus. Eur JImmunol 1999;29:2072–2081.

24 Schäble KF, Thiebe R, Bensch A,Brensing-Kuppers J, Heim V,Kirschbaum T, Lamm R, OhnrichM, Pourrajabi S, Roschenthaler F,Schwendinger J, Wichelhaus D,Zocher I, Zachau HG: Characteris-tics of the immunoglobulin Vkappagenes, pseudogenes, relics and or-phons in the mouse genome. Eur JImmunol 1999;29:2082–2086.

25 Sakano H, Huppi K, Heinrich G,Tonegawa S: Sequences at the so-matic recombination sites of immu-noglobulin light-chain genes. Nature1979;280:288–294.

26 Max EE, Seidman JG, Leder P: Se-quences of five potential recombina-tion sites encoded close to an immu-noglobulin kappa constant regiongene. Proc Natl Acad Sci USA 1979;76:3450–3454.

27 Max EE, Maizel JV Jr, Leder P: Thenucleotide sequence of a 5.5-kilo-base DNA segment containing themouse kappa immunoglobulin J andC region genes. J Biol Chem 1981;256:5116–5120.

28 Queen C, Baltimore D: Immuno-globulin gene transcription is acti-vated by downstream sequence ele-ments. Cell 1983;33:741–748.

29 Picard D, Schaffner W: A lympho-cyte-specific enhancer in the mouseimmunoglobulin kappa gene. Na-ture 1984;307:80–82.

30 Queen C, Stafford J: Fine mappingof an immunoglobulin gene activa-tor. Mol Cell Biol 1984;4:1042–1049.

31 Meyer KB, Neuberger MS: The im-munoglobulin kappa locus containsa second, stronger B-cell-specific en-hancer which is located downstreamof the constant region. EMBO J1989;8:1959–1964.

32 Giudicelli V, Lefranc MP: Ontologyfor immunogenetics: IMGT-ON-TOLOGY. Bioinformatics 1999;12:1047–1054.

33 Ruiz M, Giudicelli V, Ginestoux C,Stoehr P, Robinson J, Bödmer J,Marsh S, Bontrop R, Lemaitre M,Lefranc G, Chaume D, Lefranc MP:IMGT, the international ImMuno-GeneTics database. Nucleic AcidsRes 2000;28:219–221.

34 Lefranc MP: IMGT ImMunoGe-neTics database. Int Bioforum 2000;4:98–100.

35 Lefranc MP: IMGT, the interna-tional ImMunoGeneTics database.Nucleic Acids Res 2001;29:207–209.

36 Lefranc MP: The IMGT uniquenumbering for Immunoglobulins, Tcell receptors and Ig-like domains.Immunologist 1999;7:132–136.

37 Lefranc MP: Unique database num-bering system for immunogenetics.Immunol Today 1997;18:509.

38 Kabat EA, Wu TT, Reid-Miller M,Perry HM, Gottesman KS: Se-quences of Proteins of Immunologi-cal Interest, ed 4. Washington, Pub-lic Health Service 1987.

39 Satow Y, Cohen GH, Padlan EA,Davies DR: Phosphocholine bind-ing immunoglobulin Fab McPC603.An X-ray diffraction study at 2.7 Å.J Mol Biol 1986;190:593–604.

40 Chothia C, Lesk AM: Canonicalstructures for the hypervariable re-gions of immunoglobulins. J MolBiol 1987;196:901–917.

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