RFLP alleles and frequencies: Human
IGKV
IGKV2-29 gene
IGKV2D-29 gene
Human IGKV2-29 gene
Method: PCR and restriction enzyme mapping.
Primers AF68
(IPP700002)
and AF76
(IPP700000)
(IMGT/PRIMER-DB).
IGKV
gene name |
IGKV
allele name |
Fct |
Enzymes (1) |
Fragments (bp) (1) |
Polym. type (2) |
Frequencies (3) |
Swedish Caucasians
[1] n=206 |
Chinese Hong Kong
[1] n=232 |
| IGKV2-29 |
IGKV2-29*01 |
P |
BsmI
+
AgeI |
846 + 109 |
RS |
0.92 |
0.50 |
| IGKV2-29*02 |
F |
955 |
RS |
0.08 |
0.50 |
| IGKV2D-29 |
|
F/ORF |
742 + 214 |
|
1.00 |
1.00 |
IMGT notes:
| (1) |
The amplified band is of the same size for the IGKV2-29 and
IGKV2D-29 genes (955 bp and 956 bp respectively). The double
digest allows to remove the IGKV2D-29 band (cut by AgeI) and
to identify the polymorphic IGKV2-29*01 band (cut by BsmI)
[1].
The AgeI site (A CCGGT) is present at positions 197-202 (codons
66-68) in the IGKV2D-29 gene (according to the
IMGT
unique numbering for V-REGION).
The BsmI recognition site (GAATGC) is present at positions
311-316 (codons 104-106) of the IGKV2-29*01.
Interestingly this site corresponds to the stop codon (codon 104)
which makes IGKV2-29*01 a pseudogene. The polymorphic nucleotide
substitution a312>c in IGKV2-29*02 suppresses the stop codon and
restores the 2nd-CYS 104. The absence of the BsmI site allows
therefore to identify the functional IGKV2-29*02 allele
including, if present, the *03 and *04 alleles, as in
Black Africans [2]. |
| (2) |
Polymorphism type: RS, polymorphic Restriction Sites. |
| (3) |
n= number of alleles
Alleles IGKV2-29*03 and *04 identified in Mozambique
Black Africans [2] cannot be detected by this
restriction enzyme mapping.
|
Method: PCR and restriction enzyme mapping.
Primers 5'A183
(IPP800004)
and 3'A182
(IPP800005)
(IMGT/PRIMER-DB).
IGKV
gene name |
IGKV
allele name |
Fct |
Enzymes (1) |
Fragments (bp) |
Polym. type (2) |
Enzymes (3) |
Fragments (bp) |
Polym. type (2) |
Frequencies (4) |
Danish
Caucasians
[2] |
Greenland
Eskimos
[2] |
Mozambique
Black Africans
[2] |
| IGKV2-29 |
IGKV2-29*01 |
P |
MboI |
175 + 220 |
RS |
SphI |
395 |
RS |
0.92 |
0.55 |
0.57 |
| IGKV2-29*02 |
F |
395 |
RS |
300 + 95 |
RS |
0.08 |
0.45 |
0.23 |
| IGKV2-29*03 (4) |
F |
175 + 220 |
RS |
300 + 95 |
RS |
|
|
0.19 |
IMGT notes:
| (1) |
The MboI site ( GATC)
is present at positions 159-162 (codons 53-54) of the
IGKV2-29*01 and *03 alleles. |
| (2) |
Polymorphism type: RS, polymorphic Restriction Sites. |
| (3) |
The SphI site (GCATG C) is present at
positions 311-316 (codons 104-105) of the IGKV2-29*02 and *03
alleles. The presence of the SphI site, that corresponds to the codon of
2nd-CYS 104, allows to identify the functional IGKV2-29 alleles,
whereas the absence of the SphI site, that corresponds to a
stop codon, allows to identify the pseudogene IGKV2-29*01 allele. |
| (4) |
The IGKV2-29*03 (L-PART2 g12>a) allele is probably not amplified
with primer 5'A183
(IPP800004).
|
References:
Human IGKV2D-29 gene
Method: PCR and restriction enzyme mapping.
Primers AF103
(IPP800001)
and AF68
(IPP700002)
(IMGT/PRIMER-DB).
IGKV
gene name |
IGKV
allele name |
Fct |
Enzymes (1) |
Fragments (bp) (1) |
Polym. type (2) |
Enzymes (3) |
Fragments (3) |
Polym. type (2) |
Frequencies (4) |
Swedish Caucasians
[1] n=206 |
Chinese Hong Kong
[1] n=232 |
| IGKV2D-29 |
IGKV2D-29*01 |
F |
BsmAI (or isoschizomer Alw261) |
555 |
RS |
Tsp4CI |
472 + 87 |
RS |
0.90 |
0.53 |
| IGKV2D-29*02 |
F |
309 + 246 |
RS |
472 + 87 |
RS |
0.05 |
0.43 |
| ORF |
555 |
RS |
0.05 |
0.04 |
IMGT notes:
| (1) |
The BsmAI recognition site GTCTC is present at
positions 144-148 (codons 48-50) of the IGKV2D-29*02 alleles
(F and ORF). The c145>t polymorphic nucleotide substitution
corresponds to the P49>S in the IGKV2D-29*02 alleles. |
| (2) |
Polymorphism type: RS, polymorphic Restriction Sites. |
| (3) |
The Tsp4CI site
ACN GT is present at positions
2-6 of the V-HEPTAMER (CACAGTG) of the functional IGKV2D-29*01
and *02 alleles, but absent of the IGKV2D-29*02 ORF allele
due to a mutation at position 6 (CACAGAG). |
| (4) |
n= number of alleles. |
Reference:
Created: 01/12/2003
Author: Marie-Paule Lefranc
Marie-Paule.Lefranc@igh.cnrs.fr
Editor: Chantal Ginestoux
Contact: Marie-Paule Lefranc
Software material and data coming from IMGT server may be used for academic research only,
provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics
information system® http://www.imgt.org
(founder and director: Marie-Paule Lefranc, Montpellier, France)."
References to cite:
Lefranc, M.-P. et al.,
Nucleic Acids Research, 27, 209-212 (1999)
Cover of NAR;
Ruiz, M. et al.,
Nucleic Acids Research, 28, 219-221 (2000);
Lefranc, M.-P.,
Nucleic Acids Research, 29, 207-209 (2001);
Lefranc, M.-P.,
Nucleic Acids Res., 31, 307-310 (2003);
Lefranc, M.-P. et al.,
In Silico Biol., 5, 0006 (2004) [Epub],
5, 45-60 (2005);
Lefranc, M.-P. et al.,
Nucleic Acids Res., 33, D593-D597 (2005)
Full text;
Lefranc, M.-P. et al.,
Nucleic Acids Research 2009 37:
D1006-D1012; doi:10.1093/nar/gkn838
Full text.
