Table II.
Cloned nurse shark Igk
| Clone name a BAC# - coordinate |
VL gene b | PCR product L-V-J size c |
Number VL | Pst I d fragment |
function e |
|---|---|---|---|---|---|
| BAC1 - Ba010G16 | Vk1 | 1.25 kb | 1 | 1.2 kb | functional |
| BAC2 - Ba011G2 | psVk2a Vk2b |
1.15 1.05 |
2 | 1.4 1.5 |
RSS cgc functional |
| BAC4 - Ba017J16 | psVk18 Vk30 |
1.1 1.1 |
2 | 1.4 | RSS cgc functional |
| BAC5 - Ba017K15 | Vk5 | 1.1 | 1 | 1.5 | functional |
| BAC6 - Ba028C1 | psVk6a Vk6b Vk6c |
1.1 1.1 1.1 |
3 | 1.4 | RSS cgc Vk6b defective CL functional |
| BAC7 - Ba036O8 | psVk8 | 1.1 | 1 | 1.4 | RSS cgc |
| BAC9 - Ba044C13 | psVk8 | 1.1 | 1 | 1.4 | RSS cgc |
| BAC10- Ba050O1 | VkR7 | 0.55 | 1 | 0.8 | VkR7 in-frame VJ |
| BAC11- Ba057N16 | psVk11 | 1.1 | 1 | 4.4 | Stop in CDR2 |
| BAC12- Ba068L10 | psVk12 | 1.1 | 1 | 1.4 | Splice site defect; RSS cag; stop |
| BAC14- Ba085G1 | psVk8 | 1.1 | 1 | 1.4 | BAC7-Ba036O8 |
| BAC16- Ba099E18 | Vk16 | 1.1 | 1 | 1.5 | functional |
| BAC17- Ba104M1 | VkRE18 | 0.55 | 1 | 1.4 | VkRE18 in-frame VJ |
| BAC18- Ba107M16 | Vk18b psVk18 |
1.1 1.1 |
2 | 1.4 | functional RSS cgc |
| BAC19- Ba109L24 | Vk19 | 1.1 | 1 | 1.4 | functional |
| BAC21- Ba116A15 | Vk6b | 1.1 | 1 | 1.4 | functional |
| BAC22- Ba121B18 | (ND) psVk8 |
1.15 1.1 |
2 | 1.5 1.4 |
(ND) BAC7 - Ba036O8 |
| BAC23- Ba141C21 | Vk5 psVk18 |
1.1 1.1 |
3 | 1.5 1.4 |
functional RSS cgc |
| VkR7 | 0.55 | 0.8 | VkR7 in-frame VJ | ||
| BAC26- Ba156I14 | psVk18 | 1.1 | 1 | 1.4 | RSS cgc |
| BAC27- Ba176B16 | psVk27 | 1.1 | 1 | 1.4 | RSS cgc |
| BAC29- Ba199O6 | psVk8 | 1.1 | 1 | 1.4 | BAC7 - Ba036O8 |
| BAC30- Ba202P14 | Vk30 | 1.1 | 1 | 1.5 | functional |
| BAC36- Ba215F13 | Vk36 | 1.1 | 1 | 1.4 | functional |
| BAC38- Ba217B20 | psVk2a Vk2b |
1.1 1.1 |
2 | 1.4 1.5 |
BAC2-Ba011G2 |
| BAC41- Ba237L13 | psVk8 | 1.1 | 1 | 1.4 | BAC7-Ba036O8 |
| BAC43- Ba311O24 | Vk43 | 1.1 | 1 | 1.4 | functional |
| BAC45- Ba329G13 | Vk45 | 1.1 | 1 | 1.5 | functional |
| BAC46- Ba648D9 | Vk18b psVk18 |
1.1 1.1 |
2 | 1.4 1.4 |
BAC18-Ba107M16 |
| BAC49- Ba671L7 | Vk36 psVk49 |
1.1 1.1 |
2 | 1.4 1.5 |
functional RSS cgc |
| BAC50- Ba722N1 | psVk2a Vk50 |
1.1 1.1 |
2 | 1.4 1.3 |
RSS cgc functional |
| BAC51- Ba735C14 | psVk18 | 1.1 | 1 | 1.4 | BAC26-Ba156I14 |
| Bacteriophage clones f | |||||
| 9-NS4 | Vk52 | 1.1 | functional | ||
| 28-NS4 (S10) | Vk53 | 1.1 | functional | ||
| 7-NS4 | psVk54 | 1.1 | stop in FR2 | ||
| R4 | VkR4 | 0.55 | in-frame VJ | ||
| R6 | psVkR6 | 0.55 | insertion in FR1 | ||
| R18 | VkR18 | 0.55 | in-frame VJ | ||
| R19 | psVkR19 | 0.55 | insertion in FR1 |
BAC# is our nomenclature, whereas coordinates refer to plate addresses of the shark library from Arizona Genomics Institute.
Sequence submitted to GenBank. “ps” prefix indicates pseudogene, R indicates GL-joined VJ.
PCR primers in leader and JL. PCR fragment of 0.55 kb indicates GL-joined VJ (highlighted rows) and one >1 kb a split gene with ~500 bp intersegmental region.
Southern blotting of BAC DNA, filter probed with kappa probes to VL or CL.
VL gene determined non-functional “ps” prefix due to (1) mutation in RSS (RSS cgc), (2) splice motif defect, (3) insertions or stop codon that destroy the reading frame, or (4) defective C exon, where noted.
Genomic clones containing kappa genes, obtained from shark-Y DNA in previous study [26]. They are listed by their former phage names.