Table 3.
Comparisons of constant region exon sequences and positions of IGHM, IGHG and IGHE in BAC 27N5 (AY386696) with those in chrUn0439
| A. IGHM in BAC 27N5 (AY386696) constant region exon positions | chrUn0439 NW_003159763 positions | Number of confirming traces (yes) | ||||
|---|---|---|---|---|---|---|
| 3302-5095 | 74083-72286 | |||||
| Exon | Codon position | Codon position | yes | no | ||
| 1 | 3346-3348 | Gly GGT | Gly GGC | 74038-74036 | 8 | 0 |
| 3412-3414 | Val GTC | Ser ATC | 73975-73973 | 3 | 3 | |
| 3511-3513 | Ser TCG | STOP TCA | 73873-73871 | 3 | 4 | |
| 3583-3585 | Ser AGC | Asp GAC | 73801-73799 | 1 | 2 | |
| 2 | 3860-3862 | Leu CTG | Leu CTA | 73525-73523 | 2 | 5 |
| 3 | 4327-4330 | Ile ATC | Ile ATT | 73057-73055 | 1 | 0 |
| 4408-4410 | Ser AGC | Ser AGT | 72974-72972 | 1 | 0 | |
| 4 | 4901-4903 | Pro CCA | Pro CCG | 72483-72481 | 6 | 0 |
| B. IGHG in BAC 27N5 (AY386696) positions | ||||||
| 55582-56945 | 24231-22868 | |||||
| Exon | Codon position | Codon position | Yes | no | ||
| Hinge | 56073-56074 | [A]CAa Thr | [A]CG Met | 23742-23741 | 3 | 0 |
| Hinge | 56094-56096 | ACGb | ATGb | 23719-23717 | 1 | 2 |
| 2 | 56434-56436 | Thr ACGc | Ala GCGc | 23383-23381 | 4 | 0 |
| C. IGHE in BAC 27N5 (AY386696) positions | ||||||
| 69248-70872 | 9172-10797 | |||||
| Exond | Codon position | Codon position (−) | Yes | no | ||
| 1 | 69356-69358 | Pro CCG | Pro CCA | 10689-10687 | 4 | 0 |
| 69377-69379 | Ala GCC | Ala GCT | 10669-10667 | 4 | 0 | |
| 4 | 70543-70545 | Thr ACC | Ala GCC | 9500-9498 | 6 | 0 |
| 70676-70678 | Ser AGT | Ser AGC | 9363-9361 | 5 | 0 | |
This is a silent difference in an Ala codon formed by splicing [A] at position 56107 of exon 1 to the hinge region. The CA or CG are in the second and third codon positions.
These codons define the d12 allotype of the BAC donor rabbits and d11 predicted from serum typing of Thorbecke rabbits to be heterozygous d11/d12 with both codons present.
These codons define the e14 allotype of the BAC donor rabbits and e15 allotype predicted from serum typing to be encoded in Thorbecke rabbits (Table 1).
The sequence of BAC 27N5 (AY386696) between 69248 and 70872 is 99% identical to the reverse strand of chrUn0439 between 9172 and 10797 with seven differences (one a gap). Two silent changes are in exon 1 (69248-69594), and two changes, one replacement and one silent are in exon 4 (70532-70872) of BAC 27N5 (AY386696). Three additional differences, one a gap, are in introns.