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Notes
The genotyping protocol(s) presented here have been optimized for reagents and conditions used by The Jackson Laboratory (JAX).
To genotype animals, JAX recommends researchers validate the assay independently upon receipt of animals into their facility.
Reaction cycling temperature and times may require additional optimization based on the specific genotyping reagents used.
Expected Results
Mutant = ~300 bp
Heterozygote = ~300 bp and 310 bp
Wild type = 310 bp
>chr12:50486796+50487105 310bp ACCCTGCCCTGTGAGTCTT TTCTCCCACATTGCACCTC
Please note close band sizes. If gelling, suggest separating.
Sequence
Wt Sequence:
GGGGACTGTCTGATTATTTCACACATCAAAATCAGGGGTCTTCTTCCAACCCTTTAATACATTAACATCCGGGGGACCAGACTGTAAGTGAacGTTTTACACACATTTGCATTGTAA
Mutant Sequence:
GGGCAATGGTGCGCCTGCTGGAAGATGGCGATTAGGTCGACGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGGCCGCCACCGCGGTGGCTAGTTCGAGGTCGACGGTAtcGTTTTACACACATTTGCATTGTAAATGATAATTAAAAAAATAAGTCCAGGTATTTTTTATTAAGCCCCCCCTCCCCATTTCTGTACGTTTGTTCAGTCTTTAGGGTTGTTTACTATTCTA
JAX Protocol
Protocol Primers
| Primer | 5' Label | Sequence 5' → 3' | 3' Label | Primer Type | Reaction | Note |
|---|---|---|---|---|---|---|
| 18991 | TAG TGA AAC AGG GGC AAT GG | Mutant Forward | A | |||
| 33896 | ACC CTG CCC TGT GAG TCT T | Wild type Forward | A | |||
| 33897 | TTC TCC CAC ATT GCA CCT C | Common | A |
Reaction A
| Component | Final Concentration |
|---|---|
| ddH2O | |
| Kapa 2G HS buffer | 1.30 X |
| MgCl2 | 2.60 mM |
| dNTP KAPA | 0.26 mM |
| 18991 | 0.50 uM |
| 33896 | 0.50 uM |
| 33897 | 0.50 uM |
| Glycerol | 6.50 % |
| Dye | 1.00 X |
| Kapa 2G HS taq polym | 0.03 U/ul |
| DNA |
Cycling
| Step | Temp °C | Time | Note |
|---|---|---|---|
| 1 | 94.0 | -- | |
| 2 | 94.0 | -- | |
| 3 | 65.0 | -- | -0.5 C per cycle decrease |
| 4 | 68.0 | -- | |
| 5 | -- | repeat steps 2-4 for 10 cycles (Touchdown) | |
| 6 | 94.0 | -- | |
| 7 | 60.0 | -- | |
| 8 | 72.0 | -- | |
| 9 | -- | repeat steps 6-8 for 28 cycles | |
| 10 | 72.0 | -- | |
| 11 | 10.0 | -- | hold |
JAX uses a very high speed Taq (~1000 bp/sec), use cycling times recommended for your reagents.
JAX uses a 'touchdown' cycling protocol and therefore has not calculated the optimal annealing temperature for each set of primers.
Strains Using This Protocol
This is the only strain that uses this protocol.