Protocol 34818: Probe Assay - Ccdc117<em1(IMPC)J>
Version 1.0

Notes

Taqman qPCR protocols are run on a real time PCR instrument. Use an appropriate instrument specific Fluorophore/Quencher combination.

 

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

>chr11:5534128-5534235 108bp CACAGCTGGTGCTGACACCT TTCTGTTCCCTAGTCTCCATGC

Mut= 113 bp

Wt= 108 bp

Fam=Mut

Hex=Wt

Sequence

Wt Sequence (deletion in lower case):

 TGAAACTTAAACATAAAATAAATGGATGTTTTTTAACTAAATGAGTTTTAGCTGGGCCTGGTAAGCTCTCTCCTCAGTCCCAGCACTCTAGGCAGAAGCAGGCAGAACTCTGAATGAGGCCAGACATAGATACAGAGTGAGACTTTGTCCCAAAAATATATCTTTTTTAATTCGTTAGAGAAATgtcttacatttcgtctataatggattgcttttcttccttccctctcttcccgctgctttcctcctcctaggtgtccagtaagaaagaaacgactgactgaagctgaactcggtgcagttactgatgaatgggctctcggcgcacatcagggaagagaaggtcatggggtaaacacgtgtcctagcagcctttctatgcccagcatgctagatgtggtctgtgaggaaatggatcagacaactggagaaccacagtgtgaagtcgcccgaaggcggctgcaagagattgaggacaggtactgactgcgcgtcacatgtgctgtggtcctgtgtcagctctcctctcctaggctgctcggggtcacgtcctggtgctggagatggggaatgaacaacagacacttagtggtagatggaatagagcttgactaagccttttactgaccgtgtcaagctccgttttcctggacacttcttctaacttgactctattccaaacctttctcggtgaaaaacagcctcatttggccacttttctcagagttgtagcttacatgatctctcgctgcagcacctgtgggtttttcttttagtttcaaattttgtttgttcatttgctacaagaaacacacagtgccttgagtgattttttttttttctttctccaatttattatttaggataattgacgaagatgaagaggttgaaagtgacagaaatgttagccacctcccaagtcttgtcctttctgacaccatgaaaacgggtttgaagagggaatttgatgaagtcttcacaaagaggatgattgagtctatgtaagtgcacagctggtgctgacacctgggaaggctcttgccaagcctgttctcttaaagctgggggggGACAGCAGCAGCCACTCAGGCTCAGCATGGAGACTAGGGAACAGAAGGTGATGTGTCAGATTAGTGACAGTTGACATTGCTATCACGAAGCCCACAAACTAGCACAGCCGTCTGTGGTCATTTTAGTGTTTTAACTCTTGGATTTGTTTTG

This mutation is an 886 bp deletion beginning at Chromosome 11 position 5,534,174 bp and ending after 5,535,059 bp (GRCm38/mm10).

JAX Protocol

Protocol Primers

Primer 5' Label Sequence 5' → 3' 3' Label Primer Type Reaction Note
44556 CAC AGC TGG TGC TGA CAC CT Wild type Forward A
44557 TTC TGT TCC CTA GTC TCC ATG C Common A
44558 GGC CAG ACA TAG ATA CAG AGT GAG Mutant Forward A
44559 Fluorophore-1 AAG GCT CTT GCC AAG CCT Quencher-1 WT Probe
44560 Fluorophore-2 TTC GTT AGA GAA ATG ACA GCA GC Quencher-2 MUT Probe

Reaction A

Component Final Concentration
Kapa Probe Fast QPCR 1.00 X
ddH2O
44556 0.40 uM
44557 0.40 uM
44558 0.40 uM
Wt Probe 0.15 uM
Mutant Probe 0.15 uM
DNA

Cycling

Step Temp °C Time Note
1 95.0 --
2 95.0 --
3 60.0 --
4 -- repeat steps 2-3 for 40 cycles
5 40.0 -- Forever
JAX uses a very high speed Taq (~1000 bp/sec), use cycling times recommended for your reagents.

Strains Using This Protocol

This is the only strain that uses this protocol.