Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5232
Trapped Gene
Dapk3 (ENSMUSG00000034974)
Vector Insertion
Chr 10: 80646821 - 80652683
Public Clones YTA407 (baygenomics) 5SE305D08 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 5% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000349168 (Chr10:80646663..80646820 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CATGTCCACATTCAGGCAAG Chr10:80646758..80646777 60.11 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000349168 (Chr10:80646663..80646820 +)
Downstram Exon
ENSMUSE00000302799 (Chr10:80652684..80653044 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CATGTCCACATTCAGGCAAG Chr10:80646758..80646777 60.11 50 CCTCCGTCAATGACTCCTTC Chr10:80652964..80652983 59.65 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000349168 Chr10:80646663..80646820 CATGTCCACATTCAGGCAAG Chr10:80646758..80646777 60.11 50

*** Putative Vector Insertion (Chr 10: 80646821 - 80652683) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000302799 Chr10:80652684..80653044 CCTCCGTCAATGACTCCTTC Chr10:80652964..80652983 59.65 55
downstream ENSMUSE00000302787 Chr10:80653127..80653256 GTGCTTGTCCAGCAACATGA Chr10:80653159..80653178 60.88 50
downstream ENSMUSE00000574672 Chr10:80653343..80653391 AGCCAAGTGGCTCATAGTTCA Chr10:80653377..80653397 59.89 47.62
downstream ENSMUSE00000302769 Chr10:80653787..80653813 TGTAGGTGATGACGCCAATG Chr10:80653812..80653831 60.54 50
downstream ENSMUSE00000302762 Chr10:80654504..80654656 AGATGTTCGTCAGCGTCTCC Chr10:80654565..80654584 60.42 55
downstream ENSMUSE00000302754 Chr10:80655042..80655087 No primer for this exon
downstream ENSMUSE00000302750 Chr10:80655171..80655729 GGGACTTGAGGCTGTACTCG Chr10:80655258..80655277 59.87 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAGTGTGGGCTGACTCAGGT Chr10:80646850..80646870 59.76 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAGTGTGGGCTGACTCAGGT Chr10:80646850..80646870 59.76 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034974