Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13300
Trapped Gene
Cdc123 (ENSMUSG00000039128)
Vector Insertion
Chr 2: 5725022 - 5725956
Public Clones CMHD-GT_329A12-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 69% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000313185 (Chr2:5725957..5726079 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTGCAGATGCATTCAAGACTTT Chr2:5725997..5726018 59.89 36.36 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000313185 (Chr2:5725957..5726079 -)
Downstram Exon
ENSMUSE00000313177 (Chr2:5724993..5725021 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTGCAGATGCATTCAAGACTTT Chr2:5725997..5726018 59.89 36.36 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000647790 Chr2:5765881..5765987 TGGTACCCACTTTTCCGAAG Chr2:5765896..5765915 59.96 50
upstream ENSMUSE00000313235 Chr2:5762999..5763070 GATGATGGGACTCTGGTGGT Chr2:5763008..5763027 59.77 55
upstream ENSMUSE00000313230 Chr2:5754702..5754759 GCTCCCAGTCAGACAGTGGT Chr2:5754723..5754742 60.31 60
upstream ENSMUSE00000313225 Chr2:5754127..5754159 GTCCGATGATGAGAGCACAG Chr2:5754138..5754157 59.37 55
upstream ENSMUSE00000313217 Chr2:5744148..5744243 CTTAACTGGAGTGCCCCAAG Chr2:5744149..5744168 59.73 55
upstream ENSMUSE00000313205 Chr2:5742322..5742428 TGCGTACTGGATAGCGATGA Chr2:5742407..5742426 60.39 50
upstream ENSMUSE00000313200 Chr2:5731842..5731890 GCACTGATGACTCTCCAGACC Chr2:5731859..5731879 59.86 57.14
upstream ENSMUSE00000647789 Chr2:5730969..5731064 GCCACAACCTACCTGCTCTC Chr2:5730994..5731013 59.87 60
upstream ENSMUSE00000313190 Chr2:5728477..5728552 GGCTGAATTCCGATGTTTTG Chr2:5728498..5728517 60.45 45
upstream ENSMUSE00000313185 Chr2:5725957..5726079 TTGCAGATGCATTCAAGACTTT Chr2:5725997..5726018 59.89 36.36

*** Putative Vector Insertion (Chr 2: 5725022 - 5725956) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000313177 Chr2:5724993..5725021 No primer for this exon
downstream ENSMUSE00000313169 Chr2:5719407..5719535 TGACCTCCCCAAATGGATTA Chr2:5719471..5719490 60.13 45
downstream ENSMUSE00000313161 Chr2:5716595..5716732 CCGGTGGAAAGGTCTACAAA Chr2:5716610..5716629 59.96 50
downstream ENSMUSE00000364658 Chr2:5715713..5715926 CTCAGTCGTCCTCTTGCTCA Chr2:5715877..5715896 59.28 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGGTGCAATGAAGTGAGACC Chr2:5725920..5725940 59.68 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGGTGCAATGAAGTGAGACC Chr2:5725920..5725940 59.68 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039128