Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI18836
Trapped Gene
Cdc123 (ENSMUSG00000039128)
Vector Insertion
Chr 2: 5731891 - 5742321
Public Clones IST13969C2 (tigm) IST10115E3 (tigm) IST12093G2 (tigm) IST10115E3 (tigm)
Private Clones OST413314 (lexicon)
Severity of mutation (?) Insertion after 76% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000313205 (Chr2:5742322..5742428 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCGTACTGGATAGCGATGA Chr2:5742407..5742426 60.39 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000313205 (Chr2:5742322..5742428 -)
Downstram Exon
ENSMUSE00000313200 (Chr2:5731842..5731890 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCGTACTGGATAGCGATGA Chr2:5742407..5742426 60.39 50 CAAGGGTCTGGAGAGTCATCA Chr2:5731833..5731853 60.24 52.38

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

*** Putative Vector Insertion (Chr 2: 5731891 - 5742321) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000313200 Chr2:5731842..5731890 CAAGGGTCTGGAGAGTCATCA Chr2:5731833..5731853 60.24 52.38
downstream ENSMUSE00000647789 Chr2:5730969..5731064 GGAGAGCAGGTAGGTTGTGG Chr2:5730971..5730990 59.72 60
downstream ENSMUSE00000313190 Chr2:5728477..5728552 CACACCATTTTCGGAGAACA Chr2:5728509..5728528 59.54 45
downstream ENSMUSE00000313185 Chr2:5725957..5726079 TTGAATGCATCTGCAAATTTCT Chr2:5725981..5726002 59.73 31.82
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 TATAATCGCCTTGCAGCACA Chr2:5742252..5742272 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCTACGTGACTGGGAAAACC Chr2:5736254..5736274 59.6 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TTTTCCCACCAATTTTGTCA Chr2:5733452..5733472 58.84 35 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GTGTGTGTATGCGTGACTGG Chr2:5742369..5742389 58.57 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039128