Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9237
Trapped Gene
Cdc5l (ENSMUSG00000023932)
Vector Insertion
Chr 17: 45563631 - 45564887
Public Clones RRC285 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 6% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000136462 (Chr17:45564888..45564991 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GATTGCCTCATTGCTGCATA Chr17:45564919..45564938 59.8 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000136462 (Chr17:45564888..45564991 -)
Downstram Exon
ENSMUSE00000402096 (Chr17:45563469..45563630 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GATTGCCTCATTGCTGCATA Chr17:45564919..45564938 59.8 45 CCTATGATCGGAGCAATGGT Chr17:45563489..45563508 59.92 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000502094 Chr17:45570340..45570686 GCGCCGTTACTACTTTCTCG Chr17:45570427..45570446 60.04 55
upstream ENSMUSE00000136462 Chr17:45564888..45564991 GATTGCCTCATTGCTGCATA Chr17:45564919..45564938 59.8 45

*** Putative Vector Insertion (Chr 17: 45563631 - 45564887) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000402096 Chr17:45563469..45563630 CCTATGATCGGAGCAATGGT Chr17:45563489..45563508 59.92 50
downstream ENSMUSE00000389518 Chr17:45562801..45562928 CTTAAGCTTTCGGGGGTCAT Chr17:45562846..45562865 60.44 50
downstream ENSMUSE00000543081 Chr17:45561450..45561549 CCTCGGAGAGCATCTCAAGT Chr17:45561504..45561523 59.56 55
downstream ENSMUSE00000136475 Chr17:45556550..45556768 CTGCTCGAAGCTCTCGTCTT Chr17:45556706..45556725 60.03 55
downstream ENSMUSE00000367198 Chr17:45553894..45554038 CCACTGGTTTGGAGGATAGC Chr17:45553924..45553943 59.55 55
downstream ENSMUSE00000607325 Chr17:45552502..45552690 TTCTCAGAGCGATGCTGTTG Chr17:45552518..45552537 60.29 50
downstream ENSMUSE00000136467 Chr17:45550071..45550219 GTGGGGTATTAAGCCCACCT Chr17:45550131..45550150 60.07 55
downstream ENSMUSE00000394171 Chr17:45548777..45548939 GGGTGGCATTAGTGACTGGT Chr17:45548844..45548863 59.85 55
downstream ENSMUSE00000136466 Chr17:45547723..45547887 GTTCCTTCTCGGCATTTTCA Chr17:45547766..45547785 60.19 45
downstream ENSMUSE00000136463 Chr17:45545285..45545365 TCCTTTACACGCTCAGCATC Chr17:45545315..45545334 59.03 50
downstream ENSMUSE00000312815 Chr17:45544745..45544987 TTTCCAGATGGTTCGTAGGG Chr17:45544826..45544845 59.93 50
downstream ENSMUSE00000312798 Chr17:45541543..45541740 CCATGGCTCATTCCTTGTTT Chr17:45541663..45541682 59.93 45
downstream ENSMUSE00000396781 Chr17:45529942..45530154 TTCAAAAGTGCGTAGCTCCA Chr17:45529965..45529984 59.61 45
downstream ENSMUSE00000543072 Chr17:45528841..45529253 ACGGTGCTGGGTAACTTGTC Chr17:45529027..45529046 60.03 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAGTGCAAAGCCAGATGGTA Chr17:45564883..45564903 59.86 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGTGCAAAGCCAGATGGTA Chr17:45564883..45564903 59.86 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000023932