Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5543
Trapped Gene
Cdc5l (ENSMUSG00000023932)
Vector Insertion
Chr 17: 45561550 - 45562800
Public Clones YTA190 (baygenomics) IST10993G11 (tigm) IST10993G11 (tigm)
Private Clones OST422663 (lexicon)
Severity of mutation (?) Insertion after 18% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000389518 (Chr17:45562801..45562928 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCCGATAGACATGGATGAGG Chr17:45562801..45562820 60.29 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000389518 (Chr17:45562801..45562928 -)
Downstram Exon
ENSMUSE00000543081 (Chr17:45561450..45561549 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCCGATAGACATGGATGAGG Chr17:45562801..45562820 60.29 55 CCTCGGAGAGCATCTCAAGT Chr17:45561504..45561523 59.56 55

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
upstream ENSMUSE00000402096 Chr17:45563469..45563630 No primer for this exon
upstream ENSMUSE00000389518 Chr17:45562801..45562928 CCCGATAGACATGGATGAGG Chr17:45562801..45562820 60.29 55

*** Putative Vector Insertion (Chr 17: 45561550 - 45562800) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 GGGAGTGCTCAGCTCACTGT Chr17:45562765..45562785 60.62 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGGAGTGCTCAGCTCACTGT Chr17:45562765..45562785 60.62 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CTAATCGCCTTGCAGCACAT Chr17:45562859..45562879 61.32 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCCAAAGGGACAATGAAGAA Chr17:45562896..45562916 59.9 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000023932