Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13706
Trapped Gene
Dennd4a (ENSMUSG00000035492)
Vector Insertion
Chr 9: 64757507 - 64757737
Public Clones CMHD-GT_270D10-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000345774 (Chr9:64757308..64757506 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCCCGAAGTATTCAGATCC Chr9:64757335..64757354 60.04 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000345774 (Chr9:64757308..64757506 +)
Downstram Exon
ENSMUSE00000252625 (Chr9:64757738..64757992 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCCCGAAGTATTCAGATCC Chr9:64757335..64757354 60.04 50 TGCCACTGTTATTGCATGGT Chr9:64757872..64757891 59.99 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000584221 Chr9:64736767..64737151 GTGTCTGCTGCGTCACTGTT Chr9:64736789..64736808 60.1 55
upstream ENSMUSE00000584220 Chr9:64737397..64737538 No primer for this exon
upstream ENSMUSE00000584219 Chr9:64741093..64741209 GGGGAAAAGGAGAAAAGAGG Chr9:64741173..64741192 59.14 50
upstream ENSMUSE00000584218 Chr9:64742205..64742336 AACATCCGGAGAATGTGAGG Chr9:64742317..64742336 59.93 50
upstream ENSMUSE00000584217 Chr9:64744141..64748749 CATTTCGGGAAGGATCTCAA Chr9:64745059..64745078 60.01 45
upstream ENSMUSE00000389381 Chr9:64744617..64745237 CATTTCGGGAAGGATCTCAA Chr9:64745059..64745078 60.01 45
upstream ENSMUSE00000410808 Chr9:64751957..64752146 TGAAGATGTCTGCCACGAGT Chr9:64752028..64752047 59.42 50
upstream ENSMUSE00000352500 Chr9:64753808..64753902 CCTTGCCTGGAAAATCAGAG Chr9:64753826..64753845 59.81 50
upstream ENSMUSE00000252713 Chr9:64754645..64754820 GGTGTAGGACCTGCGACTGT Chr9:64754667..64754686 60.18 60
upstream ENSMUSE00000252679 Chr9:64754910..64755044 ACTTTGCAAGTCGGACAAGG Chr9:64754948..64754967 60.29 50
upstream ENSMUSE00000345774 Chr9:64757308..64757506 TGCCCGAAGTATTCAGATCC Chr9:64757335..64757354 60.04 50

*** Putative Vector Insertion (Chr 9: 64757507 - 64757737) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000252625 Chr9:64757738..64757992 TGCCACTGTTATTGCATGGT Chr9:64757872..64757891 59.99 45
downstream ENSMUSE00000252609 Chr9:64759472..64759589 GTACAAGGGTTGCCCTGGAT Chr9:64759573..64759592 61.13 55
downstream ENSMUSE00000467381 Chr9:64759694..64759720 No primer for this exon
downstream ENSMUSE00000386635 Chr9:64760161..64760323 GGCCCATAGACATCGTTCAT Chr9:64760272..64760291 59.78 50
downstream ENSMUSE00000532771 Chr9:64760483..64760547 CCAGTGCCACAAGTGAGAGA Chr9:64760529..64760548 60.02 55
downstream ENSMUSE00000584216 Chr9:64764766..64765395 GTTTTTCGGCATTCCATCAC Chr9:64764883..64764902 60.32 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTAATCGCCTTGCAGCACAT Chr9:64757557..64757577 61.32 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAATCCGTGACTGGGAAAAC Chr9:64757553..64757573 60.35 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000035492