Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5588
Trapped Gene
Dbr1 (ENSMUSG00000032469)
Vector Insertion
Chr 9: 99477120 - 99478859
Public Clones YTA280 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 20% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000219906 (Chr9:99476995..99477119 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGGTAGCGCCGAATATTTA Chr9:99477092..99477111 60.42 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000219906 (Chr9:99476995..99477119 +)
Downstram Exon
ENSMUSE00000219902 (Chr9:99478860..99478940 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGGTAGCGCCGAATATTTA Chr9:99477092..99477111 60.42 45 CAGAGATGCCACCAATCCTTA Chr9:99478912..99478932 60.08 47.62

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000398835 Chr9:99476225..99476544 CCAAGTACCGTCACATGCAG Chr9:99476514..99476533 60.17 55
upstream ENSMUSE00000219906 Chr9:99476995..99477119 TGGGTAGCGCCGAATATTTA Chr9:99477092..99477111 60.42 45

*** Putative Vector Insertion (Chr 9: 99477120 - 99478859) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000219902 Chr9:99478860..99478940 CAGAGATGCCACCAATCCTTA Chr9:99478912..99478932 60.08 47.62
downstream ENSMUSE00000325617 Chr9:99479776..99479861 No primer for this exon
downstream ENSMUSE00000219905 Chr9:99480558..99480782 AGAACCAGTACGCAGGCTGT Chr9:99480741..99480760 59.94 55
downstream ENSMUSE00000219899 Chr9:99482441..99482521 AAGTCTCTGTGTGGCAAGCA Chr9:99482517..99482536 59.62 50
downstream ENSMUSE00000219901 Chr9:99482736..99482881 CTTGTGTGCAGACCGTTGTC Chr9:99482884..99482903 60.36 55
downstream ENSMUSE00000451723 Chr9:99483731..99484873 AGACTCCACCGTTTCACCAC Chr9:99484307..99484326 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACCCTATGGTGGCTGGGTAG Chr9:99477080..99477100 61.14 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGCTCGTGACTGGGAAAAC Chr9:99477166..99477186 60.83 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032469