Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI35640
Trapped Gene
Pde9a (ENSMUSG00000041119)
Vector Insertion
Chr 17: 31585397 - 31590346
Public Clones IST11592F9 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 30% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000315965 (Chr17:31585312..31585396 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAAAAGATGCGGGAGGAGTT Chr17:31585359..31585378 60.07 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000315965 (Chr17:31585312..31585396 +)
Downstram Exon
ENSMUSE00000315946 (Chr17:31590347..31590425 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAAAAGATGCGGGAGGAGTT Chr17:31585359..31585378 60.07 45 ACATCACGTCGAGGTGTCAA Chr17:31590412..31590431 60.16 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000393277 Chr17:31523196..31523301 GGTGAAAAAGTCCAAGTGCAG Chr17:31523201..31523221 59.77 47.62
upstream ENSMUSE00000316049 Chr17:31551046..31551116 TCAGCAAGTACTGCAACTCCA Chr17:31551053..31551073 59.65 47.62
upstream ENSMUSE00000316035 Chr17:31552225..31552302 GAACACCACCATCTCCCTTTT Chr17:31552225..31552245 60.22 47.62
upstream ENSMUSE00000316020 Chr17:31557190..31557233 GGCTGTGAAGCAAGTGTCTG Chr17:31557214..31557233 59.62 55
upstream ENSMUSE00000316006 Chr17:31580111..31580165 No primer for this exon
upstream ENSMUSE00000315987 Chr17:31580783..31580853 AAGCCGAAGTTGCAAATCAC Chr17:31580806..31580825 60.26 45
upstream ENSMUSE00000315965 Chr17:31585312..31585396 AAAAAGATGCGGGAGGAGTT Chr17:31585359..31585378 60.07 45

*** Putative Vector Insertion (Chr 17: 31585397 - 31590346) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000315946 Chr17:31590347..31590425 ACATCACGTCGAGGTGTCAA Chr17:31590412..31590431 60.16 50
downstream ENSMUSE00000315919 Chr17:31591999..31592073 TAGGGCTTCGATGGTCTCTG Chr17:31592034..31592053 60.35 55
downstream ENSMUSE00000315882 Chr17:31596020..31596106 GAAGTCCCTGACCAGACCAA Chr17:31596076..31596095 60.09 55
downstream ENSMUSE00000315854 Chr17:31596846..31596950 TGGAAGGGGTTGTTCCTGTA Chr17:31596886..31596905 60.35 50
downstream ENSMUSE00000315822 Chr17:31597124..31597206 TTGTTGTACCCTGGGTGGTC Chr17:31597206..31597225 60.67 55
downstream ENSMUSE00000315806 Chr17:31598516..31598672 GTTCTCCAGCGGTGAGATGT Chr17:31598582..31598601 60.27 55
downstream ENSMUSE00000315784 Chr17:31603300..31603413 ATGTCGGTAGCCAGGATCAA Chr17:31603334..31603353 60.48 50
downstream ENSMUSE00000315767 Chr17:31606739..31606843 GGACGGACTTCATTGGAGAT Chr17:31606791..31606810 58.94 50
downstream ENSMUSE00000315751 Chr17:31607626..31607754 CACTTTGTCTCGGTCCATGA Chr17:31607688..31607707 59.68 50
downstream ENSMUSE00000315729 Chr17:31608704..31608799 TGCTTCAGCTCCTCGTAGTG Chr17:31608780..31608799 59.34 55
downstream ENSMUSE00000315702 Chr17:31610103..31610224 GGAGAATGGCCTTCACTGTC Chr17:31610197..31610216 59.66 55
downstream ENSMUSE00000351292 Chr17:31612870..31613254 CACAGGCCACAATTCATCTG Chr17:31612911..31612930 60.11 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGGAGTTGGCAGCTAGGAA Chr17:31588372..31588392 59.57 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGGAGTTGGCAGCTAGGAA Chr17:31588372..31588392 59.57 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000041119