Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI81
Trapped Gene
Stmn2 (ENSMUSG00000027500)
Vector Insertion
Chr 3: 8509631 - 8541840
Public Clones GC0347 (tigem) RRJ569 (baygenomics) XG803 (baygenomics) HMA310 (baygenomics)
RRT508 (baygenomics) RRA012 (baygenomics) RRJ526 (baygenomics) RRT509 (baygenomics)
A025E05 (ggtc) PST3205-NL (escells)
Private Clones not available
Severity of mutation (?) Insertion after 4% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000382200 (Chr3:8509521..8509630 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACAGCTGGACCCTTCTCCTT Chr3:8509555..8509574 60.25 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000382200 (Chr3:8509521..8509630 +)
Downstram Exon
ENSMUSE00000311839 (Chr3:8541841..8541936 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACAGCTGGACCCTTCTCCTT Chr3:8509555..8509574 60.25 55 GCAGGAGCAGATCAGTGACA Chr3:8541896..8541915 60.15 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000382200 Chr3:8509521..8509630 ACAGCTGGACCCTTCTCCTT Chr3:8509555..8509574 60.25 55
upstream ENSMUSE00000705955 Chr3:8509565..8509630 No primer for this exon

*** Putative Vector Insertion (Chr 3: 8509631 - 8541840) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000311839 Chr3:8541841..8541936 GCAGGAGCAGATCAGTGACA Chr3:8541896..8541915 60.15 55
downstream ENSMUSE00000170117 Chr3:8545573..8545745 GGTGGCTTCAAGATCAGCTC Chr3:8545642..8545661 59.96 55
downstream ENSMUSE00000569583 Chr3:8554792..8554983 TTTCCTGCAGACGTTCAATG Chr3:8554984..8555003 59.84 45
downstream ENSMUSE00000170122 Chr3:8560266..8561604 TAATGCAGCAACCAGCTCAC Chr3:8561280..8561299 60.02 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGCAGACACTGAATGCACA Chr3:8539635..8539655 59.6 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGCAGACACTGAATGCACA Chr3:8539635..8539655 59.6 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027500