Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13556
Trapped Gene
Vapa (ENSMUSG00000024091)
Vector Insertion
Chr 17: 65930188 - 65931919
Public Clones CMHD-GT_306F8-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 79% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000138301 (Chr17:65931920..65932093 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAGCGACTCCAGGGAGAAAT Chr17:65931954..65931973 60.21 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000138301 (Chr17:65931920..65932093 -)
Downstram Exon
ENSMUSE00000381941 (Chr17:65929396..65930187 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAGCGACTCCAGGGAGAAAT Chr17:65931954..65931973 60.21 50 CCAGGTTTATCCGAATGTGC Chr17:65930119..65930138 60.33 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000306239 Chr17:65962560..65962836 CTCGACCCTCCTTCAGACCT Chr17:65962571..65962590 60.78 60
upstream ENSMUSE00000540917 Chr17:65944242..65944394 CGGGGTCAATTGTGACTGTT Chr17:65944246..65944265 60.81 50
upstream ENSMUSE00000138298 Chr17:65942780..65942883 TTGCTCCACCAAACATTTCA Chr17:65942795..65942814 60.09 40
upstream ENSMUSE00000138302 Chr17:65941631..65941711 TGTTTGAAATGCCGAATGAA Chr17:65941643..65941662 60.05 35
upstream ENSMUSE00000138301 Chr17:65931920..65932093 AAGCGACTCCAGGGAGAAAT Chr17:65931954..65931973 60.21 50

*** Putative Vector Insertion (Chr 17: 65930188 - 65931919) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000381941 Chr17:65929396..65930187 CCAGGTTTATCCGAATGTGC Chr17:65930119..65930138 60.33 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCAGAAGAAAACCGACACCTG Chr17:65931921..65931942 60.28 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCAGAAGAAAACCGACACCTG Chr17:65931921..65931942 60.28 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024091