Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3071
Trapped Gene
Vapa (ENSMUSG00000024091)
Vector Insertion
Chr 17: 65942884 - 65944241
Public Clones DC0258 (sanger)
Private Clones OST451896 (lexicon) OST338827 (lexicon) OST202025 (lexicon)
Severity of mutation (?) Insertion after 31% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000540917 (Chr17:65944242..65944394 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGGGGTCAATTGTGACTGTT Chr17:65944246..65944265 60.81 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000540917 (Chr17:65944242..65944394 -)
Downstram Exon
ENSMUSE00000138298 (Chr17:65942780..65942883 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGGGGTCAATTGTGACTGTT Chr17:65944246..65944265 60.81 50 CTGAAATGTTTGGTGGAGCA Chr17:65942772..65942791 59.69 45

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

*** Putative Vector Insertion (Chr 17: 65942884 - 65944241) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000138298 Chr17:65942780..65942883 CTGAAATGTTTGGTGGAGCA Chr17:65942772..65942791 59.69 45
downstream ENSMUSE00000138302 Chr17:65941631..65941711 TTCATTCGGCATTTCAAACA Chr17:65941621..65941640 60.05 35
downstream ENSMUSE00000138301 Chr17:65931920..65932093 AGTCGCTTGCACTCTTCCAT Chr17:65931944..65931963 60.02 50
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 TTAATCGCCTTGCAGCACAT Chr17:65944171..65944191 61.69 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGCCCAACAGTGGGATTATT Chr17:65944268..65944288 60.94 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024091