Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4412
Trapped Gene
Mtf2 (ENSMUSG00000029267)
Vector Insertion
Chr 5: 108516416 - 108516959
Public Clones AD0746 (sanger) XE829 (baygenomics) XE827 (baygenomics) XE830 (baygenomics)
XE828 (baygenomics) W245E04 (ggtc) W245E02 (ggtc) W240B01 (ggtc)
W246D03 (ggtc) W245D04 (ggtc) PST20157-NL (escells)
Private Clones OST55165 (lexicon)
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000596082 (Chr5:108516315..108516415 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTTGTCGACAGTGCGTTTTT Chr5:108516381..108516400 59.37 40 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000596082 (Chr5:108516315..108516415 +)
Downstram Exon
ENSMUSE00000596081 (Chr5:108516960..108517108 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTTGTCGACAGTGCGTTTTT Chr5:108516381..108516400 59.37 40 GTCCTTTCTTAAGCGCACCA Chr5:108516987..108517006 60.39 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000692471 Chr5:108494732..108494984 CGGGAACGAGATTGCTTCTA Chr5:108494920..108494939 60.34 50
upstream ENSMUSE00000692514 Chr5:108494761..108494984 CGGGAACGAGATTGCTTCTA Chr5:108494920..108494939 60.34 50
upstream ENSMUSE00000720649 Chr5:108494761..108494984 CGGGAACGAGATTGCTTCTA Chr5:108494920..108494939 60.34 50
upstream ENSMUSE00000692473 Chr5:108494763..108494984 CGGGAACGAGATTGCTTCTA Chr5:108494920..108494939 60.34 50
upstream ENSMUSE00000692470 Chr5:108498181..108498542 CTACTATGCCTCCCCCTTCC Chr5:108498340..108498359 59.92 60
upstream ENSMUSE00000541254 Chr5:108509844..108510042 CAAGCGGTCTCCTTTACGTC Chr5:108509877..108509896 59.88 55
upstream ENSMUSE00000692469 Chr5:108509844..108510042 CAAGCGGTCTCCTTTACGTC Chr5:108509877..108509896 59.88 55
upstream ENSMUSE00000596085 Chr5:108510156..108510237 TCCAAATCCTGGGTTCTCTG Chr5:108510201..108510220 60.04 50
upstream ENSMUSE00000692467 Chr5:108510156..108510237 TCCAAATCCTGGGTTCTCTG Chr5:108510201..108510220 60.04 50
upstream ENSMUSE00000596083 Chr5:108516018..108516113 AGAAGCTCCCAATGAAATGGT Chr5:108516070..108516090 59.95 42.86
upstream ENSMUSE00000692465 Chr5:108516018..108516113 AGAAGCTCCCAATGAAATGGT Chr5:108516070..108516090 59.95 42.86
upstream ENSMUSE00000596082 Chr5:108516315..108516415 TTTGTCGACAGTGCGTTTTT Chr5:108516381..108516400 59.37 40

*** Putative Vector Insertion (Chr 5: 108516416 - 108516959) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000596081 Chr5:108516960..108517108 GTCCTTTCTTAAGCGCACCA Chr5:108516987..108517006 60.39 50
downstream ENSMUSE00000596080 Chr5:108521080..108521175 TCTGAAGGCATTGGACACAA Chr5:108521156..108521175 60.24 45
downstream ENSMUSE00000596079 Chr5:108522357..108522425 CTGGTCCAGAACTGCAGACA Chr5:108522400..108522419 60.02 55
downstream ENSMUSE00000596078 Chr5:108523144..108523267 CTCCAGGGTGCAATCTATCC Chr5:108523268..108523287 59.51 55
downstream ENSMUSE00000596077 Chr5:108528138..108528205 TCAGATTTGGGTGTGTCTGC Chr5:108528163..108528182 59.68 50
downstream ENSMUSE00000596076 Chr5:108529832..108530002 GAGGAACACGAATTCGCAAC Chr5:108529899..108529918 60.65 50
downstream ENSMUSE00000596075 Chr5:108533039..108533144 TTGTATATGGGCCAGGAGGA Chr5:108533112..108533131 60.29 50
downstream ENSMUSE00000596074 Chr5:108533285..108533337 TCCAACGTAGGATTCTCTGAAA Chr5:108533320..108533341 58.83 40.91
downstream ENSMUSE00000596073 Chr5:108533445..108533549 TGCTAGCCGAGGTAGTTTCG Chr5:108533536..108533555 60.53 55
downstream ENSMUSE00000491639 Chr5:108535607..108538023 AAGGCGACCTCTTCTTCTCC Chr5:108535694..108535713 59.96 55
downstream ENSMUSE00000692461 Chr5:108535607..108536643 AAGGCGACCTCTTCTTCTCC Chr5:108535694..108535713 59.96 55
downstream ENSMUSE00000692472 Chr5:108535607..108536104 AAGGCGACCTCTTCTTCTCC Chr5:108535694..108535713 59.96 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTTTGTCGACAGTGCGTTT Chr5:108516380..108516400 61.41 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCTTTGTCGACAGTGCGTTT Chr5:108516380..108516400 61.41 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029267