Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1075
Trapped Gene
Tfdp2 (ENSMUSG00000032411)
Vector Insertion
Chr 9: 96195547 - 96198042
Public Clones CC0048 (sanger) CC0182 (sanger)
Private Clones OST405791 (lexicon) OST297979 (lexicon) OST42358 (lexicon)
Severity of mutation (?) Insertion after 26% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000530945 (Chr9:96195384..96195546 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAGAAAGTTCAGCGGAAAGG Chr9:96195448..96195467 59.05 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000530945 (Chr9:96195384..96195546 +)
Downstram Exon
ENSMUSE00000693779 (Chr9:96198043..96198189 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAGAAAGTTCAGCGGAAAGG Chr9:96195448..96195467 59.05 50 CCTGAGCAGAATTGGTAGGC Chr9:96198175..96198194 59.84 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000634876 Chr9:96096767..96096979 GCCTTGACCCTTCCTGCACT Chr9:96096799..96096818 63.94 60
upstream ENSMUSE00000634875 Chr9:96102550..96102607 GCTGAAGAGAGAGCCCTGAT Chr9:96102581..96102600 58.72 55
upstream ENSMUSE00000693791 Chr9:96133101..96133167 GCAGAGCTGAGGGGCTTTAT Chr9:96133122..96133141 60.87 55
upstream ENSMUSE00000693790 Chr9:96147469..96147507 AAGTGGAATTGCTGGGTCAT Chr9:96147485..96147504 59.41 45
upstream ENSMUSE00000219556 Chr9:96174258..96174361 TTTCAAGCACCAACTCACCA Chr9:96174285..96174304 60.28 45
upstream ENSMUSE00000489999 Chr9:96188020..96188141 CGCAATGGTCACTCAGACTC Chr9:96188091..96188110 59.42 55
upstream ENSMUSE00000233223 Chr9:96190999..96191046 No primer for this exon
upstream ENSMUSE00000530945 Chr9:96195384..96195546 GAGAAAGTTCAGCGGAAAGG Chr9:96195448..96195467 59.05 50

*** Putative Vector Insertion (Chr 9: 96195547 - 96198042) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000693779 Chr9:96198043..96198189 CCTGAGCAGAATTGGTAGGC Chr9:96198175..96198194 59.84 55
downstream ENSMUSE00000462451 Chr9:96198046..96198189 CCTGAGCAGAATTGGTAGGC Chr9:96198175..96198194 59.84 55
downstream ENSMUSE00000530944 Chr9:96200791..96200859 TCTATCCGCCTCTGCTTCTC Chr9:96200816..96200835 59.68 55
downstream ENSMUSE00000530943 Chr9:96207219..96207370 TAAATGGCAGCTGAATGGTG Chr9:96207318..96207337 59.69 45
downstream ENSMUSE00000530942 Chr9:96210941..96211107 TGTCGTCGTGGATCTCAAAG Chr9:96210993..96211012 59.83 50
downstream ENSMUSE00000530941 Chr9:96217896..96218001 CCAAGAAGGTCCTGTGGAGA Chr9:96217921..96217940 60.23 55
downstream ENSMUSE00000459397 Chr9:96218207..96219400 CGTAAAAGCTTGCTCCGTTC Chr9:96218934..96218953 60.02 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATAATCGCCTTGCAGCACA Chr9:96195596..96195616 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGGCAGCTGATTCGGTAAGT Chr9:96195534..96195554 60.8 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032411