Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10407
Trapped Gene
Tfdp2 (ENSMUSG00000032411)
Vector Insertion
Chr 9: 96133168 - 96147468
Public Clones (sanger) (sanger) (sanger) (sanger) D072C11 (ggtc) (ggtc)
D133B07 (ggtc) IST14666B2 (tigm) IST11606G5 (tigm) IST10088D5 (tigm)
IST10457E9 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000693791 (Chr9:96133101..96133167 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCAGAGCTGAGGGGCTTTAT Chr9:96133122..96133141 60.87 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000693791 (Chr9:96133101..96133167 +)
Downstram Exon
ENSMUSE00000693790 (Chr9:96147469..96147507 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCAGAGCTGAGGGGCTTTAT Chr9:96133122..96133141 60.87 55 GACCCAGCAATTCCACTTGTA Chr9:96147504..96147524 59.99 47.62

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

*** Putative Vector Insertion (Chr 9: 96133168 - 96147468) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000693790 Chr9:96147469..96147507 GACCCAGCAATTCCACTTGTA Chr9:96147504..96147524 59.99 47.62
downstream ENSMUSE00000219556 Chr9:96174258..96174361 GGCCCTAAGGTTTTCGGTAA Chr9:96174336..96174355 60.31 50
downstream ENSMUSE00000489999 Chr9:96188020..96188141 CAATTCTCTGCGGTGTGCTT Chr9:96188047..96188066 61.38 50
downstream ENSMUSE00000233223 Chr9:96190999..96191046 No primer for this exon
downstream ENSMUSE00000530945 Chr9:96195384..96195546 TTCCGCTGAACTTTCTCACA Chr9:96195467..96195486 59.57 45
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 TTCTAATCGCCTTGCAGCAC Chr9:96139216..96139236 61.44 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCAGGTGTGGTTTAGCTGTTGT Chr9:96139130..96139152 59.7 45.46 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032411