Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI37224
Trapped Gene
Tfdp1 (ENSMUSG00000038482)
Vector Insertion
Chr 8: 13370647 - 13370878
Public Clones CMHD-GT_453C10-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 39% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000514215 (Chr8:13370481..13370646 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGCCGACAACCACATTCTA Chr8:13370615..13370634 59.72 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000514215 (Chr8:13370481..13370646 +)
Downstram Exon
ENSMUSE00000272546 (Chr8:13370879..13371022 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGCCGACAACCACATTCTA Chr8:13370615..13370634 59.72 50 AAGTTCTGGCACTCCTGAGC Chr8:13371021..13371040 59.6 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000610192 Chr8:13338806..13338920 No primer for this exon
upstream ENSMUSE00000469325 Chr8:13339665..13339739 TCTGTGGAGGGTACGCAGTT Chr8:13339680..13339699 60.71 55
upstream ENSMUSE00000455008 Chr8:13357043..13357109 No primer for this exon
upstream ENSMUSE00000455017 Chr8:13365089..13365195 TTCGGACAGTCCAATGTCAA Chr8:13365160..13365179 60.09 45
upstream ENSMUSE00000272558 Chr8:13369459..13369580 GACTCCTCACCTTGGTCTGC Chr8:13369558..13369577 59.84 60
upstream ENSMUSE00000514215 Chr8:13370481..13370646 CTGCCGACAACCACATTCTA Chr8:13370615..13370634 59.72 50

*** Putative Vector Insertion (Chr 8: 13370647 - 13370878) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000272546 Chr8:13370879..13371022 AAGTTCTGGCACTCCTGAGC Chr8:13371021..13371040 59.6 55
downstream ENSMUSE00000272513 Chr8:13371352..13371420 TGGAGCTGTGACTGCTTCTG Chr8:13371407..13371426 60.33 55
downstream ENSMUSE00000272506 Chr8:13372466..13372617 ATGAAGGGCAAGTGGATGAC Chr8:13372566..13372585 59.93 50
downstream ENSMUSE00000272500 Chr8:13372936..13373102 CATCGTGGATCTCAAACGTG Chr8:13372985..13373004 60.11 50
downstream ENSMUSE00000272493 Chr8:13373845..13373923 CGTGACGAATACTCCACCAA Chr8:13373885..13373904 59.57 50
downstream ENSMUSE00000472934 Chr8:13377142..13378446 CAACTGTTGAGGGGCAAAAT Chr8:13377613..13377632 59.97 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCGACAACCACATTCTACC Chr8:13370618..13370638 60.38 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCGACAACCACATTCTACC Chr8:13370618..13370638 60.38 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000038482