Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14212
Trapped Gene
RP23-166A1.1 (ENSMUSG00000078901)
Vector Insertion
Chr 2: 175108926 - 175109130
Public Clones CMHD-GT_84B9-3 (cmhd)
Private Clones OST62757 (lexicon)
Severity of mutation (?) Insertion after 68% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000678884 (Chr2:175108799..175108925 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTCAGGAAGAGTGGGCTTTG Chr2:175108836..175108855 59.98 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000678884 (Chr2:175108799..175108925 +)
Downstram Exon
ENSMUSE00000638700 (Chr2:175109131..175109191 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTCAGGAAGAGTGGGCTTTG Chr2:175108836..175108855 59.98 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000678885 Chr2:175100626..175100704 TGTGATGTGTTCTGCGTGAC Chr2:175100634..175100653 59.27 50
upstream ENSMUSE00000678884 Chr2:175108799..175108925 CTCAGGAAGAGTGGGCTTTG Chr2:175108836..175108855 59.98 55

*** Putative Vector Insertion (Chr 2: 175108926 - 175109130) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000638700 Chr2:175109131..175109191 No primer for this exon
downstream ENSMUSE00000678883 Chr2:175109131..175112306 TTGGCACACGTGAAATTGTT Chr2:175110335..175110354 60.01 40
downstream ENSMUSE00000678882 Chr2:175112418..175112466 CTTGGCAGTATGGATTGTTTCA Chr2:175112451..175112472 60 40.91

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATCGCCTTGCAGCACATC Chr2:175108977..175108997 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000078901