Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1729
Trapped Gene
Znfx1 (ENSMUSG00000039501)
Vector Insertion
Chr 2: 166865770 - 166867193
Public Clones CG0425 (sanger)
Private Clones OST433085 (lexicon)
Severity of mutation (?) Insertion after 54% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000461429 (Chr2:166867194..166867339 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACACCATCGCCACACTAAG Chr2:166867237..166867256 60.17 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000461429 (Chr2:166867194..166867339 -)
Downstram Exon
ENSMUSE00000639038 (Chr2:166865659..166865769 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACACCATCGCCACACTAAG Chr2:166867237..166867256 60.17 55 TCACTTTTACCAGCCGTTCA Chr2:166865666..166865685 59.32 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000679510 Chr2:166888010..166888515 CCTATCACGCACCTGCTTCT Chr2:166888059..166888078 60.42 55
upstream ENSMUSE00000514356 Chr2:166885532..166885642 TAACGAAGTCAGGCGAAGGT Chr2:166885616..166885635 59.88 50
upstream ENSMUSE00000234975 Chr2:166880654..166882441 TTCCAAGCGACTGCTGTATG Chr2:166881173..166881192 60.01 50
upstream ENSMUSE00000234968 Chr2:166875814..166875945 AGACATTCCCCATCTTGGTG Chr2:166875854..166875873 59.78 50
upstream ENSMUSE00000511240 Chr2:166873933..166874081 GGGTGTCAGAAGACCAGCAT Chr2:166874054..166874073 60.12 55
upstream ENSMUSE00000234950 Chr2:166873041..166873190 AGCAGCACCTGGAGAAGTACA Chr2:166873085..166873105 60.07 52.38
upstream ENSMUSE00000234944 Chr2:166872392..166872506 CCTCGAAGCACTCCATGATT Chr2:166872462..166872481 60.22 50
upstream ENSMUSE00000400189 Chr2:166869496..166869743 CAAGCGGACAGAGTGATTGA Chr2:166869644..166869663 59.98 50
upstream ENSMUSE00000639041 Chr2:166868862..166868912 No primer for this exon
upstream ENSMUSE00000639040 Chr2:166868048..166868187 TGGAGCTTCGCAAACTGAAT Chr2:166868125..166868144 60.91 45
upstream ENSMUSE00000639039 Chr2:166867550..166867704 TCCTCAAAGATGCCGAAGTT Chr2:166867569..166867588 59.81 45
upstream ENSMUSE00000461429 Chr2:166867194..166867339 CACACCATCGCCACACTAAG Chr2:166867237..166867256 60.17 55

*** Putative Vector Insertion (Chr 2: 166865770 - 166867193) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000639038 Chr2:166865659..166865769 TCACTTTTACCAGCCGTTCA Chr2:166865666..166865685 59.32 45
downstream ENSMUSE00000639037 Chr2:166865277..166865372 TCCAGATCCTGGTAAATGTGG Chr2:166865292..166865312 59.8 47.62
downstream ENSMUSE00000519670 Chr2:166861299..166864663 GGACCTGCTCAAGTCGAGTC Chr2:166862745..166862764 59.99 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
  No PCR available

Come back to gene ENSMUSG00000039501