Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29634
Trapped Gene
Gabpb1 (ENSMUSG00000027361)
Vector Insertion
Chr 2: 126488726 - 126501192
Public Clones (sanger) (sanger) (sanger) (sanger) D001C03 (ggtc) E132A06 (ggtc)
D131A06 (ggtc) D001C03 (ggtc) E054G05 (ggtc) D081A11 (ggtc) (ggtc)
D144B12 (ggtc) IST13573G1 (tigm) IST14175C7 (tigm) IST11261C1 (tigm)
IST14557G6 (tigm) IST14233D6 (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
ENSMUSE00000597120 (Chr2:126501092..126501191 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000597120 (Chr2:126501092..126501191 -)
Downstram Exon
ENSMUSE00000661643 (Chr2:126488727..126488824 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon AGCTGGTCAGCAGGTAGGAG Chr2:126488778..126488797 59.62 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000683920 Chr2:126501770..126502073 TGAAGAGGACAGGCATCCTT Chr2:126501823..126501842 59.8 50
upstream ENSMUSE00000398603 Chr2:126501092..126501304 GACTTTTCGGTGGGGATTTT Chr2:126501250..126501269 60.17 45
upstream ENSMUSE00000597120 Chr2:126501092..126501191 No primer for this exon
upstream ENSMUSE00000661644 Chr2:126501092..126501280 GACTTTTCGGTGGGGATTTT Chr2:126501250..126501269 60.17 45
upstream ENSMUSE00000661647 Chr2:126501092..126501328 GACTTTTCGGTGGGGATTTT Chr2:126501250..126501269 60.17 45
upstream ENSMUSE00000661643 Chr2:126488727..126488824 TCCTACCTGCTGACCAGCTC Chr2:126488799..126488818 60.56 60

*** Putative Vector Insertion (Chr 2: 126488726 - 126501192) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000641451 Chr2:126484206..126484313 CCATCAAAATGCGAACTTCA Chr2:126484213..126484232 59.66 40
downstream ENSMUSE00000718562 Chr2:126484206..126484313 CCATCAAAATGCGAACTTCA Chr2:126484213..126484232 59.66 40
downstream ENSMUSE00000168730 Chr2:126479291..126479458 TCGGAGAAGAACCTCTGTGG Chr2:126479368..126479387 60.38 55
downstream ENSMUSE00000168732 Chr2:126477969..126478163 AAAGCTCCACCACCTCTTGA Chr2:126478051..126478070 59.84 50
downstream ENSMUSE00000168727 Chr2:126476245..126476356 GTGTGGCAGCGTGTATTGTC Chr2:126476265..126476284 60.19 55
downstream ENSMUSE00000168731 Chr2:126475804..126475917 No primer for this exon
downstream ENSMUSE00000597119 Chr2:126475804..126475917 No primer for this exon
downstream ENSMUSE00000641435 Chr2:126473484..126475917 GGTGCTGAGGCTTCAAACTC Chr2:126475125..126475144 60 55
downstream ENSMUSE00000322272 Chr2:126472299..126472484 TCTGCGGTAACCACTTCCTC Chr2:126472432..126472451 60.26 55
downstream ENSMUSE00000597113 Chr2:126472299..126472484 TCTGCGGTAACCACTTCCTC Chr2:126472432..126472451 60.26 55
downstream ENSMUSE00000661646 Chr2:126472299..126472481 TCTGCGGTAACCACTTCCTC Chr2:126472432..126472451 60.26 55
downstream ENSMUSE00000322266 Chr2:126464965..126465080 CCCGGCTCTCAATTATTTCC Chr2:126464963..126464982 60.76 50
downstream ENSMUSE00000597117 Chr2:126464965..126465080 CCCGGCTCTCAATTATTTCC Chr2:126464963..126464982 60.76 50
downstream ENSMUSE00000661640 Chr2:126464917..126465080 CCCGGCTCTCAATTATTTCC Chr2:126464963..126464982 60.76 50
downstream ENSMUSE00000683919 Chr2:126464372..126465080 TTGAGGGCTTGCCATATGTT Chr2:126464752..126464771 60.47 45
downstream ENSMUSE00000661642 Chr2:126454651..126456118 ATGGTCGCCAGTAAAACCAG Chr2:126455211..126455230 59.99 50
downstream ENSMUSE00000597112 Chr2:126454649..126456118 ATGGTCGCCAGTAAAACCAG Chr2:126455211..126455230 59.99 50
downstream ENSMUSE00000358516 Chr2:126453178..126456118 ATGGTCGCCAGTAAAACCAG Chr2:126455211..126455230 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTAATCGCCTTGCAGCACATC Chr2:126495121..126495142 63.08 52.38 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AATGTCATCATTCCTGCCAAT Chr2:126501178..126501199 59.26 38.1 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027361