Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8342
Trapped Gene
Notch2 (ENSMUSG00000027878)
Vector Insertion
Chr 3: 97915666 - 97916932
Public Clones STA005 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 32% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000391377 (Chr3:97915473..97915665 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATGTGAATGGTTTCCGGTGT Chr3:97915545..97915564 60.1 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000391377 (Chr3:97915473..97915665 +)
Downstram Exon
ENSMUSE00000173837 (Chr3:97916933..97917078 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATGTGAATGGTTTCCGGTGT Chr3:97915545..97915564 60.1 45 CCAGGTTATTGCACGTTCCT Chr3:97917042..97917061 59.99 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000409345 Chr3:97851650..97851732 GTGTCGAGGTGGTCAAGAGC Chr3:97851658..97851677 60.87 60
upstream ENSMUSE00000404985 Chr3:97874783..97875042 AAAAACCGCTGTCAGAATGG Chr3:97874835..97874854 60.11 45
upstream ENSMUSE00000244757 Chr3:97876510..97876845 ATCTCATCCCTGCGAAAATG Chr3:97876541..97876560 60.04 45
upstream ENSMUSE00000173829 Chr3:97885840..97885962 CCTGTGAGCGGAATATCGAC Chr3:97885855..97885874 60.62 55
upstream ENSMUSE00000244740 Chr3:97902019..97902252 TCGATGACTGTGCCTATGCT Chr3:97902160..97902179 59.42 50
upstream ENSMUSE00000565998 Chr3:97903347..97903502 CCTGAACGGGCAGTACATTT Chr3:97903420..97903439 59.99 50
upstream ENSMUSE00000410900 Chr3:97904123..97904311 GAGTGTCTGAAGGGCTACGC Chr3:97904185..97904204 60.02 60
upstream ENSMUSE00000173851 Chr3:97905444..97905557 AAGTCAACCGCTTCCAGTGT Chr3:97905525..97905544 59.77 50
upstream ENSMUSE00000372606 Chr3:97906249..97906362 AGTGTGCCAGATCGACATTG Chr3:97906262..97906281 59.71 50
upstream ENSMUSE00000173865 Chr3:97908272..97908505 GGATGGGATCGACTCCTACA Chr3:97908345..97908364 59.89 55
upstream ENSMUSE00000173842 Chr3:97910970..97911080 ACCCTTGTATGCACGGAGTC Chr3:97911009..97911028 60 55
upstream ENSMUSE00000391377 Chr3:97915473..97915665 ATGTGAATGGTTTCCGGTGT Chr3:97915545..97915564 60.1 45

*** Putative Vector Insertion (Chr 3: 97915666 - 97916932) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000173837 Chr3:97916933..97917078 CCAGGTTATTGCACGTTCCT Chr3:97917042..97917061 59.99 50
downstream ENSMUSE00000357324 Chr3:97919155..97919268 GGTTGGAGGCACACTCATCT Chr3:97919199..97919218 60.12 55
downstream ENSMUSE00000406771 Chr3:97920624..97920743 TCTCAAAATTGGGTGCCTCT Chr3:97920713..97920732 59.67 45
downstream ENSMUSE00000392832 Chr3:97921116..97921268 TAGCTGCCCTGAGTGTTGTG Chr3:97921203..97921222 60.05 55
downstream ENSMUSE00000173846 Chr3:97924650..97924878 GCACTTGTCCCCTATGAAGC Chr3:97924738..97924757 59.7 55
downstream ENSMUSE00000173840 Chr3:97925827..97926028 CTGACAGTTTTTCCCGGTGT Chr3:97926031..97926050 60.01 50
downstream ENSMUSE00000173839 Chr3:97927668..97927821 GGACACGTTGAGCACATCAC Chr3:97927799..97927818 60.17 55
downstream ENSMUSE00000357630 Chr3:97928072..97928256 CATGGATTGGATGCACACTC Chr3:97928210..97928229 59.92 50
downstream ENSMUSE00000173862 Chr3:97930035..97930167 TGGCACTCGTCCACTTCATA Chr3:97930090..97930109 60.26 50
downstream ENSMUSE00000491540 Chr3:97935121..97935357 GACAGGCATTCGTTGATGTC Chr3:97935277..97935296 59.09 50
downstream ENSMUSE00000173859 Chr3:97938482..97938594 GGGACAACGACAGATGAAGC Chr3:97938594..97938613 60.67 55
downstream ENSMUSE00000671895 Chr3:97938482..97938499 No primer for this exon
downstream ENSMUSE00000173831 Chr3:97939249..97939754 TACTGGCACATCCTGACTCG Chr3:97939387..97939406 59.85 55
downstream ENSMUSE00000173834 Chr3:97941198..97941551 TTGTTTAATGCGCAAGTTGG Chr3:97941432..97941451 59.74 40
downstream ENSMUSE00000671894 Chr3:97941218..97941551 TTGTTTAATGCGCAAGTTGG Chr3:97941432..97941451 59.74 40
downstream ENSMUSE00000410647 Chr3:97942309..97942451 ACTGTCGGTTGTCGATCTCC Chr3:97942346..97942365 60.12 55
downstream ENSMUSE00000637280 Chr3:97942565..97942668 ACCGCGAGCAGATAGAGAAG Chr3:97942616..97942635 59.74 55
downstream ENSMUSE00000637278 Chr3:97942674..97942700 No primer for this exon
downstream ENSMUSE00000637277 Chr3:97942705..97942775 ATCCTGTCCCACAGGTTCAC Chr3:97942764..97942783 59.82 55
downstream ENSMUSE00000173843 Chr3:97943509..97943605 CTCTGACACTTGCACGGAGA Chr3:97943536..97943555 60.18 55
downstream ENSMUSE00000410856 Chr3:97945387..97945552 GTTCTGCCTGAGGAGGAGTG Chr3:97945516..97945535 59.99 60
downstream ENSMUSE00000173830 Chr3:97946816..97947117 GAAGCCAGCATCAGTGGAGT Chr3:97946846..97946865 60.42 55
downstream ENSMUSE00000173849 Chr3:97948285..97948432 GGGGGTAGTACCATCGTTCA Chr3:97948347..97948366 59.67 55
downstream ENSMUSE00000173847 Chr3:97949045..97949142 TATCTCTGTTGGCCCCATTC Chr3:97949131..97949150 59.89 50
downstream ENSMUSE00000507053 Chr3:97949976..97951367 TGAGAGCGCAGAAGTCAAGA Chr3:97950194..97950213 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCCACGGAAACTGTACTGGAG Chr3:97915636..97915657 60.16 52.38 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCCACGGAAACTGTACTGGAG Chr3:97915636..97915657 60.16 52.38 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027878