Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1476
Trapped Gene
Plcb4 (ENSMUSG00000039943)
Vector Insertion
Chr 2: 135735836 - 135735981
Public Clones CD0291 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 6% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000167685 (Chr2:135735837..135735980 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAGGGCGGATATTGTGTGTC Chr2:135735892..135735911 59.82 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000167685 (Chr2:135735837..135735980 +)
Downstram Exon
ENSMUSE00000682803 (Chr2:135735837..135735980 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAGGGCGGATATTGTGTGTC Chr2:135735892..135735911 59.82 50 GCCCTTCCAGATCATTTTCA Chr2:135735900..135735919 60.01 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000682812 Chr2:135567566..135567623 TACCTGGGAGGATTCTCGAC Chr2:135567592..135567611 59.09 55
upstream ENSMUSE00000497642 Chr2:135631284..135631341 GCAGGATTTGATCGGGTAGA Chr2:135631292..135631311 60.04 50
upstream ENSMUSE00000682811 Chr2:135631285..135631341 GCAGGATTTGATCGGGTAGA Chr2:135631292..135631311 60.04 50
upstream ENSMUSE00000711482 Chr2:135703119..135703217 CATGGCCAAACCTTACGAAT Chr2:135703133..135703152 59.82 45
upstream ENSMUSE00000712135 Chr2:135703119..135703217 CATGGCCAAACCTTACGAAT Chr2:135703133..135703152 59.82 45
upstream ENSMUSE00000716356 Chr2:135703119..135703217 CATGGCCAAACCTTACGAAT Chr2:135703133..135703152 59.82 45
upstream ENSMUSE00000167688 Chr2:135733235..135733315 TTTGTGTTTGAGCCCAACTG Chr2:135733241..135733260 59.73 45
upstream ENSMUSE00000682805 Chr2:135733235..135733315 TTTGTGTTTGAGCCCAACTG Chr2:135733241..135733260 59.73 45
upstream ENSMUSE00000167690 Chr2:135734086..135734145 TCAACAGTATTCGCCAAGCA Chr2:135734114..135734133 60.4 45
upstream ENSMUSE00000682804 Chr2:135734086..135734145 TCAACAGTATTCGCCAAGCA Chr2:135734114..135734133 60.4 45

*** Putative Vector Insertion (Chr 2: 135735836 - 135735981) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000167685 Chr2:135735837..135735980 GCCCTTCCAGATCATTTTCA Chr2:135735900..135735919 60.01 45
downstream ENSMUSE00000682803 Chr2:135735837..135735980 GCCCTTCCAGATCATTTTCA Chr2:135735900..135735919 60.01 45
downstream ENSMUSE00000396929 Chr2:135755691..135755770 CATCGGACTGACGTTGTTTG Chr2:135755756..135755775 60.15 50
downstream ENSMUSE00000682802 Chr2:135755691..135755770 CATCGGACTGACGTTGTTTG Chr2:135755756..135755775 60.15 50
downstream ENSMUSE00000350832 Chr2:135757985..135758038 TTGGTCAGAAAGGCCAGTTT Chr2:135758014..135758033 59.71 45
downstream ENSMUSE00000682801 Chr2:135757985..135758038 TTGGTCAGAAAGGCCAGTTT Chr2:135758014..135758033 59.71 45
downstream ENSMUSE00000378637 Chr2:135763996..135764077 TGAGGGCTTGAAAGATCACC Chr2:135764054..135764073 60.19 50
downstream ENSMUSE00000682800 Chr2:135763996..135764077 TGAGGGCTTGAAAGATCACC Chr2:135764054..135764073 60.19 50
downstream ENSMUSE00000291202 Chr2:135764946..135765046 ATGCAGCAGGTTCAATTTCA Chr2:135764973..135764992 59.28 40
downstream ENSMUSE00000682799 Chr2:135764946..135765046 ATGCAGCAGGTTCAATTTCA Chr2:135764973..135764992 59.28 40
downstream ENSMUSE00000291194 Chr2:135765683..135765740 No primer for this exon
downstream ENSMUSE00000682798 Chr2:135765683..135765740 No primer for this exon
downstream ENSMUSE00000291187 Chr2:135772782..135772890 TTTCATTCAGCCGAGGATCT Chr2:135772812..135772831 59.77 45
downstream ENSMUSE00000682797 Chr2:135772782..135772890 TTTCATTCAGCCGAGGATCT Chr2:135772812..135772831 59.77 45
downstream ENSMUSE00000291181 Chr2:135775948..135776158 AGGTGTTGTGGGAGGAACTG Chr2:135776088..135776107 60 55
downstream ENSMUSE00000682795 Chr2:135775948..135776158 AGGTGTTGTGGGAGGAACTG Chr2:135776088..135776107 60 55
downstream ENSMUSE00000291175 Chr2:135777729..135777822 TCGGTTCCTGATCTTCACCT Chr2:135777781..135777800 59.65 50
downstream ENSMUSE00000682794 Chr2:135777729..135777822 TCGGTTCCTGATCTTCACCT Chr2:135777781..135777800 59.65 50
downstream ENSMUSE00000291169 Chr2:135780082..135780161 GCAGTGGTTTTCGAAGGAGA Chr2:135780162..135780181 60.38 50
downstream ENSMUSE00000682793 Chr2:135780082..135780161 GCAGTGGTTTTCGAAGGAGA Chr2:135780162..135780181 60.38 50
downstream ENSMUSE00000291160 Chr2:135780651..135780735 TTCAACAGGAGATCCCCAAA Chr2:135780716..135780735 60.43 45
downstream ENSMUSE00000682791 Chr2:135780651..135780735 TTCAACAGGAGATCCCCAAA Chr2:135780716..135780735 60.43 45
downstream ENSMUSE00000291156 Chr2:135783791..135783881 GGTCATTAGGAGACGGCAAG Chr2:135783830..135783849 59.69 55
downstream ENSMUSE00000682790 Chr2:135783791..135783881 GGTCATTAGGAGACGGCAAG Chr2:135783830..135783849 59.69 55
downstream ENSMUSE00000557975 Chr2:135784378..135784473 CCAGCTTCCATCATGCTTTT Chr2:135784417..135784436 60.21 45
downstream ENSMUSE00000682789 Chr2:135784378..135784473 CCAGCTTCCATCATGCTTTT Chr2:135784417..135784436 60.21 45
downstream ENSMUSE00000557972 Chr2:135787455..135787555 AACCGCTTCCTTGTGACTGT Chr2:135787540..135787559 59.77 50
downstream ENSMUSE00000682788 Chr2:135787455..135787555 AACCGCTTCCTTGTGACTGT Chr2:135787540..135787559 59.77 50
downstream ENSMUSE00000682809 Chr2:135790788..135790823 No primer for this exon
downstream ENSMUSE00000291129 Chr2:135792761..135792902 GGATGGATGTTCGTGGTAGC Chr2:135792840..135792859 60.35 55
downstream ENSMUSE00000682787 Chr2:135792761..135792902 GGATGGATGTTCGTGGTAGC Chr2:135792840..135792859 60.35 55
downstream ENSMUSE00000291125 Chr2:135793653..135793737 GCCAACCGACTCGTTAAAAG Chr2:135793702..135793721 59.75 50
downstream ENSMUSE00000682786 Chr2:135793653..135793737 GCCAACCGACTCGTTAAAAG Chr2:135793702..135793721 59.75 50
downstream ENSMUSE00000291120 Chr2:135794057..135794181 CAACCAGCGTTCCAGAAAAT Chr2:135794152..135794171 60.11 45
downstream ENSMUSE00000682785 Chr2:135794057..135794181 CAACCAGCGTTCCAGAAAAT Chr2:135794152..135794171 60.11 45
downstream ENSMUSE00000291114 Chr2:135796130..135796181 CCGCATGATCCATTATACTCAA Chr2:135796182..135796203 59.82 40.91
downstream ENSMUSE00000682784 Chr2:135796130..135796181 CCGCATGATCCATTATACTCAA Chr2:135796182..135796203 59.82 40.91
downstream ENSMUSE00000291107 Chr2:135797494..135797596 GTCCACAGGGGTTTCAGAGA Chr2:135797569..135797588 60.09 55
downstream ENSMUSE00000682782 Chr2:135797494..135797596 GTCCACAGGGGTTTCAGAGA Chr2:135797569..135797588 60.09 55
downstream ENSMUSE00000291096 Chr2:135798648..135798812 GCAGCCCGTACATATCGACT Chr2:135798720..135798739 60.12 55
downstream ENSMUSE00000682781 Chr2:135798648..135798812 GCAGCCCGTACATATCGACT Chr2:135798720..135798739 60.12 55
downstream ENSMUSE00000291091 Chr2:135801835..135802039 AGCTAGGTCAGGCAGGATCA Chr2:135801858..135801877 59.97 55
downstream ENSMUSE00000682779 Chr2:135801835..135802039 AGCTAGGTCAGGCAGGATCA Chr2:135801858..135801877 59.97 55
downstream ENSMUSE00000291083 Chr2:135807769..135807857 TTGGATCGGATAAAGCATCC Chr2:135807798..135807817 59.86 45
downstream ENSMUSE00000682778 Chr2:135807769..135807857 TTGGATCGGATAAAGCATCC Chr2:135807798..135807817 59.86 45
downstream ENSMUSE00000380377 Chr2:135808712..135808862 GTCACTGGGCACATCTGCTA Chr2:135808741..135808760 59.86 55
downstream ENSMUSE00000682777 Chr2:135808712..135808862 GTCACTGGGCACATCTGCTA Chr2:135808741..135808760 59.86 55
downstream ENSMUSE00000682808 Chr2:135808712..135808748 GTCACTGGGCACATCTGCTA Chr2:135808741..135808760 59.86 55
downstream ENSMUSE00000682807 Chr2:135808976..135809001 No primer for this exon
downstream ENSMUSE00000404645 Chr2:135813216..135813265 No primer for this exon
downstream ENSMUSE00000682776 Chr2:135813216..135813265 No primer for this exon
downstream ENSMUSE00000359180 Chr2:135813573..135813638 No primer for this exon
downstream ENSMUSE00000395037 Chr2:135820030..135820145 GTCATACTGGGCCACGATTT Chr2:135820095..135820114 59.82 50
downstream ENSMUSE00000291042 Chr2:135824413..135824488 ATCCGTTGTCAGGGTCTGAA Chr2:135824479..135824498 60.51 50
downstream ENSMUSE00000291035 Chr2:135825870..135826045 TGAGCATTGATGAGCAGCTT Chr2:135826009..135826028 59.7 45
downstream ENSMUSE00000291027 Chr2:135828295..135828396 GATGGCCTTGCTATTTTCCA Chr2:135828358..135828377 60.04 45
downstream ENSMUSE00000291019 Chr2:135833076..135833133 TGCTGTTCAACTCCCTGACTC Chr2:135833100..135833120 60.44 52.38
downstream ENSMUSE00000291013 Chr2:135833559..135833645 No primer for this exon
downstream ENSMUSE00000682775 Chr2:135836672..135836708 GGACACTGCATGACAGGATTT Chr2:135836700..135836720 59.99 47.62
downstream ENSMUSE00000460557 Chr2:135838702..135838804 ATCTCGGCTTCCAATTTCAC Chr2:135838745..135838764 59.13 45
downstream ENSMUSE00000682774 Chr2:135838702..135838804 ATCTCGGCTTCCAATTTCAC Chr2:135838745..135838764 59.13 45
downstream ENSMUSE00000682810 Chr2:135838702..135840329 GGGCATGATCTTCTGGTGTT Chr2:135838829..135838848 59.93 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTCTCGAAGCTGTTGGAAA Chr2:135735856..135735876 60.66 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAAATGCGTGACTGGGAAAA Chr2:135735881..135735901 60.48 40 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039943