Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1872
Trapped Gene
Ints3 (ENSMUSG00000027933)
Vector Insertion
Chr 3: 90207520 - 90207906
Public Clones AZ0168 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 42% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000304126 (Chr3:90207907..90207986 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGGTCATGCATCACTCCAT Chr3:90207956..90207975 59.51 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000304126 (Chr3:90207907..90207986 -)
Downstram Exon
ENSMUSE00000304120 (Chr3:90207428..90207519 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGGTCATGCATCACTCCAT Chr3:90207956..90207975 59.51 50 GCCAAGACTCGTTTCTCCAC Chr3:90207406..90207425 59.85 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000457149 Chr3:90236726..90237558 TTGTTCCTCTTGCTCCTCGT Chr3:90236955..90236974 59.99 50
upstream ENSMUSE00000457133 Chr3:90227926..90228009 AGGTTGGAAAGGTGCATGAG Chr3:90227990..90228009 60.11 50
upstream ENSMUSE00000457126 Chr3:90225658..90225741 No primer for this exon
upstream ENSMUSE00000457121 Chr3:90219415..90219528 GGACTTGGCTCTGGTGAGTC Chr3:90219501..90219520 59.84 60
upstream ENSMUSE00000457119 Chr3:90219080..90219164 GAGTGGAGTTCTGGGAGCTG Chr3:90219116..90219135 59.99 60
upstream ENSMUSE00000457114 Chr3:90217452..90217518 GGATATCCTGACGGAGCAGA Chr3:90217453..90217472 60.18 55
upstream ENSMUSE00000457109 Chr3:90215123..90215267 TTCGGCAGAAGGAAGTTGAC Chr3:90215150..90215169 60.38 50
upstream ENSMUSE00000457105 Chr3:90213920..90214049 CAGGCCTTGAGTCCTCAGTT Chr3:90213925..90213944 59.45 55
upstream ENSMUSE00000457100 Chr3:90212424..90212521 CATGGAAACGAAGCTCCTCT Chr3:90212438..90212457 59.43 50
upstream ENSMUSE00000457096 Chr3:90210096..90210287 CGCTGTGACCTCATTCGATA Chr3:90210190..90210209 59.82 50
upstream ENSMUSE00000304132 Chr3:90208436..90208523 GCTGTTCTTCAGCCCAGAAA Chr3:90208457..90208476 60.52 50
upstream ENSMUSE00000304126 Chr3:90207907..90207986 CTGGTCATGCATCACTCCAT Chr3:90207956..90207975 59.51 50

*** Putative Vector Insertion (Chr 3: 90207520 - 90207906) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000304120 Chr3:90207428..90207519 GCCAAGACTCGTTTCTCCAC Chr3:90207406..90207425 59.85 55
downstream ENSMUSE00000304115 Chr3:90207001..90207107 GCATGGACCGAAGCTCTTTA Chr3:90207030..90207049 60.35 50
downstream ENSMUSE00000174429 Chr3:90206230..90206349 GAGGTGGTTGTCCATTTCCA Chr3:90206284..90206303 60.76 50
downstream ENSMUSE00000174433 Chr3:90205765..90205894 TCCTCCACGACAGTCTCCTT Chr3:90205821..90205840 59.83 55
downstream ENSMUSE00000174430 Chr3:90205327..90205381 TAACCTCACACTGGGCCTCT Chr3:90205334..90205353 59.72 55
downstream ENSMUSE00000174432 Chr3:90204990..90205093 ACCTCTTCAGGCAACACCTC Chr3:90204977..90204996 59.31 55
downstream ENSMUSE00000174427 Chr3:90204517..90204561 No primer for this exon
downstream ENSMUSE00000174438 Chr3:90204226..90204345 GAAGCTGCTGTTGTCCTCCT Chr3:90204287..90204306 59.6 55
downstream ENSMUSE00000174434 Chr3:90200300..90200453 GCATAGCAGTCGCACATCAT Chr3:90200305..90200324 59.86 50
downstream ENSMUSE00000174441 Chr3:90199060..90199128 GCCACAATCATGTTCAGCAG Chr3:90199057..90199076 60.27 50
downstream ENSMUSE00000174436 Chr3:90198245..90198320 TGAGTCCTTCCGAAACATGA Chr3:90198239..90198258 59.22 45
downstream ENSMUSE00000174443 Chr3:90197996..90198109 CTGCTCAAACGTTTCCCAGT Chr3:90198056..90198075 60.29 50
downstream ENSMUSE00000174442 Chr3:90197668..90197716 CCGTAGCTGAAGCAGGAGAC Chr3:90197654..90197673 60.16 60
downstream ENSMUSE00000174437 Chr3:90197018..90197185 TGGTGAACTGGTCATCAGGA Chr3:90197099..90197118 60.09 50
downstream ENSMUSE00000304170 Chr3:90196713..90196813 TGCTTGGTGTTGGCTAGGTT Chr3:90196696..90196715 60.69 50
downstream ENSMUSE00000174431 Chr3:90196450..90196522 CTTGTGAGCTTCGTCACAGC Chr3:90196433..90196452 59.78 55
downstream ENSMUSE00000304160 Chr3:90196134..90196290 CTTGGGTGGCTTAGTGGAAG Chr3:90196208..90196227 59.73 55
downstream ENSMUSE00000490758 Chr3:90195915..90196027 TTCGTTTTCGTTTGGTAGGC Chr3:90195963..90195982 60.11 45
downstream ENSMUSE00000395515 Chr3:90195310..90196027 TAATGACCACCGTCCACAGA Chr3:90195593..90195612 59.96 50
downstream ENSMUSE00000488281 Chr3:90195310..90195833 TAATGACCACCGTCCACAGA Chr3:90195593..90195612 59.96 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTCATGTGCCGAGTAAGTGC Chr3:90207897..90207917 59.87 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGCAGTGTTGAATCCGTGA Chr3:90207850..90207870 59.84 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027933