Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7204
Trapped Gene
Bnc2 (ENSMUSG00000028487)
Vector Insertion
Chr 4: 84192108 - 84192238
Public Clones RRU542 (baygenomics)
Private Clones OST304427 (lexicon) OST103438 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000662706 (Chr4:84192109..84192237 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATGGCAAAACGCTGACACTA Chr4:84192135..84192154 59.35 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000662706 (Chr4:84192109..84192237 -)
Downstram Exon
ENSMUSE00000443683 (Chr4:84192109..84192309 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATGGCAAAACGCTGACACTA Chr4:84192135..84192154 59.35 45 GTTCTGGTTCCGAACTGCAT Chr4:84192163..84192182 60.12 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000672378 Chr4:84320879..84320990 CCGCTAAGAGGAGACCAAGA Chr4:84320916..84320935 59.57 55
upstream ENSMUSE00000632105 Chr4:84201683..84201808 CATTTTAAGGTCCCGTGCTG Chr4:84201708..84201727 60.49 50
upstream ENSMUSE00000443683 Chr4:84192109..84192309 ATGGCAAAACGCTGACACTA Chr4:84192135..84192154 59.35 45
upstream ENSMUSE00000662706 Chr4:84192109..84192237 ATGGCAAAACGCTGACACTA Chr4:84192135..84192154 59.35 45

*** Putative Vector Insertion (Chr 4: 84192108 - 84192238) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000468368 Chr4:84152432..84152515 AAGTCTGCACCCAGCACTCT Chr4:84152453..84152472 60.06 55
downstream ENSMUSE00000603220 Chr4:84060150..84060252 CACACGTGCAGTTTACCAATG Chr4:84060197..84060217 60.08 47.62
downstream ENSMUSE00000469416 Chr4:84036793..84037028 ATGTCAAACACCACGTTGGA Chr4:84036928..84036947 59.85 45
downstream ENSMUSE00000179656 Chr4:83937597..83939566 CCATGTTGCAACCTTCAATG Chr4:83938779..83938798 59.96 45
downstream ENSMUSE00000518854 Chr4:83920999..83922351 ATTTGGAGTGTCCGTTCTGG Chr4:83921647..83921666 59.97 50
downstream ENSMUSE00000672376 Chr4:83920748..83922351 ATTTGGAGTGTCCGTTCTGG Chr4:83921647..83921666 59.97 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAACCATAATCGCCTTGCAG Chr4:84192173..84192193 60.61 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AACCACGTGACTGGGAAAAC Chr4:84192172..84192192 59.87 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028487