Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27168
Trapped Gene
Nbn (ENSMUSG00000028224)
Vector Insertion
Chr 4: 15885258 - 15889457
Public Clones (sanger) (sanger)
Private Clones OST67987 (lexicon)
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000346939 (Chr4:15885115..15885257 +)
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
ENSMUSE00000346939 (Chr4:15885115..15885257 +)
Downstram Exon
ENSMUSE00000251302 (Chr4:15889458..15889591 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon TCCTCCCAACAACGTACTCC Chr4:15889508..15889527 59.97 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000346939 Chr4:15885115..15885257 No primer for this exon

*** Putative Vector Insertion (Chr 4: 15885258 - 15889457) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000251302 Chr4:15889458..15889591 TCCTCCCAACAACGTACTCC Chr4:15889508..15889527 59.97 55
downstream ENSMUSE00000177365 Chr4:15890919..15891067 CTGTCTTCAACGTGCAGGAA Chr4:15891030..15891049 60.03 50
downstream ENSMUSE00000177364 Chr4:15891394..15891553 TAACTGCCGACATGACAAGG Chr4:15891542..15891561 59.72 50
downstream ENSMUSE00000177367 Chr4:15892281..15892384 GGACGTCCACAAATGAGTGC Chr4:15892312..15892331 61.54 55
downstream ENSMUSE00000177362 Chr4:15896488..15896605 GGTTCATCAATGGGTGGGTA Chr4:15896514..15896533 60.44 50
downstream ENSMUSE00000177363 Chr4:15897868..15898061 GCTCTGTTCCTCTTCGTCGT Chr4:15897951..15897970 59.6 55
downstream ENSMUSE00000177370 Chr4:15898913..15899010 CAATCCAATCTCCGCTTCAG Chr4:15898955..15898974 60.73 50
downstream ENSMUSE00000177357 Chr4:15903182..15903311 CTTGGTCCTGGAGTCGTTGT Chr4:15903212..15903231 60.15 55
downstream ENSMUSE00000177371 Chr4:15906288..15906560 GGTGCATGGCTGGAAGTAGT Chr4:15906555..15906574 60.14 55
downstream ENSMUSE00000177360 Chr4:15908454..15908895 CTGATGCTCCTTGCTTTTCC Chr4:15908580..15908599 59.96 50
downstream ENSMUSE00000251251 Chr4:15911101..15911169 TGTTGACCACGACTCTGTCTG Chr4:15911156..15911176 59.92 52.38
downstream ENSMUSE00000251244 Chr4:15913656..15913811 CTGGAGGTGGAGTTGTGGTT Chr4:15913759..15913778 60 55
downstream ENSMUSE00000177361 Chr4:15916149..15916262 CGGTATTCTTTCGAGCATGG Chr4:15916233..15916252 60.6 50
downstream ENSMUSE00000177368 Chr4:15918329..15918378 GCAAGAGATTCCTCCTTTGCT Chr4:15918365..15918385 59.98 47.62
downstream ENSMUSE00000416563 Chr4:15919581..15919735 ACAGCTTCCTTTACAAGGTTCAA Chr4:15919631..15919653 59.36 39.13

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTAATCGCCTTGCAGCACAT Chr4:15885308..15885328 61.2 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTCCCTTCGTAAACGTGACTG Chr4:15885296..15885317 60.15 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028224