Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2422
Trapped Gene
Lmnb1 (ENSMUSG00000024590)
Vector Insertion
Chr 18: 56892992 - 56899474
Public Clones AC0463 (sanger) XB206 (baygenomics) XA130 (baygenomics) XA152 (baygenomics)
H004B04 (ggtc) H004B04 (ggtc)
Private Clones OST45900 (lexicon)
Severity of mutation (?) Insertion after 53% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000143562 (Chr18:56892866..56892991 +)
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
ENSMUSE00000143562 (Chr18:56892866..56892991 +)
Downstram Exon
ENSMUSE00000143565 (Chr18:56899475..56899695 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon GTAGGCGCTGATCTCCATGT Chr18:56899669..56899688 60.25 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000625385 Chr18:56867467..56868128 AGCCCGAGAGGAAACAAAGT Chr18:56867514..56867533 60.25 50
upstream ENSMUSE00000143569 Chr18:56888055..56888211 GCCCTAGGGGACAAAAAGAG Chr18:56888149..56888168 60.07 55
upstream ENSMUSE00000143564 Chr18:56888941..56889066 GGATTTGGAGAATCGCTGTC Chr18:56889000..56889019 59.63 50
upstream ENSMUSE00000143567 Chr18:56890624..56890794 TGGGCGTCAGATTGAGTATG Chr18:56890677..56890696 59.67 50
upstream ENSMUSE00000143562 Chr18:56892866..56892991 No primer for this exon

*** Putative Vector Insertion (Chr 18: 56892992 - 56899474) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000143565 Chr18:56899475..56899695 GTAGGCGCTGATCTCCATGT Chr18:56899669..56899688 60.25 55
downstream ENSMUSE00000143571 Chr18:56900341..56900566 CCGACTCCTCCACATCAACT Chr18:56900456..56900475 60.11 55
downstream ENSMUSE00000494265 Chr18:56902865..56902969 No primer for this exon
downstream ENSMUSE00000491699 Chr18:56907631..56907750 CATCTTCACCAGTACCCCAAG Chr18:56907720..56907740 59.46 52.38
downstream ENSMUSE00000492660 Chr18:56909353..56909463 No primer for this exon
downstream ENSMUSE00000489632 Chr18:56912261..56913076 AGCTTGAGGAAGATCGACCA Chr18:56912338..56912357 59.95 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTTTGAGCAGGACTGAGGT Chr18:56899007..56899027 59.45 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTTTGAGCAGGACTGAGGT Chr18:56899007..56899027 59.45 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024590