Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26052
Trapped Gene
Nup43 (ENSMUSG00000040034)
Vector Insertion
Chr 10: 7387923 - 7389350
Public Clones IST10099A11 (tigm) IST10099A11 (tigm)
Private Clones OST142674 (lexicon)
Severity of mutation (?) Insertion after 21% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000355550 (Chr10:7387800..7387922 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GATTCTGACGGAGGGTTTGA Chr10:7387845..7387864 60.05 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000355550 (Chr10:7387800..7387922 +)
Downstram Exon
ENSMUSE00000323106 (Chr10:7389351..7389428 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GATTCTGACGGAGGGTTTGA Chr10:7387845..7387864 60.05 50 ACACAGCCTGTTGACGAAGC Chr10:7389400..7389419 61.46 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000323125 Chr10:7387342..7387479 CCTGCAGACCACAGAGACCT Chr10:7387434..7387453 60.46 60
upstream ENSMUSE00000355550 Chr10:7387800..7387922 GATTCTGACGGAGGGTTTGA Chr10:7387845..7387864 60.05 50

*** Putative Vector Insertion (Chr 10: 7387923 - 7389350) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000323106 Chr10:7389351..7389428 ACACAGCCTGTTGACGAAGC Chr10:7389400..7389419 61.46 55
downstream ENSMUSE00000323097 Chr10:7390737..7390917 CACTGCTGATTGACGGACAG Chr10:7390762..7390781 60.46 55
downstream ENSMUSE00000348903 Chr10:7393383..7393518 CTCAGGAGTTCGAAGGAAGG Chr10:7393438..7393457 59.01 55
downstream ENSMUSE00000374602 Chr10:7394804..7394955 GCCACCGGTAGCTACAACAT Chr10:7394879..7394898 60.02 55
downstream ENSMUSE00000323066 Chr10:7396038..7396160 CCAATGCCAGAGAGATCCAT Chr10:7396117..7396136 60.03 50
downstream ENSMUSE00000323055 Chr10:7398366..7398675 GACAGAGTCCTGCTGGGAAG Chr10:7398510..7398529 59.99 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCATGGGGATGTCATGGATT Chr10:7387899..7387919 60.96 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCATGGGGATGTCATGGATT Chr10:7387899..7387919 60.96 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040034