Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12106
Trapped Gene
Ccdc55 (ENSMUSG00000037958)
Vector Insertion
Chr 11: 76861964 - 76862774
Public Clones A042D03 (ggtc) A042C03 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 31% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000293687 (Chr11:76862775..76862982 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGAGAGATGGAAAACGGAGA Chr11:76862876..76862895 60.33 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000293687 (Chr11:76862775..76862982 -)
Downstram Exon
ENSMUSE00000293678 (Chr11:76861855..76861963 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGAGAGATGGAAAACGGAGA Chr11:76862876..76862895 60.33 50 TCTGCTTGGTCACATCCAAA Chr11:76861918..76861937 60.24 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000661751 Chr11:76891881..76891937 AGCGGAGACGGGAACAAGAT Chr11:76891899..76891918 63.34 55
upstream ENSMUSE00000661750 Chr11:76890156..76890246 CGTTGCACCGAGTTTTACAG Chr11:76890195..76890214 59.39 50
upstream ENSMUSE00000293705 Chr11:76868446..76868502 GTGAGCGAAAGCCTTCAGAG Chr11:76868477..76868496 60.28 55
upstream ENSMUSE00000293697 Chr11:76864086..76864214 AAGAAAACAACCCCAAGCTG Chr11:76864107..76864126 59.22 45
upstream ENSMUSE00000293687 Chr11:76862775..76862982 CGAGAGATGGAAAACGGAGA Chr11:76862876..76862895 60.33 50

*** Putative Vector Insertion (Chr 11: 76861964 - 76862774) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000293678 Chr11:76861855..76861963 TCTGCTTGGTCACATCCAAA Chr11:76861918..76861937 60.24 45
downstream ENSMUSE00000661749 Chr11:76857794..76860256 GGCCTCTCTGTGCCTATGAG Chr11:76859823..76859842 59.97 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTGCTCTGGAAGGTATGGA Chr11:76862766..76862786 60.36 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCTGCTCTGGAAGGTATGGA Chr11:76862766..76862786 60.36 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037958