Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26111
Trapped Gene
Ccdc55 (ENSMUSG00000037958)
Vector Insertion
Chr 11: 76890247 - 76891880
Public Clones Ayu21-T93 (egtc)
Private Clones OST136958 (lexicon)
Severity of mutation (?) Insertion after 1% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000661751 (Chr11:76891881..76891937 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCGGAGACGGGAACAAGAT Chr11:76891899..76891918 63.34 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000661751 (Chr11:76891881..76891937 -)
Downstram Exon
ENSMUSE00000661750 (Chr11:76890156..76890246 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCGGAGACGGGAACAAGAT Chr11:76891899..76891918 63.34 55 CCCAAACACTGACGGTTTCT Chr11:76890155..76890174 60.01 50

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

*** Putative Vector Insertion (Chr 11: 76890247 - 76891880) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000661750 Chr11:76890156..76890246 CCCAAACACTGACGGTTTCT Chr11:76890155..76890174 60.01 50
downstream ENSMUSE00000293705 Chr11:76868446..76868502 CTCTGAAGGCTTTCGCTCAC Chr11:76868455..76868474 60.28 55
downstream ENSMUSE00000293697 Chr11:76864086..76864214 GCTTGGGGTTGTTTTCTTCC Chr11:76864087..76864106 60.84 50
downstream ENSMUSE00000293687 Chr11:76862775..76862982 TCCGTTTTCCATCTCTCGTT Chr11:76862856..76862875 59.67 45
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 GAGTGATGGGGAAGTTAGGG Chr11:76891857..76891877 58.45 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGTGATGGGGAAGTTAGGG Chr11:76891857..76891877 58.45 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037958