Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7437
Trapped Gene
Rabgef1 (ENSMUSG00000025340)
Vector Insertion
Chr 5: 130673819 - 130673987
Public Clones RRS789 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 24% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000709554 (Chr5:130673817..130673986 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATTGAGACGGACCGAGTGAC Chr5:130673870..130673889 60.12 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000709554 (Chr5:130673817..130673986 +)
Downstram Exon
ENSMUSE00000149947 (Chr5:130673820..130673986 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATTGAGACGGACCGAGTGAC Chr5:130673870..130673889 60.12 55 GTCCGTCTCAATGCTGGTTT Chr5:130673884..130673903 60.12 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000712071 Chr5:130647668..130647764 AGGGAGCCGAGTGACTGAAG Chr5:130647700..130647719 61.91 60
upstream ENSMUSE00000714179 Chr5:130663031..130663456 CTGGAGGGAGGAGTACCACA Chr5:130663391..130663410 60.1 60
upstream ENSMUSE00000310054 Chr5:130663050..130663456 CTGGAGGGAGGAGTACCACA Chr5:130663391..130663410 60.1 60
upstream ENSMUSE00000711184 Chr5:130663271..130663456 CTGGAGGGAGGAGTACCACA Chr5:130663391..130663410 60.1 60
upstream ENSMUSE00000149942 Chr5:130666747..130666913 AACCCGAAAAGTCACCACAG Chr5:130666849..130666868 60.01 50
upstream ENSMUSE00000709554 Chr5:130673817..130673986 ATTGAGACGGACCGAGTGAC Chr5:130673870..130673889 60.12 55

*** Putative Vector Insertion (Chr 5: 130673819 - 130673987) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000149947 Chr5:130673820..130673986 GTCCGTCTCAATGCTGGTTT Chr5:130673884..130673903 60.12 50
downstream ENSMUSE00000149944 Chr5:130682879..130682960 ACGGGTCTGCATTCTTTCAG Chr5:130682956..130682975 60.26 50
downstream ENSMUSE00000149946 Chr5:130684556..130684688 No primer for this exon
downstream ENSMUSE00000718174 Chr5:130684556..130684622 No primer for this exon
downstream ENSMUSE00000149948 Chr5:130686294..130686385 CATCTGAGGCGTTACCCAGT Chr5:130686324..130686343 60.13 55
downstream ENSMUSE00000149945 Chr5:130687732..130687988 GCCCTTCAGGACGATGTAGA Chr5:130687892..130687911 60.22 55
downstream ENSMUSE00000344215 Chr5:130688704..130690206 GGCCAACTCTCAGACTCCTG Chr5:130688828..130688847 59.99 60
downstream ENSMUSE00000709075 Chr5:130688704..130690212 GGCCAACTCTCAGACTCCTG Chr5:130688828..130688847 59.99 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAAACCAGTAATCGCCTTGC Chr5:130673862..130673882 60.64 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000025340