Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7823
Trapped Gene
Tcp1 (ENSMUSG00000068039)
Vector Insertion
Chr 17: 13111038 - 13112216
Public Clones RRP033 (baygenomics) RRO044 (baygenomics) PST25650-NR (escells)
Private Clones OST53912 (lexicon)
Severity of mutation (?) Insertion after 17% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000555827 (Chr17:13110909..13111037 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCAGCCAAAGTTCTGTGTGA Chr17:13110969..13110988 60.03 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000555827 (Chr17:13110909..13111037 +)
Downstram Exon
ENSMUSE00000555826 (Chr17:13112217..13112314 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCAGCCAAAGTTCTGTGTGA Chr17:13110969..13110988 60.03 50 CAGGCAAGACGATAGCCACT Chr17:13112314..13112333 60.42 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000555829 Chr17:13109331..13109495 AGCTTTGCTTCGTTTCCTGA Chr17:13109410..13109429 60.13 45
upstream ENSMUSE00000555828 Chr17:13110664..13110749 GCCAGTTGGCTTGGATAAAA Chr17:13110710..13110729 60.07 45
upstream ENSMUSE00000555827 Chr17:13110909..13111037 GCAGCCAAAGTTCTGTGTGA Chr17:13110969..13110988 60.03 50

*** Putative Vector Insertion (Chr 17: 13111038 - 13112216) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000555826 Chr17:13112217..13112314 CAGGCAAGACGATAGCCACT Chr17:13112314..13112333 60.42 55
downstream ENSMUSE00000555822 Chr17:13112681..13112791 No primer for this exon
downstream ENSMUSE00000555820 Chr17:13113142..13113323 ACCACACAATTGAGCGCATA Chr17:13113315..13113334 60.14 45
downstream ENSMUSE00000555817 Chr17:13113606..13113732 TGCAGGCTGAAGTCAAGACA Chr17:13113663..13113682 60.74 50
downstream ENSMUSE00000555815 Chr17:13114969..13115144 TGCAACATGCTTCAGGTCTC Chr17:13115134..13115153 59.99 50
downstream ENSMUSE00000555811 Chr17:13115475..13115598 AAATTGGCCAGCGTAGACAG Chr17:13115505..13115524 60.27 50
downstream ENSMUSE00000555808 Chr17:13116084..13116276 GGACAGGGCAGCTTCTACAG Chr17:13116249..13116268 60.01 60
downstream ENSMUSE00000555804 Chr17:13116396..13116559 TAGCAAGCTGTTCCCGAGAT Chr17:13116420..13116439 59.98 50
downstream ENSMUSE00000555801 Chr17:13117126..13117422 GCGAACTTCAGGCTCTTCAC Chr17:13117224..13117243 60.14 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGTGAGACGCTACCAGGAAA Chr17:13111038..13111058 60.26 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTGAGACGCTACCAGGAAA Chr17:13111038..13111058 60.26 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000068039