Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2170
Trapped Gene
Tsc22d1 (ENSMUSG00000022010)
Vector Insertion
Chr 14: 76905105 - 76906223
Public Clones XT0138 (sanger) RRJ565 (baygenomics) CMHD-GT_163B12-3 (cmhd)
Private Clones OST18579 (lexicon) OST8557 (lexicon)
Severity of mutation (?) Insertion after 41% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000122900 (Chr14:76905056..76905104 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCTGGTGCAAGTGTGGTAGC Chr14:76905057..76905076 59.9 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000122900 (Chr14:76905056..76905104 +)
Downstram Exon
ENSMUSE00000685771 (Chr14:76906224..76906977 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCTGGTGCAAGTGTGGTAGC Chr14:76905057..76905076 59.9 55 TACTGGGGAGAAAGCGAGAA Chr14:76906643..76906662 59.95 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000685776 Chr14:76814768..76815524 No primer for this exon
upstream ENSMUSE00000555055 Chr14:76815499..76815524 No primer for this exon
upstream ENSMUSE00000403113 Chr14:76815628..76818816 CTGTGGGAGTGGTTTCCAGT Chr14:76817055..76817074 60 55
upstream ENSMUSE00000555054 Chr14:76815724..76816796 ACTAGCGTTACTCCGGCTCA Chr14:76816229..76816248 60.04 55
upstream ENSMUSE00000685775 Chr14:76815724..76816796 ACTAGCGTTACTCCGGCTCA Chr14:76816229..76816248 60.04 55
upstream ENSMUSE00000706438 Chr14:76815953..76818816 CTGTGGGAGTGGTTTCCAGT Chr14:76817055..76817074 60 55
upstream ENSMUSE00000555053 Chr14:76817043..76818816 CTGTGGGAGTGGTTTCCAGT Chr14:76817055..76817074 60 55
upstream ENSMUSE00000685772 Chr14:76888243..76888482 GGTCAGGTTCGAGCATCTGT Chr14:76888293..76888312 60.27 55
upstream ENSMUSE00000685770 Chr14:76903636..76903653 No primer for this exon
upstream ENSMUSE00000122901 Chr14:76904321..76904648 GTAGACCAGTGGCGATGGAT Chr14:76904540..76904559 59.96 55
upstream ENSMUSE00000122900 Chr14:76905056..76905104 TCTGGTGCAAGTGTGGTAGC Chr14:76905057..76905076 59.9 55
upstream ENSMUSE00000647340 Chr14:76905056..76905104 TCTGGTGCAAGTGTGGTAGC Chr14:76905057..76905076 59.9 55

*** Putative Vector Insertion (Chr 14: 76905105 - 76906223) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000685769 Chr14:76906224..76907569 TCGCAAGACTTCAGCAGCTA Chr14:76907377..76907396 60.03 50
downstream ENSMUSE00000685771 Chr14:76906224..76906977 TACTGGGGAGAAAGCGAGAA Chr14:76906643..76906662 59.95 50
downstream ENSMUSE00000685774 Chr14:76906224..76907569 TCGCAAGACTTCAGCAGCTA Chr14:76907377..76907396 60.03 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCACAAAATAATCGCCTTG Chr14:76905147..76905167 59.7 40 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAAAACGTGACTGGGAAAAC Chr14:76905151..76905171 58.1 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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