Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25907
Trapped Gene
Skp1a (ENSMUSG00000036309)
Vector Insertion
Chr 11: 52051836 - 52056088
Public Clones IST14171D7 (tigm)
Private Clones OST152564 (lexicon)
Severity of mutation (?) Insertion after 20% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000579923 (Chr11:52051753..52051835 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTATGGATCAGATGCTCTTGAA Chr11:52051762..52051784 59.72 39.13 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000579923 (Chr11:52051753..52051835 +)
Downstram Exon
ENSMUSE00000292750 (Chr11:52056089..52056162 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTATGGATCAGATGCTCTTGAA Chr11:52051762..52051784 59.72 39.13 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000678943 Chr11:52045539..52045620 TGGCCTTGTTCTCGATACTTC Chr11:52045542..52045562 59.33 47.62
upstream ENSMUSE00000678940 Chr11:52045691..52046114 TCTGGCGTCAATTAGCTCCT Chr11:52046060..52046079 59.98 50
upstream ENSMUSE00000292755 Chr11:52050339..52050435 No primer for this exon
upstream ENSMUSE00000710103 Chr11:52050339..52050435 No primer for this exon
upstream ENSMUSE00000579923 Chr11:52051753..52051835 TGTATGGATCAGATGCTCTTGAA Chr11:52051762..52051784 59.72 39.13

*** Putative Vector Insertion (Chr 11: 52051836 - 52056088) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000292750 Chr11:52056089..52056162 No primer for this exon
downstream ENSMUSE00000292744 Chr11:52057117..52057260 GGAGGGTCATCTTTGTGGTG Chr11:52057157..52057176 60.36 55
downstream ENSMUSE00000292739 Chr11:52058483..52058623 CATATTGGCCACAGTCTTGC Chr11:52058548..52058567 59.15 50
downstream ENSMUSE00000653682 Chr11:52059487..52060360 GTTTCTCCACCTGGGAACAA Chr11:52060225..52060244 59.94 50
downstream ENSMUSE00000706076 Chr11:52059487..52059748 TGAAGACAAGGCGATGTTTG Chr11:52059638..52059657 59.84 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTTAAAGGTAATCGCCTTGC Chr11:52054878..52054899 60.23 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAGCTTAAAGGCGTGACTGG Chr11:52054876..52054896 58.2 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036309