Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9066
Trapped Gene
Skp1a (ENSMUSG00000036309)
Vector Insertion
Chr 11: 52058624 - 52059486
Public Clones XK187 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 93% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000292739 (Chr11:52058483..52058623 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCAAGACTGTGGCCAATATG Chr11:52058526..52058545 59.15 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000292739 (Chr11:52058483..52058623 +)
Downstram Exon
ENSMUSE00000706076 (Chr11:52059487..52059748 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCAAGACTGTGGCCAATATG Chr11:52058526..52058545 59.15 50 TGAAGACAAGGCGATGTTTG Chr11:52059638..52059657 59.84 45

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
upstream ENSMUSE00000292750 Chr11:52056089..52056162 TGGGAATGGATGATGAAGGA Chr11:52056092..52056111 61.22 45
upstream ENSMUSE00000292744 Chr11:52057117..52057260 TCCTGTTTGGGACCAAGAAT Chr11:52057200..52057219 59.38 45
upstream ENSMUSE00000292739 Chr11:52058483..52058623 GCAAGACTGTGGCCAATATG Chr11:52058526..52058545 59.15 50

*** Putative Vector Insertion (Chr 11: 52058624 - 52059486) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 ATAATCGCCTTGCAGCACAT Chr11:52058674..52058694 60.64 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAGAGGAAGAGGCCCAGGTA Chr11:52058608..52058628 60.2 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036309