Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20976
Trapped Gene
Pkig (ENSMUSG00000035268)
Vector Insertion
Chr 2: 163529292 - 163546863
Public Clones IST10455E8 (tigm)
Private Clones OST346905 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000328300 (Chr2:163529222..163529291 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAGGCAGGAAAACGGAATTA Chr2:163529266..163529285 60.07 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000328300 (Chr2:163529222..163529291 +)
Downstram Exon
ENSMUSE00000328292 (Chr2:163546864..163547037 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAGGCAGGAAAACGGAATTA Chr2:163529266..163529285 60.07 45 TCCGAGTAGGAGGACTCGAC Chr2:163546918..163546937 59.4 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000427413 Chr2:163484135..163484228 No primer for this exon
upstream ENSMUSE00000639334 Chr2:163484187..163484228 No primer for this exon
upstream ENSMUSE00000639333 Chr2:163484886..163484971 AATGCAGTGGAGGCTGTTGT Chr2:163484893..163484912 60.72 50
upstream ENSMUSE00000680142 Chr2:163519773..163519892 No primer for this exon
upstream ENSMUSE00000328300 Chr2:163529222..163529291 CAGGCAGGAAAACGGAATTA Chr2:163529266..163529285 60.07 45

*** Putative Vector Insertion (Chr 2: 163529292 - 163546863) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000328292 Chr2:163546864..163547037 TCCGAGTAGGAGGACTCGAC Chr2:163546918..163546937 59.4 60
downstream ENSMUSE00000427401 Chr2:163551193..163551886 CACAGGCAGACTCAGGATGA Chr2:163551286..163551305 59.98 55
downstream ENSMUSE00000639332 Chr2:163551193..163551894 CACAGGCAGACTCAGGATGA Chr2:163551286..163551305 59.98 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACTCCCCAGAGCTGTGTTTG Chr2:163544320..163544340 60.3 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGGCAGGAAAACGGAATTA Chr2:163538267..163538287 60.07 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000035268