Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8604
Trapped Gene
Pcnp (ENSMUSG00000071533)
Vector Insertion
Chr 16: 56024782 - 56029715
Public Clones (sanger) XG526 (baygenomics) P030B10 (ggtc) D001B10 (ggtc) Q023C05 (ggtc)
W223B03 (ggtc) PST4393-NR (escells) PST12696-NL (escells) PST12013-NR (escells)
Private Clones not available
Severity of mutation (?) Insertion after 15% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000717002 (Chr16:56029716..56029809 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGGAGAGGAGAAGCCAGAGA Chr16:56029743..56029762 61.01 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000717002 (Chr16:56029716..56029809 -)
Downstram Exon
ENSMUSE00000699358 (Chr16:56024647..56024781 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGGAGAGGAGAAGCCAGAGA Chr16:56029743..56029762 61.01 60 GCTGTCACCTACTGACCCAAC Chr16:56024632..56024652 59.64 57.14

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000655002 Chr16:56029716..56029830 GGGAGAGGAGAAGCCAGAGA Chr16:56029743..56029762 61.01 60
upstream ENSMUSE00000717002 Chr16:56029716..56029809 GGGAGAGGAGAAGCCAGAGA Chr16:56029743..56029762 61.01 60

*** Putative Vector Insertion (Chr 16: 56024782 - 56029715) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000699358 Chr16:56024647..56024781 GCTGTCACCTACTGACCCAAC Chr16:56024632..56024652 59.64 57.14
downstream ENSMUSE00000618093 Chr16:56024337..56024551 AGGTCTGCAGCTTCGTCTTC Chr16:56024412..56024431 59.75 55
downstream ENSMUSE00000720388 Chr16:56024337..56024741 GGAGCAGCAACCTCAAAAAG Chr16:56024586..56024605 59.99 50
downstream ENSMUSE00000618092 Chr16:56022168..56022242 GCTGCTGCTACCGACAGAGT Chr16:56022165..56022184 60.76 60
downstream ENSMUSE00000618091 Chr16:56018585..56018640 TCTTTGCTTCTGGAGGCATT Chr16:56018585..56018604 59.96 45
downstream ENSMUSE00000718790 Chr16:56018233..56018640 TCTTTGCTTCTGGAGGCATT Chr16:56018585..56018604 59.96 45
downstream ENSMUSE00000699357 Chr16:56017304..56017430 GTCTTGGTCGTGGACGTTTC Chr16:56017288..56017307 60.56 55
downstream ENSMUSE00000699366 Chr16:56015621..56017430 CTAGAATGGCCCGAAACAAA Chr16:56016719..56016738 60.07 45
downstream ENSMUSE00000717074 Chr16:56007358..56007595 GCAGAGTGAGTGCTGCTGTC Chr16:56007408..56007427 59.93 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGGAGAGGAGAAGCCAGAGA Chr16:56026741..56026761 61.01 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGAGAGGAGAAGCCAGAGAAG Chr16:56026739..56026760 59.71 57.14 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TAATCGCCTTGCAGCACATC Chr16:56026739..56026759 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GCCACCTTGAACCTGCTTATAC Chr16:56026785..56026807 60.03 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000071533