Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14767
Trapped Gene
Pxn (ENSMUSG00000029528)
Vector Insertion
Chr 5: 116002031 - 116002112
Public Clones PST15516-NL (escells)
Private Clones not available
Severity of mutation (?) Insertion after 60% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000189826 (Chr5:116001860..116002030 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTCTGCAGTCCGACCTGAAC Chr5:116001945..116001964 60.87 60 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000189826 (Chr5:116001860..116002030 +)
Downstram Exon
ENSMUSE00000189816 (Chr5:116002113..116002286 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTCTGCAGTCCGACCTGAAC Chr5:116001945..116001964 60.87 60 GATGGGTCCGTTGCAGTAGT Chr5:116002283..116002302 60 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000650726 Chr5:115956721..115956877 No primer for this exon
upstream ENSMUSE00000690307 Chr5:115956817..115956877 No primer for this exon
upstream ENSMUSE00000690306 Chr5:115993084..115993096 No primer for this exon
upstream ENSMUSE00000650725 Chr5:115994352..115994578 AAACGGCCAGTGTTCTTGTC Chr5:115994396..115994415 60.16 50
upstream ENSMUSE00000267355 Chr5:115994890..115995005 GCGAGGAAGAGCACGTCTAC Chr5:115994984..115995003 60.16 60
upstream ENSMUSE00000267348 Chr5:115995381..115995517 ACTTGACCGGCTGTTACTGG Chr5:115995456..115995475 60.17 55
upstream ENSMUSE00000267342 Chr5:115995613..115995814 AGAGAAGCCAAAGCGAAATG Chr5:115995716..115995735 59.59 45
upstream ENSMUSE00000189819 Chr5:115996822..115996957 TGGCGTCACTGTCAGATTTC Chr5:115996935..115996954 59.84 50
upstream ENSMUSE00000650711 Chr5:116001497..116001598 GCCTGGAACAGAGAGTGGAT Chr5:116001504..116001523 59.26 55
upstream ENSMUSE00000189826 Chr5:116001860..116002030 GTCTGCAGTCCGACCTGAAC Chr5:116001945..116001964 60.87 60

*** Putative Vector Insertion (Chr 5: 116002031 - 116002112) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000189816 Chr5:116002113..116002286 GATGGGTCCGTTGCAGTAGT Chr5:116002283..116002302 60 55
downstream ENSMUSE00000189810 Chr5:116002773..116002854 GGGCACAGAAGAAGTGTTCC Chr5:116002830..116002849 59.7 55
downstream ENSMUSE00000189813 Chr5:116002987..116003135 GGTGTTGAGGGCTGAAATGT Chr5:116003108..116003127 59.97 50
downstream ENSMUSE00000480796 Chr5:116003878..116005988 AGATACCCCGACCTCGTCTT Chr5:116005867..116005886 59.96 55
downstream ENSMUSE00000650708 Chr5:116003878..116004987 GTGAGGTGCTGGCTCTTAGG Chr5:116004429..116004448 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GACCTCTAATCGCCTTGCAG Chr5:116002076..116002096 59.98 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACCTCCGTGACTGGGAAAAC Chr5:116002077..116002097 61.32 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029528