Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI420
Trapped Gene
Nptn (ENSMUSG00000032336)
Vector Insertion
Chr 9: 58491610 - 58492267
Public Clones BC0563 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 84% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000511494 (Chr9:58491336..58491609 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCTCTGGTCGCTTCTTCATC Chr9:58491349..58491368 60.1 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000511494 (Chr9:58491336..58491609 +)
Downstram Exon
ENSMUSE00000698207 (Chr9:58492268..58492277 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCTCTGGTCGCTTCTTCATC Chr9:58491349..58491368 60.1 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000507475 Chr9:58430197..58430333 TCTCGCTCTTGCTGGTCTCT Chr9:58430277..58430296 60.43 55
upstream ENSMUSE00000707048 Chr9:58430214..58430333 TCTCGCTCTTGCTGGTCTCT Chr9:58430277..58430296 60.43 55
upstream ENSMUSE00000584306 Chr9:58466470..58466817 AGAATAACCCGGCTCACCTT Chr9:58466682..58466701 59.96 50
upstream ENSMUSE00000253189 Chr9:58471494..58471662 AACTCACTGCCACCCGTAAG Chr9:58471620..58471639 60.17 55
upstream ENSMUSE00000253174 Chr9:58475641..58475735 GAGGATTCAGGCGAATACCA Chr9:58475660..58475679 60.04 50
upstream ENSMUSE00000698206 Chr9:58477038..58477062 No primer for this exon
upstream ENSMUSE00000472506 Chr9:58488476..58488609 ATATGGCGCAAGAAGGAGAA Chr9:58488577..58488596 59.81 45
upstream ENSMUSE00000511494 Chr9:58491336..58491609 GCTCTGGTCGCTTCTTCATC Chr9:58491349..58491368 60.1 55

*** Putative Vector Insertion (Chr 9: 58491610 - 58492267) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000698207 Chr9:58492268..58492277 No primer for this exon
downstream ENSMUSE00000512433 Chr9:58498304..58498325 No primer for this exon
downstream ENSMUSE00000513121 Chr9:58499065..58499139 TTTCTCTGGCGCAAGTTTTT Chr9:58499118..58499137 60 40
downstream ENSMUSE00000709977 Chr9:58499065..58499125 TTTCTCTGGCGCAAGTTTTT Chr9:58499118..58499137 60 40
downstream ENSMUSE00000714674 Chr9:58499065..58499125 TTTCTCTGGCGCAAGTTTTT Chr9:58499118..58499137 60 40
downstream ENSMUSE00000506268 Chr9:58499666..58500685 GTACCGCATGAGAACCCAGT Chr9:58500583..58500602 60 55
downstream ENSMUSE00000707045 Chr9:58499666..58500676 GTACCGCATGAGAACCCAGT Chr9:58500583..58500602 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCAGATGAGGTTCCTGATGG Chr9:58491592..58491612 60.47 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032336