Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10322
Trapped Gene
Nptn (ENSMUSG00000032336)
Vector Insertion
Chr 9: 58471663 - 58475640
Public Clones LST018 (baygenomics)
Private Clones OST323632 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000253189 (Chr9:58471494..58471662 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AACTCACTGCCACCCGTAAG Chr9:58471620..58471639 60.17 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000253189 (Chr9:58471494..58471662 +)
Downstram Exon
ENSMUSE00000253174 (Chr9:58475641..58475735 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AACTCACTGCCACCCGTAAG Chr9:58471620..58471639 60.17 55 TGGTATTCGCCTGAATCCTC Chr9:58475682..58475701 60.04 50

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

*** Putative Vector Insertion (Chr 9: 58471663 - 58475640) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000253174 Chr9:58475641..58475735 TGGTATTCGCCTGAATCCTC Chr9:58475682..58475701 60.04 50
downstream ENSMUSE00000698206 Chr9:58477038..58477062 TGGGAAGGTCCACTACTGACA Chr9:58477061..58477081 60.55 52.38
downstream ENSMUSE00000472506 Chr9:58488476..58488609 CTTCTTGCGCCATATCCACT Chr9:58488594..58488613 60.24 50
downstream ENSMUSE00000511494 Chr9:58491336..58491609 GATGAAGAAGCGACCAGAGC Chr9:58491371..58491390 60.1 55
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 AAGGTGGTATAATCGCCTTGC Chr9:58474705..58474726 60.35 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCAAGGTGGTACGTGACTGG Chr9:58471703..58471723 59.59 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032336