Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20943
Trapped Gene
Ryk (ENSMUSG00000032547)
Vector Insertion
Chr 9: 102737570 - 102764203
Public Clones not available
Private Clones OST347742 (lexicon) OST347703 (lexicon)
Severity of mutation (?) Insertion after 10% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000321294 (Chr9:102737250..102737569 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCTACCTGAGCGAGGACGAG Chr9:102737534..102737553 60.69 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000321294 (Chr9:102737250..102737569 +)
Downstram Exon
ENSMUSE00000321268 (Chr9:102764204..102764325 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCTACCTGAGCGAGGACGAG Chr9:102737534..102737553 60.69 60 TGTCTCACTGGGCACTAGCA Chr9:102764292..102764311 60.62 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000321294 Chr9:102737250..102737569 TCTACCTGAGCGAGGACGAG Chr9:102737534..102737553 60.69 60

*** Putative Vector Insertion (Chr 9: 102737570 - 102764203) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000321268 Chr9:102764204..102764325 TGTCTCACTGGGCACTAGCA Chr9:102764292..102764311 60.62 55
downstream ENSMUSE00000321249 Chr9:102769885..102769984 GATAAAGTGCGTGGGACCTC Chr9:102769985..102770004 59.56 55
downstream ENSMUSE00000220661 Chr9:102771604..102771738 CTTTGCCGGTACAAGAAAGC Chr9:102771639..102771658 59.88 50
downstream ENSMUSE00000220653 Chr9:102774058..102774111 GTGTTTTTGTCCAAGGCTGAA Chr9:102774099..102774119 60.14 42.86
downstream ENSMUSE00000220651 Chr9:102778069..102778213 ATGAAGGTGCAAAACGGCTA Chr9:102778187..102778206 60.64 45
downstream ENSMUSE00000220647 Chr9:102783984..102784084 GTCTGGGTAGACGGCTGAGA Chr9:102784037..102784056 60.41 60
downstream ENSMUSE00000220656 Chr9:102788324..102788458 TGGCTTCCAGAAGAGTGACA Chr9:102788395..102788414 59.54 50
downstream ENSMUSE00000220655 Chr9:102790800..102790886 ATGGAAAATACGCCCAAAAG Chr9:102790825..102790844 58.94 40
downstream ENSMUSE00000220649 Chr9:102793546..102793615 GAGCATCATCGTCACCTGAA Chr9:102793583..102793602 59.79 50
downstream ENSMUSE00000220654 Chr9:102799532..102799664 TAATTTGCACTGCCGAAGAA Chr9:102799646..102799665 59.44 40
downstream ENSMUSE00000220652 Chr9:102800789..102800898 GACCAGATCTTGCTGGGAAA Chr9:102800815..102800834 60.19 50
downstream ENSMUSE00000220645 Chr9:102801021..102801180 CCTGTTCTCGTTGTCCCCTA Chr9:102801120..102801139 60.1 55
downstream ENSMUSE00000220657 Chr9:102808367..102808503 TGGGCTATTCGGTAACCATC Chr9:102808482..102808501 59.78 50
downstream ENSMUSE00000382229 Chr9:102809180..102810637 AAACAAGCGATTTTCCATGC Chr9:102809903..102809922 60.08 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTTGTTTCGCCTCAAGATGG Chr9:102752547..102752567 60.64 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGTCACTGCTGGCGATTTCT Chr9:102752583..102752603 60.02 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032547