Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9940
Trapped Gene
Rhpn2 (ENSMUSG00000030494)
Vector Insertion
Chr 7: 36166551 - 36168987
Public Clones XD013 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 69% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000199768 (Chr7:36166356..36166550 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGATTGACGCTCCAGATGTC Chr7:36166527..36166546 59.79 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000199768 (Chr7:36166356..36166550 +)
Downstram Exon
ENSMUSE00000297055 (Chr7:36168988..36169064 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGATTGACGCTCCAGATGTC Chr7:36166527..36166546 59.79 50 GGAAAAGTCGGGGAAGGTTA Chr7:36169034..36169053 60.29 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000596560 Chr7:36119333..36119430 ATGACCGATACGCTGCTACC Chr7:36119362..36119381 60.12 55
upstream ENSMUSE00000596559 Chr7:36119343..36119430 ATGACCGATACGCTGCTACC Chr7:36119362..36119381 60.12 55
upstream ENSMUSE00000518772 Chr7:36138751..36138866 TTGTAATCCCCTTGCACAAA Chr7:36138753..36138772 59.01 40
upstream ENSMUSE00000514886 Chr7:36145999..36146127 CTCAACATCTCCGTGGGAGT Chr7:36146093..36146112 60.11 55
upstream ENSMUSE00000516669 Chr7:36148636..36148711 AAGCGTTCACCATTCCTCTG Chr7:36148638..36148657 60.26 50
upstream ENSMUSE00000199777 Chr7:36155728..36155805 TGAGGATGACATTGCAGACC Chr7:36155769..36155788 59.64 50
upstream ENSMUSE00000199767 Chr7:36156134..36156258 CACATGGGGCTCCTGTTTAC Chr7:36156236..36156255 60.38 55
upstream ENSMUSE00000297094 Chr7:36157324..36157490 GCTTAGAGAGCGCTGTGGAT Chr7:36157452..36157471 59.75 55
upstream ENSMUSE00000297087 Chr7:36161179..36161366 AACGAGTTCTTCGTGCTGGT Chr7:36161322..36161341 59.91 50
upstream ENSMUSE00000297078 Chr7:36161993..36162149 ATGAGCCAGGAACCAGTGAA Chr7:36162026..36162045 60.66 50
upstream ENSMUSE00000199769 Chr7:36164584..36164703 AGACGAGGACCACCAAGAGA Chr7:36164597..36164616 59.83 55
upstream ENSMUSE00000199768 Chr7:36166356..36166550 TGATTGACGCTCCAGATGTC Chr7:36166527..36166546 59.79 50

*** Putative Vector Insertion (Chr 7: 36166551 - 36168987) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000297055 Chr7:36168988..36169064 GGAAAAGTCGGGGAAGGTTA Chr7:36169034..36169053 60.29 50
downstream ENSMUSE00000297049 Chr7:36169657..36169803 GGTGTTCCCTCGTAAGGTGA Chr7:36169764..36169783 59.97 55
downstream ENSMUSE00000199773 Chr7:36170346..36170501 GAGGCTCACGACCTTCATCT Chr7:36170483..36170502 59.41 55
downstream ENSMUSE00000442866 Chr7:36175774..36177304 GGTCACCAGGGCAACTTCTA Chr7:36176338..36176357 60.11 55
downstream ENSMUSE00000533307 Chr7:36175774..36176329 AGAGTTGAGCAGGCTGAAGG Chr7:36176019..36176038 59.74 55
downstream ENSMUSE00000533306 Chr7:36176628..36177300 CAGCCTGTTTCGGTTTTGTT Chr7:36176708..36176727 60.15 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGATTGACGCTCCAGATGTC Chr7:36166528..36166548 59.79 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGATTGACGCTCCAGATGTC Chr7:36166528..36166548 59.79 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030494