Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2396
Trapped Gene
Dnaja2 (ENSMUSG00000031701)
Vector Insertion
Chr 8: 88064352 - 88070411
Public Clones AD0583 (sanger) AD0051 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 63% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000212040 (Chr8:88070412..88070608 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGGCATGAAACATGGACAGA Chr8:88070498..88070517 59.09 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000212040 (Chr8:88070412..88070608 -)
Downstram Exon
ENSMUSE00000212039 (Chr8:88064207..88064351 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGGCATGAAACATGGACAGA Chr8:88070498..88070517 59.09 45 CACCACAATCTGACGAGCAT Chr8:88064216..88064235 59.71 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000400893 Chr8:88079069..88079237 CGAAGCTGTACGACATCCTG Chr8:88079108..88079127 59.47 55
upstream ENSMUSE00000212042 Chr8:88077816..88077875 GCCAAAGAATACCACCCTGA Chr8:88077841..88077860 59.93 50
upstream ENSMUSE00000212047 Chr8:88077086..88077309 GGCTTTATGGGCAATCAGAG Chr8:88077137..88077156 59.67 50
upstream ENSMUSE00000212044 Chr8:88072781..88072861 No primer for this exon
upstream ENSMUSE00000212041 Chr8:88072463..88072596 TGTGCTCCGACTGTAATGGA Chr8:88072467..88072486 60.26 50
upstream ENSMUSE00000212040 Chr8:88070412..88070608 AGGCATGAAACATGGACAGA Chr8:88070498..88070517 59.09 45

*** Putative Vector Insertion (Chr 8: 88064352 - 88070411) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000212039 Chr8:88064207..88064351 CACCACAATCTGACGAGCAT Chr8:88064216..88064235 59.71 50
downstream ENSMUSE00000212046 Chr8:88063949..88064076 TCACCTCGAACAACACGAAC Chr8:88064030..88064049 59.73 50
downstream ENSMUSE00000212043 Chr8:88062531..88063306 CAAACCCATTGTGTGCAAAG Chr8:88062629..88062648 60 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCTCAGCAGGGTAATGTGT Chr8:88067390..88067410 59.32 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGCTCAGCAGGGTAATGTGT Chr8:88067390..88067410 59.32 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000031701