Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI36199
Trapped Gene
Pdzd3 (ENSMUSG00000032105)
Vector Insertion
Chr 9: 44056638 - 44057127
Public Clones IST14789A12 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 71% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000216581 (Chr9:44056930..44057126 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCATTGTCGTCGATCCTGAG Chr9:44056951..44056970 59.79 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000216581 (Chr9:44056930..44057126 -)
Downstram Exon
ENSMUSE00000216585 (Chr9:44056639..44056845 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCATTGTCGTCGATCCTGAG Chr9:44056951..44056970 59.79 50 TGTCTTCAACCGGAAGATCC Chr9:44056736..44056755 60.05 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000365748 Chr9:44059523..44059547 No primer for this exon
upstream ENSMUSE00000343067 Chr9:44059081..44059108 GGACACGGCCTTGTTAACTC Chr9:44059082..44059101 59.6 55
upstream ENSMUSE00000216579 Chr9:44058866..44058939 GGCATTGACAATCCTGTCCT Chr9:44058895..44058914 59.93 50
upstream ENSMUSE00000216578 Chr9:44058334..44058545 TGTCTGTTGAGCAAGGAGGA Chr9:44058497..44058516 59.54 50
upstream ENSMUSE00000216573 Chr9:44057926..44058115 CCGGTTGTGCCATGTAGTAA Chr9:44057962..44057981 59.46 50
upstream ENSMUSE00000216575 Chr9:44057694..44057830 GTCGAGGTCCTTTCTGGTTG Chr9:44057808..44057827 59.7 55
upstream ENSMUSE00000216577 Chr9:44057318..44057522 AAAGGACCTGAAGGCTTTGG Chr9:44057359..44057378 60.6 50
upstream ENSMUSE00000216581 Chr9:44056930..44057126 TCATTGTCGTCGATCCTGAG Chr9:44056951..44056970 59.79 50
upstream ENSMUSE00000216585 Chr9:44056639..44056845 GGATCTTCCGGTTGAAGACA Chr9:44056758..44056777 60.05 50

*** Putative Vector Insertion (Chr 9: 44056638 - 44057127) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000216576 Chr9:44056314..44056514 CCCACAGGATATCCGTTCAC Chr9:44056413..44056432 60.19 55
downstream ENSMUSE00000347034 Chr9:44055401..44056099 CCACAGCGTCATCTTCTTGA Chr9:44055730..44055749 59.98 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTCAGGGGAGAGCAGTGAAG Chr9:44057140..44057160 59.99 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTCAGGGGAGAGCAGTGAAG Chr9:44057140..44057160 59.99 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032105