Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI17865
Trapped Gene
Papd4 (ENSMUSG00000042167)
Vector Insertion
Chr 13: 93955853 - 93956257
Public Clones not available
Private Clones OST434672 (lexicon)
Severity of mutation (?) Insertion after 9% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000303890 (Chr13:93956258..93956431 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTCAATTTTGGGTCGTCCAC Chr13:93956364..93956383 60.35 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000303890 (Chr13:93956258..93956431 -)
Downstram Exon
ENSMUSE00000303881 (Chr13:93955763..93955852 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTCAATTTTGGGTCGTCCAC Chr13:93956364..93956383 60.35 50 TTCCATATGTCAGGGGCTGT Chr13:93955790..93955809 60.34 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000303901 Chr13:93962049..93962238 GCCTTAGGCTCGTGACTCTC Chr13:93962195..93962214 59.19 60
upstream ENSMUSE00000303890 Chr13:93956258..93956431 CTCAATTTTGGGTCGTCCAC Chr13:93956364..93956383 60.35 50

*** Putative Vector Insertion (Chr 13: 93955853 - 93956257) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000303881 Chr13:93955763..93955852 TTCCATATGTCAGGGGCTGT Chr13:93955790..93955809 60.34 50
downstream ENSMUSE00000303868 Chr13:93954034..93954271 GCCGTTTACCATCAAGAGGA Chr13:93954206..93954225 60.07 50
downstream ENSMUSE00000303857 Chr13:93945653..93945767 TTGCTTGCTGCTGACAAGTT Chr13:93945697..93945716 59.79 45
downstream ENSMUSE00000303849 Chr13:93945474..93945565 AAGCATAAATCGCCATCACTG Chr13:93945471..93945491 60.11 42.86
downstream ENSMUSE00000303838 Chr13:93944595..93944673 No primer for this exon
downstream ENSMUSE00000303822 Chr13:93941778..93941847 ATTGGCACTTTTGCTCGAAT Chr13:93941780..93941799 59.71 40
downstream ENSMUSE00000303809 Chr13:93938346..93938422 No primer for this exon
downstream ENSMUSE00000303799 Chr13:93937881..93938009 TCACCAGCACTAATGGACGA Chr13:93937955..93937974 60.26 50
downstream ENSMUSE00000303786 Chr13:93929600..93929643 AAGGATGGGTTCAGGTAGGG Chr13:93929602..93929621 60.18 55
downstream ENSMUSE00000303776 Chr13:93924880..93925016 GCATGATGAACAAGGTGCAG Chr13:93924951..93924970 60.27 50
downstream ENSMUSE00000303769 Chr13:93920639..93920730 TGGCTTCACGAACTGAAATC Chr13:93920674..93920693 58.85 45
downstream ENSMUSE00000303759 Chr13:93918836..93918915 CTGCTTCTCATGCACAGCTC Chr13:93918847..93918866 59.89 55
downstream ENSMUSE00000344724 Chr13:93917355..93917620 AAGGCAGCACACTGTTCAGA Chr13:93917550..93917569 59.62 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTTTGATAATCGCCTTGCAG Chr13:93956192..93956212 58.53 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTCTTTGACGTGACTGGGAAA Chr13:93956193..93956214 60.28 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042167