Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29382
Trapped Gene
Ccnl2 (ENSMUSG00000029068)
Vector Insertion
Chr 4: 155192097 - 155192647
Public Clones Ayu18-71 (egtc)
Private Clones not available
Severity of mutation (?) Insertion after 42% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000185197 (Chr4:155192032..155192096 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACACCTGGTCCAGACTGCAT Chr4:155192076..155192095 60.6 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000185197 (Chr4:155192032..155192096 +)
Downstram Exon
ENSMUSE00000705418 (Chr4:155192648..155192669 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACACCTGGTCCAGACTGCAT Chr4:155192076..155192095 60.6 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000523689 Chr4:155186621..155186918 CTCATCACCTTGGAAAACTGC Chr4:155186766..155186786 59.73 47.62
upstream ENSMUSE00000185195 Chr4:155187277..155187351 CTACAGGGCAGGTGCTGTTC Chr4:155187287..155187306 60.85 60
upstream ENSMUSE00000185200 Chr4:155187568..155187677 AATGTATTCCATCGCCTTCG Chr4:155187640..155187659 59.92 45
upstream ENSMUSE00000185199 Chr4:155189352..155189472 CTCAAGGAGTTGGGCTTTTG Chr4:155189428..155189447 59.85 50
upstream ENSMUSE00000185197 Chr4:155192032..155192096 ACACCTGGTCCAGACTGCAT Chr4:155192076..155192095 60.6 55
upstream ENSMUSE00000185203 Chr4:155192032..155192067 No primer for this exon

*** Putative Vector Insertion (Chr 4: 155192097 - 155192647) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000705418 Chr4:155192648..155192669 No primer for this exon
downstream ENSMUSE00000185194 Chr4:155194438..155194537 ATCTGTGCGAAGGCTGTCAT Chr4:155194471..155194490 60.83 50
downstream ENSMUSE00000523690 Chr4:155194893..155194997 TGTGGACGATTGGGTAAAGG Chr4:155194918..155194937 60.74 50
downstream ENSMUSE00000185201 Chr4:155195082..155195223 CTCCAGATGCGTCAAATCAA Chr4:155195105..155195124 59.8 45
downstream ENSMUSE00000185193 Chr4:155195921..155196029 GGAAGGCTTGCCTCCTTTAC Chr4:155195958..155195977 60.21 55
downstream ENSMUSE00000185192 Chr4:155196114..155196206 CTGCTCACGACTCCTGCTTT Chr4:155196165..155196184 60.73 55
downstream ENSMUSE00000228484 Chr4:155197452..155198460 AGCCACCAGGGATCCTATCT Chr4:155197828..155197847 59.92 55
downstream ENSMUSE00000414644 Chr4:155197669..155197806 AGCGCTCACGTCTTTGATCT Chr4:155197738..155197757 60.16 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACACCTGGTCCAGACTGCAT Chr4:155192077..155192097 60.6 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACACCTGGTCCAGACTGCAT Chr4:155192077..155192097 60.6 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029068