Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26226
Trapped Gene
Prkar2a (ENSMUSG00000032601)
Vector Insertion
Chr 9: 108595517 - 108616603
Public Clones IST13963A3 (tigm) IST11540C6 (tigm) IST13478G7 (tigm) IST13608D10 (tigm)
IST12879C3 (tigm) IST11593G4 (tigm) IST14656G8 (tigm) IST14892G12 (tigm)
IST14954A5 (tigm) IST12604C7 (tigm) IST11796A11 (tigm)
Private Clones OST129758 (lexicon)
Severity of mutation (?) Insertion after 21% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000404418 (Chr9:108595368..108595516 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCTTTCCGAAGACAAGAGCA Chr9:108595384..108595403 60.66 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000404418 (Chr9:108595368..108595516 +)
Downstram Exon
ENSMUSE00000239601 (Chr9:108616604..108616639 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCTTTCCGAAGACAAGAGCA Chr9:108595384..108595403 60.66 50 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000634246 Chr9:108594474..108595043 AGTGACTCGGACTCGGAAGA Chr9:108595010..108595029 59.99 55
upstream ENSMUSE00000404418 Chr9:108595368..108595516 GCTTTCCGAAGACAAGAGCA Chr9:108595384..108595403 60.66 50

*** Putative Vector Insertion (Chr 9: 108595517 - 108616603) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000239601 Chr9:108616604..108616639 No primer for this exon
downstream ENSMUSE00000239582 Chr9:108619194..108619246 CCTTGGATCGTTATCCTCCTC Chr9:108619248..108619268 59.91 52.38
downstream ENSMUSE00000439254 Chr9:108621534..108621617 TGCTCATCAGTTTTGGGATG Chr9:108621562..108621581 59.65 45
downstream ENSMUSE00000634245 Chr9:108630505..108630611 TAAAAGTTGTCCCCGTCGTC Chr9:108630602..108630621 59.97 50
downstream ENSMUSE00000239556 Chr9:108635441..108635594 CTGCCACGGTTGTCATACTG Chr9:108635515..108635534 60.17 55
downstream ENSMUSE00000221338 Chr9:108642766..108642867 No primer for this exon
downstream ENSMUSE00000221337 Chr9:108643019..108643093 AGATCTTTTCCCCGATCACA Chr9:108643067..108643086 59.48 45
downstream ENSMUSE00000221339 Chr9:108646561..108646626 TAGAAGCTGTCGGCCTTTTC Chr9:108646586..108646605 59.59 50
downstream ENSMUSE00000221335 Chr9:108647813..108647954 CTTATGGCAATGGGCAATCT Chr9:108647872..108647891 59.92 45
downstream ENSMUSE00000495082 Chr9:108649192..108651843 AGGTCTGGGGTTGGACTTCT Chr9:108651015..108651034 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCCTTCTTGTTTGCTTTGC Chr9:108610542..108610562 61.44 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGCCTTCTTGTTTGCTTTGC Chr9:108610542..108610562 61.44 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032601