Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26838
Trapped Gene
Prkar2a (ENSMUSG00000032601)
Vector Insertion
Chr 9: 108616640 - 108619193
Public Clones not available
Private Clones OST92226 (lexicon) OST45036 (lexicon)
Severity of mutation (?) Insertion after 24% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000239601 (Chr9:108616604..108616639 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000239601 (Chr9:108616604..108616639 +)
Downstram Exon
ENSMUSE00000239582 (Chr9:108619194..108619246 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon CCTTGGATCGTTATCCTCCTC Chr9:108619248..108619268 59.91 52.38

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
upstream ENSMUSE00000239601 Chr9:108616604..108616639 No primer for this exon

*** Putative Vector Insertion (Chr 9: 108616640 - 108619193) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TAATCGCCTTGCAGCACATC Chr9:108616691..108616711 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TATGCGTGACTGGGAAAACC Chr9:108616687..108616707 60.89 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032601