Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2138
Trapped Gene
Pkn2 (ENSMUSG00000004591)
Vector Insertion
Chr 3: 142493579 - 142502171
Public Clones AB0293 (sanger) XT0507 (sanger) AD0653 (sanger) XP0145 (sanger)
AB0292 (sanger) AD0652 (sanger) XA059 (baygenomics) XB006BC (baygenomics)
Private Clones OST95936 (lexicon) OST41490 (lexicon)
Severity of mutation (?) Insertion after 16% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000586388 (Chr3:142502172..142502326 -)
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
ENSMUSE00000586388 (Chr3:142502172..142502326 -)
Downstram Exon
ENSMUSE00000586387 (Chr3:142493461..142493578 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000669079 Chr3:142516843..142516848 No primer for this exon
upstream ENSMUSE00000669063 Chr3:142516628..142516678 No primer for this exon
upstream ENSMUSE00000586376 Chr3:142516378..142516597 No primer for this exon
upstream ENSMUSE00000586389 Chr3:142516378..142516678 No primer for this exon
upstream ENSMUSE00000586388 Chr3:142502172..142502326 No primer for this exon

*** Putative Vector Insertion (Chr 3: 142493579 - 142502171) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000586387 Chr3:142493461..142493578 No primer for this exon
downstream ENSMUSE00000586386 Chr3:142492148..142492293 No primer for this exon
downstream ENSMUSE00000586385 Chr3:142491845..142492058 No primer for this exon
downstream ENSMUSE00000586384 Chr3:142484483..142484668 No primer for this exon
downstream ENSMUSE00000586383 Chr3:142483501..142483610 No primer for this exon
downstream ENSMUSE00000586382 Chr3:142474878..142475021 No primer for this exon
downstream ENSMUSE00000586381 Chr3:142474491..142474566 No primer for this exon
downstream ENSMUSE00000586380 Chr3:142473655..142473829 No primer for this exon
downstream ENSMUSE00000586366 Chr3:142473325..142473451 No primer for this exon
downstream ENSMUSE00000586365 Chr3:142472788..142472918 No primer for this exon
downstream ENSMUSE00000586378 Chr3:142472606..142472681 No primer for this exon
downstream ENSMUSE00000586377 Chr3:142472437..142472528 No primer for this exon
downstream ENSMUSE00000271205 Chr3:142466518..142466694 No primer for this exon
downstream ENSMUSE00000177758 Chr3:142464004..142464066 No primer for this exon
downstream ENSMUSE00000177756 Chr3:142462769..142462845 No primer for this exon
downstream ENSMUSE00000177755 Chr3:142461867..142462009 No primer for this exon
downstream ENSMUSE00000177759 Chr3:142457352..142457459 No primer for this exon
downstream ENSMUSE00000177760 Chr3:142457067..142457147 No primer for this exon
downstream ENSMUSE00000561979 Chr3:142456266..142456978 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATAATCGCCTTGCAGCACAT Chr3:142502101..142502121 60.64 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TATCTGGACGGGGAAGAACA Chr3:142502135..142502155 60.45 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000004591