Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1282
Trapped Gene
Pdlim5 (ENSMUSG00000028273)
Vector Insertion
Chr 3: 141922257 - 141940780
Public Clones DD0421 (sanger) CSH674 (baygenomics) XH199 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 62% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000177777 (Chr3:141940781..141940965 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACCAGCGTCAAGTCACCTA Chr3:141940805..141940824 59.9 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000177777 (Chr3:141940781..141940965 -)
Downstram Exon
ENSMUSE00000177772 (Chr3:141922094..141922256 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACCAGCGTCAAGTCACCTA Chr3:141940805..141940824 59.9 55 GTTCCGCTCTCTGCACAAGT Chr3:141922127..141922146 60.6 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000562179 Chr3:142058550..142058599 No primer for this exon
upstream ENSMUSE00000586463 Chr3:142058550..142058582 No primer for this exon
upstream ENSMUSE00000562206 Chr3:142054677..142054814 AAGGTGGCAAGGATTTCAAC Chr3:142054698..142054717 59.03 45
upstream ENSMUSE00000669150 Chr3:142054677..142054815 AAGGTGGCAAGGATTTCAAC Chr3:142054698..142054717 59.03 45
upstream ENSMUSE00000332994 Chr3:142015698..142015849 AATAGGGGACGTGGTTCTCA Chr3:142015792..142015811 59.4 50
upstream ENSMUSE00000444521 Chr3:141977370..141977412 CTTCAGCTGCAGCCAAGAGT Chr3:141977391..141977410 60.88 55
upstream ENSMUSE00000562169 Chr3:141975087..141975178 GTGTGTTCCGAGTCTGCTCA Chr3:141975144..141975163 60.03 55
upstream ENSMUSE00000562201 Chr3:141975087..141975505 GTGTGTTCCGAGTCTGCTCA Chr3:141975144..141975163 60.03 55
upstream ENSMUSE00000669146 Chr3:141972492..141972508 No primer for this exon
upstream ENSMUSE00000669149 Chr3:141969248..141969262 No primer for this exon
upstream ENSMUSE00000669148 Chr3:141967669..141967686 No primer for this exon
upstream ENSMUSE00000414343 Chr3:141967261..141967433 AAACGGCTGATTGAGGACAC Chr3:141967341..141967360 60.12 50
upstream ENSMUSE00000413260 Chr3:141966907..141966943 No primer for this exon
upstream ENSMUSE00000669145 Chr3:141966292..141966385 TACGTGACTGGCACCATGAA Chr3:141966322..141966341 61.15 50
upstream ENSMUSE00000503680 Chr3:141966185..141966385 CCCACCTAAGCAGCTAGCAC Chr3:141966256..141966275 60.04 60
upstream ENSMUSE00000562178 Chr3:141966023..141966385 GAAATGACCTGACCCCTTCA Chr3:141966058..141966077 59.9 50
upstream ENSMUSE00000177777 Chr3:141940781..141940965 CACCAGCGTCAAGTCACCTA Chr3:141940805..141940824 59.9 55

*** Putative Vector Insertion (Chr 3: 141922257 - 141940780) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000177772 Chr3:141922094..141922256 GTTCCGCTCTCTGCACAAGT Chr3:141922127..141922146 60.6 55
downstream ENSMUSE00000177783 Chr3:141912294..141912474 GCCATTGTGTTTTTGCAATG Chr3:141912375..141912394 59.98 40
downstream ENSMUSE00000272616 Chr3:141910259..141910379 AACAGGACACATGCCAGGTC Chr3:141910315..141910334 61 55
downstream ENSMUSE00000177778 Chr3:141907860..141907975 TTGTTCCAAAAAGGGCGTAG Chr3:141907930..141907949 60.1 45
downstream ENSMUSE00000635583 Chr3:141904328..141905733 CGAAACGCCATCATTTCTTT Chr3:141904351..141904370 60.07 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATAATCGCCTTGCAGCAC Chr3:141937712..141937732 58.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGCTACGTGACTGGGAAAAC Chr3:141937714..141937734 60.69 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028273