Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI17682
Trapped Gene
Pdcd10 (ENSMUSG00000027835)
Vector Insertion
Chr 3: 75337517 - 75345081
Public Clones not available
Private Clones OST438239 (lexicon)
Severity of mutation (?) Insertion after 15% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000389259 (Chr3:75345082..75345300 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGAAGAAATTCGGCAGTGAA Chr3:75345231..75345250 60.19 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000389259 (Chr3:75345082..75345300 -)
Downstram Exon
ENSMUSE00000173435 (Chr3:75337463..75337516 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGAAGAAATTCGGCAGTGAA Chr3:75345231..75345250 60.19 45 GAGCTGCAGACAAATTTACTCG Chr3:75337467..75337488 59.18 45.46

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000361341 Chr3:75360644..75360707 GAATTGATCCGGGAGTTGAA Chr3:75360688..75360707 59.87 45
upstream ENSMUSE00000389259 Chr3:75345082..75345300 GGAAGAAATTCGGCAGTGAA Chr3:75345231..75345250 60.19 45

*** Putative Vector Insertion (Chr 3: 75337517 - 75345081) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000173435 Chr3:75337463..75337516 GAGCTGCAGACAAATTTACTCG Chr3:75337467..75337488 59.18 45.46
downstream ENSMUSE00000173437 Chr3:75332732..75332849 AGGAGGGACTCGGTGAAGTT Chr3:75332736..75332755 60.11 55
downstream ENSMUSE00000173433 Chr3:75331510..75331636 CCGTGCCTTTTCATTTAGGT Chr3:75331559..75331578 59.09 45
downstream ENSMUSE00000173436 Chr3:75324953..75325031 CCTGCGGTTCTGGTACTGAT Chr3:75324931..75324950 60.13 55
downstream ENSMUSE00000173434 Chr3:75324624..75324706 No primer for this exon
downstream ENSMUSE00000225572 Chr3:75321028..75321523 AATTAGCCGGTTGGCACTTA Chr3:75321465..75321484 59.61 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTCTAATCGCCTTGCAGCAC Chr3:75345013..75345033 61.44 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACTCTTCCGTGACTGGGAAA Chr3:75345017..75345037 59.7 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027835