Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9792
Trapped Gene
Cstf3 (ENSMUSG00000027176)
Vector Insertion
Chr 2: 104504515 - 104504873
Public Clones RRC014 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 91% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000166570 (Chr2:104504454..104504514 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCGAAGATGCAAGATACCAAA Chr2:104504492..104504512 60.08 42.86 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000166570 (Chr2:104504454..104504514 +)
Downstram Exon
ENSMUSE00000342603 (Chr2:104504874..104505575 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCGAAGATGCAAGATACCAAA Chr2:104504492..104504512 60.08 42.86 GATGTGGCGTTGTCATTTTG Chr2:104505333..104505352 59.97 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000376863 Chr2:104430680..104430859 TGGTGCGTACGTTGTAGTCC Chr2:104430804..104430823 59.64 55
upstream ENSMUSE00000226273 Chr2:104449028..104449129 GGTGAAGAAAGCGGAAAAGA Chr2:104449051..104449070 59.43 45
upstream ENSMUSE00000166584 Chr2:104449248..104449343 ACTTACGAACGCCTTGTTGC Chr2:104449275..104449294 60.31 50
upstream ENSMUSE00000166573 Chr2:104484446..104484478 No primer for this exon
upstream ENSMUSE00000340815 Chr2:104485136..104485233 GGGTAAACTGCCCAGCTACA Chr2:104485213..104485232 60.13 55
upstream ENSMUSE00000226254 Chr2:104486557..104486623 No primer for this exon
upstream ENSMUSE00000166559 Chr2:104486766..104486800 No primer for this exon
upstream ENSMUSE00000226243 Chr2:104486881..104487007 CGAGGTTGTGTTAATCCAATGA Chr2:104486942..104486963 59.86 40.91
upstream ENSMUSE00000166568 Chr2:104488327..104488404 No primer for this exon
upstream ENSMUSE00000166567 Chr2:104489610..104489772 GGACCAGACCCTGATAACCA Chr2:104489747..104489766 59.78 55
upstream ENSMUSE00000226232 Chr2:104491799..104491908 CGAGTAAGCTGCTTGCAGAA Chr2:104491883..104491902 59.51 50
upstream ENSMUSE00000166579 Chr2:104492602..104492718 TGAAAGAGCCATAAGCACGTTA Chr2:104492649..104492670 59.91 40.91
upstream ENSMUSE00000166575 Chr2:104493161..104493235 TCTGGCAATTGAGGACATTG Chr2:104493205..104493224 59.65 45
upstream ENSMUSE00000166565 Chr2:104494318..104494461 CCCGCCATCATGTCTATGTA Chr2:104494409..104494428 59.38 50
upstream ENSMUSE00000166560 Chr2:104495846..104495948 No primer for this exon
upstream ENSMUSE00000226206 Chr2:104499423..104499492 CCTTCCTCCTGAGAAGTCTGG Chr2:104499472..104499492 60.37 57.14
upstream ENSMUSE00000392214 Chr2:104500676..104500871 TGAAGGCAAGGAAACAGCTT Chr2:104500778..104500797 59.99 45
upstream ENSMUSE00000166562 Chr2:104503451..104503604 TCAGCCACGACATTTAGCAC Chr2:104503585..104503604 59.87 50
upstream ENSMUSE00000166566 Chr2:104504226..104504320 CCACCTCCTATCTGCTTCCA Chr2:104504300..104504319 60.21 55
upstream ENSMUSE00000166570 Chr2:104504454..104504514 CCGAAGATGCAAGATACCAAA Chr2:104504492..104504512 60.08 42.86

*** Putative Vector Insertion (Chr 2: 104504515 - 104504873) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000342603 Chr2:104504874..104505575 GATGTGGCGTTGTCATTTTG Chr2:104505333..104505352 59.97 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTCATTTTCACTGCGGAAT Chr2:104504529..104504549 60.22 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCTCATTTTCACTGCGGAAT Chr2:104504529..104504549 60.22 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027176