Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2386
Trapped Gene
Cstf3 (ENSMUSG00000027176)
Vector Insertion
Chr 2: 104449130 - 104449247
Public Clones AD0130 (sanger) RRS244 (baygenomics) CMHD-GT_359C12-3 (cmhd)
Private Clones OST379333 (lexicon) OST98508 (lexicon) OST31322 (lexicon) OST26142 (lexicon)
OST20224 (lexicon) OST15824 (lexicon) OST6891 (lexicon)
Severity of mutation (?) Insertion after 6% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000226273 (Chr2:104449028..104449129 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTGAAGAAAGCGGAAAAGA Chr2:104449051..104449070 59.43 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000226273 (Chr2:104449028..104449129 +)
Downstram Exon
ENSMUSE00000166584 (Chr2:104449248..104449343 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTGAAGAAAGCGGAAAAGA Chr2:104449051..104449070 59.43 45 GCAACAAGGCGTTCGTAAGT Chr2:104449297..104449316 60.31 50

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

*** Putative Vector Insertion (Chr 2: 104449130 - 104449247) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000166584 Chr2:104449248..104449343 GCAACAAGGCGTTCGTAAGT Chr2:104449297..104449316 60.31 50
downstream ENSMUSE00000166573 Chr2:104484446..104484478 No primer for this exon
downstream ENSMUSE00000340815 Chr2:104485136..104485233 TGTAGCTGGGCAGTTTACCC Chr2:104485235..104485254 60.13 55
downstream ENSMUSE00000226254 Chr2:104486557..104486623 No primer for this exon
downstream ENSMUSE00000166559 Chr2:104486766..104486800 No primer for this exon
downstream ENSMUSE00000226243 Chr2:104486881..104487007 No primer for this exon
downstream ENSMUSE00000166568 Chr2:104488327..104488404 No primer for this exon
downstream ENSMUSE00000166567 Chr2:104489610..104489772 CCACATGTCCACTTGCTGAG Chr2:104489705..104489724 60.31 55
downstream ENSMUSE00000226232 Chr2:104491799..104491908 TTCTGCAAGCAGCTTACTCG Chr2:104491905..104491924 59.51 50
downstream ENSMUSE00000166579 Chr2:104492602..104492718 AACGTGCTTATGGCTCTTTCA Chr2:104492671..104492691 59.9 42.86
downstream ENSMUSE00000166575 Chr2:104493161..104493235 CAATGTCCTCAATTGCCAGA Chr2:104493227..104493246 59.65 45
downstream ENSMUSE00000166565 Chr2:104494318..104494461 TCCATGAGGGCTGCAGTTAC Chr2:104494448..104494467 61.21 55
downstream ENSMUSE00000166560 Chr2:104495846..104495948 No primer for this exon
downstream ENSMUSE00000226206 Chr2:104499423..104499492 No primer for this exon
downstream ENSMUSE00000392214 Chr2:104500676..104500871 AAGCTGTTTCCTTGCCTTCA Chr2:104500800..104500819 59.99 45
downstream ENSMUSE00000166562 Chr2:104503451..104503604 GTGCTAAATGTCGTGGCTGA Chr2:104503607..104503626 59.87 50
downstream ENSMUSE00000166566 Chr2:104504226..104504320 GAGGTGGGAGCAGTTTCATC Chr2:104504309..104504328 59.66 55
downstream ENSMUSE00000166570 Chr2:104504454..104504514 TCCATCAGCTCATCCACTTG Chr2:104504488..104504507 59.79 50
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 TATAATCGCCTTGCAGCACA Chr2:104449179..104449199 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CATTCGAGAGGCACAGGTTT Chr2:104449115..104449135 60.26 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027176