Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4438
Trapped Gene
Esf1 (ENSMUSG00000045624)
Vector Insertion
Chr 2: 139949266 - 139949414
Public Clones AC0594 (sanger) RRJ473 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 83% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000467319 (Chr2:139949267..139949413 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAGCACCAGAATCTGAGCAA Chr2:139949322..139949341 59.12 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000467319 (Chr2:139949267..139949413 -)
Downstram Exon
ENSMUSE00000682682 (Chr2:139949267..139949413 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAGCACCAGAATCTGAGCAA Chr2:139949322..139949341 59.12 50 GGTGCTCCACAATCTTGTCA Chr2:139949313..139949332 59.68 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000640648 Chr2:139996213..139996294 No primer for this exon
upstream ENSMUSE00000682686 Chr2:139993802..139993903 TGAAAAGCCGATTGAAGAGAA Chr2:139993807..139993827 59.95 38.1
upstream ENSMUSE00000444523 Chr2:139993508..139994191 CAAGAGGTTTCGAGCCATGT Chr2:139994027..139994046 60.26 50
upstream ENSMUSE00000557757 Chr2:139993508..139993799 CTTTGCCCAAAGGAAAGCTA Chr2:139993590..139993609 59.47 45
upstream ENSMUSE00000557773 Chr2:139989945..139990318 TTTGTTTCCCGAAGAACCTG Chr2:139989998..139990017 60.08 45
upstream ENSMUSE00000640653 Chr2:139986119..139986232 TGCTGGCTCTGTTCAACTCA Chr2:139986155..139986174 60.74 50
upstream ENSMUSE00000640652 Chr2:139985430..139985530 TGGAAAGGAGAGGATGAAGG Chr2:139985494..139985513 59.21 50
upstream ENSMUSE00000640651 Chr2:139984216..139984368 TGCAGTAGCGGAGTGTGATT Chr2:139984295..139984314 59.47 50
upstream ENSMUSE00000640650 Chr2:139982791..139982905 CCAAGGATGTGGCCTTAGAA Chr2:139982851..139982870 60.07 50
upstream ENSMUSE00000640649 Chr2:139980530..139980677 TGGGATGAGACTGACCATGA Chr2:139980646..139980665 60.05 50
upstream ENSMUSE00000338220 Chr2:139974489..139974650 No primer for this exon
upstream ENSMUSE00000711438 Chr2:139964669..139964790 GACCCCTTGGGAACAGTTTT Chr2:139964713..139964732 60.2 50
upstream ENSMUSE00000716213 Chr2:139964669..139964790 GACCCCTTGGGAACAGTTTT Chr2:139964713..139964732 60.2 50
upstream ENSMUSE00000460610 Chr2:139954936..139955023 TCAATGATCCCTACTTTGCTGA Chr2:139954953..139954974 59.71 40.91
upstream ENSMUSE00000682684 Chr2:139954936..139955023 TCAATGATCCCTACTTTGCTGA Chr2:139954953..139954974 59.71 40.91
upstream ENSMUSE00000510249 Chr2:139950664..139950740 CAAAAGACAGCGCATCTTCA Chr2:139950694..139950713 60.13 45
upstream ENSMUSE00000682683 Chr2:139950664..139950740 CAAAAGACAGCGCATCTTCA Chr2:139950694..139950713 60.13 45
upstream ENSMUSE00000467319 Chr2:139949267..139949413 GAGCACCAGAATCTGAGCAA Chr2:139949322..139949341 59.12 50
upstream ENSMUSE00000682682 Chr2:139949267..139949413 GAGCACCAGAATCTGAGCAA Chr2:139949322..139949341 59.12 50

*** Putative Vector Insertion (Chr 2: 139949266 - 139949414) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000595799 Chr2:139945617..139946641 GCACCGGGTCTCTCAAATTA Chr2:139946097..139946116 60.07 50
downstream ENSMUSE00000682681 Chr2:139945617..139946641 GCACCGGGTCTCTCAAATTA Chr2:139946097..139946116 60.07 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTCTCCGTAGGCTGAGATGG Chr2:139949402..139949422 59.97 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTCTCCGTAGGCTGAGATGG Chr2:139949402..139949422 59.97 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000045624