Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8040
Trapped Gene
Kif15 (ENSMUSG00000036768)
Vector Insertion
Chr 9: 122913812 - 122916431
Public Clones XL528 (baygenomics) RRJ126 (baygenomics)
Private Clones OST437482 (lexicon)
Severity of mutation (?) Insertion after 76% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000254552 (Chr9:122913689..122913811 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAATGCTTCATTGGCTGACA Chr9:122913697..122913716 60.81 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000254552 (Chr9:122913689..122913811 +)
Downstram Exon
ENSMUSE00000405378 (Chr9:122916432..122916578 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAATGCTTCATTGGCTGACA Chr9:122913697..122913716 60.81 45 CTGGTCAGCTCCTCTTGAGC Chr9:122916547..122916566 60.28 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000528048 Chr9:122860182..122860270 AAGGGAGGATTCTGGTGGTC Chr9:122860201..122860220 60.31 55
upstream ENSMUSE00000404489 Chr9:122868235..122868277 No primer for this exon
upstream ENSMUSE00000359842 Chr9:122868925..122869108 ACTCTCCGGCTACACTCCAA Chr9:122869034..122869053 59.87 55
upstream ENSMUSE00000528047 Chr9:122872598..122872674 AAAAGCATTGTGGAATCATGC Chr9:122872622..122872642 59.96 38.1
upstream ENSMUSE00000528046 Chr9:122875067..122875104 CAGACTGGCTCTGGGAAGAC Chr9:122875071..122875090 59.99 60
upstream ENSMUSE00000220698 Chr9:122880807..122880904 No primer for this exon
upstream ENSMUSE00000254867 Chr9:122884767..122884946 GGAGCTGGGAAGAGTTTCCT Chr9:122884770..122884789 59.82 55
upstream ENSMUSE00000412405 Chr9:122886958..122887167 CATCCGGACCTCCTTACTCA Chr9:122887083..122887102 60.06 55
upstream ENSMUSE00000335709 Chr9:122888588..122888713 ATAAACCGATCGCTGAGCTG Chr9:122888600..122888619 60.37 50
upstream ENSMUSE00000409812 Chr9:122888858..122888980 TTTTGCTCAAAGAGCCAAGC Chr9:122888947..122888966 60.64 45
upstream ENSMUSE00000393841 Chr9:122893918..122894041 GAAATGTCAGCCAACTGCAA Chr9:122893943..122893962 59.85 45
upstream ENSMUSE00000345735 Chr9:122895263..122895339 No primer for this exon
upstream ENSMUSE00000386576 Chr9:122895560..122895769 GAGGACCAAATCATGCGTCT Chr9:122895650..122895669 60.08 50
upstream ENSMUSE00000254783 Chr9:122896964..122897141 ATGAAATCGATGCCCAGTCT Chr9:122897064..122897083 59.51 45
upstream ENSMUSE00000254769 Chr9:122900204..122900345 TGCAAGGATTTTCTCCCAAA Chr9:122900207..122900226 60.56 40
upstream ENSMUSE00000254747 Chr9:122900979..122901120 AAACCTTTTGGAGGCAACAA Chr9:122901042..122901061 59.59 40
upstream ENSMUSE00000254728 Chr9:122902961..122903158 GTGCCACCTGAGATGAGTGA Chr9:122903096..122903115 59.83 55
upstream ENSMUSE00000396286 Chr9:122904834..122904941 No primer for this exon
upstream ENSMUSE00000383048 Chr9:122905409..122905514 AAGCGATTGGACCAAACAAC Chr9:122905426..122905445 59.98 45
upstream ENSMUSE00000335687 Chr9:122906900..122907065 ATGTGCAGGTTCAGCTTCAG Chr9:122907032..122907051 59.04 50
upstream ENSMUSE00000254648 Chr9:122908293..122908443 TTCTTGAGAGCCAAGCCTGT Chr9:122908310..122908329 60.13 50
upstream ENSMUSE00000254623 Chr9:122908633..122908718 GGTGGAGCTTTTTGAAGCAG Chr9:122908638..122908657 59.99 50
upstream ENSMUSE00000254601 Chr9:122910163..122910232 GATGGCCAAGTGTGAAAAGC Chr9:122910211..122910230 60.65 50
upstream ENSMUSE00000254586 Chr9:122911153..122911239 No primer for this exon
upstream ENSMUSE00000254567 Chr9:122912688..122912792 GAAACCATAGCCACCCTGAA Chr9:122912751..122912770 59.93 50
upstream ENSMUSE00000254552 Chr9:122913689..122913811 CAATGCTTCATTGGCTGACA Chr9:122913697..122913716 60.81 45

*** Putative Vector Insertion (Chr 9: 122913812 - 122916431) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000405378 Chr9:122916432..122916578 CTGGTCAGCTCCTCTTGAGC Chr9:122916547..122916566 60.28 60
downstream ENSMUSE00000254487 Chr9:122918435..122918536 TTCTGCTCCACTTCCTCCTT Chr9:122918469..122918488 59.01 50
downstream ENSMUSE00000254476 Chr9:122918878..122919042 TTGAAAATGGGGTGGTGTTT Chr9:122918907..122918926 60.07 40
downstream ENSMUSE00000254448 Chr9:122920646..122920755 TTGCAGGAGCCAGTTTTTCT Chr9:122920720..122920739 59.99 45
downstream ENSMUSE00000254420 Chr9:122923058..122923130 No primer for this exon
downstream ENSMUSE00000254401 Chr9:122923587..122923624 No primer for this exon
downstream ENSMUSE00000254380 Chr9:122926363..122926528 TCTGGTTCGCTCAATTTCCT Chr9:122926444..122926463 59.81 45
downstream ENSMUSE00000254350 Chr9:122926705..122926836 TTGCTTTTTCAGCATTTCCA Chr9:122926731..122926750 59.42 35
downstream ENSMUSE00000254326 Chr9:122927186..122927843 TTCAGCACGCAATTTTTCTG Chr9:122927212..122927231 59.99 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCTCAGAGGACATCGAGGTAGG Chr9:122913796..122913818 60.78 54.54 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTCAGAGGACATCGAGGTAGG Chr9:122913796..122913818 60.78 54.54 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036768