Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI18390
Trapped Gene
Zwilch (ENSMUSG00000032400)
Vector Insertion
Chr 9: 64016472 - 64020624
Public Clones E078E03 (ggtc) E078G07 (ggtc) E078E03 (ggtc) PST19302-NR (escells) IST14289B6 (tigm)
IST13337H1 (tigm) IST14220D6 (tigm)
Private Clones OST424252 (lexicon) OST200478 (lexicon)
Severity of mutation (?) Insertion after 3% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000331328 (Chr9:64020625..64020715 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGGAGGAGTTTTATGCTCGT Chr9:64020633..64020652 59.34 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000331328 (Chr9:64020625..64020715 -)
Downstram Exon
ENSMUSE00000323062 (Chr9:64016420..64016471 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGGAGGAGTTTTATGCTCGT Chr9:64020633..64020652 59.34 50 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000331328 Chr9:64020625..64020715 CGGAGGAGTTTTATGCTCGT Chr9:64020633..64020652 59.34 50
upstream ENSMUSE00000711185 Chr9:64020625..64020911 CGGAGGAGTTTTATGCTCGT Chr9:64020633..64020652 59.34 50

*** Putative Vector Insertion (Chr 9: 64016472 - 64020624) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000323062 Chr9:64016420..64016471 No primer for this exon
downstream ENSMUSE00000219417 Chr9:64013170..64013265 CCTTTGCTGATCAACTGCAC Chr9:64013212..64013231 59.44 50
downstream ENSMUSE00000219419 Chr9:64012154..64012272 TGCTCTCCCAACAGGTAAGG Chr9:64012134..64012153 60.25 55
downstream ENSMUSE00000219421 Chr9:64010371..64010570 CTCAGCTCCTAGCCAACAGG Chr9:64010407..64010426 60.15 60
downstream ENSMUSE00000219416 Chr9:64009178..64009248 No primer for this exon
downstream ENSMUSE00000219420 Chr9:64008628..64008783 GAGCTCATACTGGGCAAAGC Chr9:64008729..64008748 59.99 55
downstream ENSMUSE00000322894 Chr9:64006502..64006573 CAGACAACCTCTGGACTCTCCT Chr9:64006513..64006534 59.91 54.54
downstream ENSMUSE00000322858 Chr9:64003820..64003913 GAGGCTCAAGCCATTCAGTT Chr9:64003843..64003862 59.43 50
downstream ENSMUSE00000322833 Chr9:64002971..64003026 No primer for this exon
downstream ENSMUSE00000322801 Chr9:64001358..64001457 CACCAAAGCTGTTCAGCAAA Chr9:64001350..64001369 60.03 45
downstream ENSMUSE00000362674 Chr9:64000692..64000771 TCACCACGCTGAAGACTCTG Chr9:64000683..64000702 60.18 55
downstream ENSMUSE00000322726 Chr9:63997963..63998119 GCATCTGCAGTGGGGTAGTT Chr9:63997995..63998014 60.14 55
downstream ENSMUSE00000399097 Chr9:63997206..63997234 No primer for this exon
downstream ENSMUSE00000322674 Chr9:63995077..63995213 GTTTCTGAACACGGCAAACC Chr9:63995134..63995153 60.54 50
downstream ENSMUSE00000400965 Chr9:63994632..63994727 CTGGTCTGACTGGCAACTGA Chr9:63994635..63994654 60.02 55
downstream ENSMUSE00000347367 Chr9:63991887..63991999 CCTGTGGAAACTGGAATGGT Chr9:63991869..63991888 59.82 50
downstream ENSMUSE00000390139 Chr9:63987698..63987823 AACGAAGGCTGTCCTTTCTTC Chr9:63987749..63987769 59.88 47.62
downstream ENSMUSE00000349645 Chr9:63985483..63985866 GGGATCTCCTCTCCACCTTC Chr9:63985710..63985729 60.01 60
downstream ENSMUSE00000720585 Chr9:63984951..63985866 CATGGCTCCAAAACTCCATT Chr9:63985440..63985459 59.93 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTGAGTTGTGGTTGGGGAAT Chr9:64017603..64017623 59.68 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTGAGTTGTGGTTGGGGAAT Chr9:64020603..64020623 59.68 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GGTATGTGGTCGCGTAATCG Chr9:64017659..64017679 61.3 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GCCTCTGACGTCATTGTCTGG Chr9:64017725..64017746 63.16 57.14 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032400