Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14108
Trapped Gene
OTTMUSG00000003947 (ENSMUSG00000075410)
Vector Insertion
Chr 11: 116521142 - 116529345
Public Clones (ggtc) (ggtc) CMHD-GT_106F10-3 (cmhd) PSTVUpb13c2 (vanderbilt) PSTVUpb18g2 (vanderbilt)
PSTVUpb14f3 (vanderbilt) IST12531A12HMF1 (tigm)
Private Clones OST31874 (lexicon) OST28762 (lexicon) OST27752 (lexicon) OST23875 (lexicon)
OST23683 (lexicon) OST23232 (lexicon) OST21366 (lexicon) OST20722 (lexicon)
OST20367 (lexicon) OST18185 (lexicon) OST18135 (lexicon) OST18007 (lexicon)
OST17746 (lexicon) OST17011 (lexicon) OST16753 (lexicon) OST13223 (lexicon)
OST11554 (lexicon) OST11323 (lexicon)
Severity of mutation (?) Insertion after 92% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000645982 (Chr11:116521047..116521141 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGAGAAACGGTCATGGAGAA Chr11:116521121..116521140 60.05 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000645982 (Chr11:116521047..116521141 +)
Downstram Exon
ENSMUSE00000705775 (Chr11:116529346..116529605 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGAGAAACGGTCATGGAGAA Chr11:116521121..116521140 60.05 50 ATGGTAGAGACGCGATGCTT Chr11:116529439..116529458 59.87 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000714145 Chr11:116514848..116515291 TCTCCGAGCTAGAAGGCATC Chr11:116514910..116514929 59.68 55
upstream ENSMUSE00000720642 Chr11:116514848..116515291 TCTCCGAGCTAGAAGGCATC Chr11:116514910..116514929 59.68 55
upstream ENSMUSE00000669684 Chr11:116518436..116518621 CTTCTTCAGCGGAGTTGGTC Chr11:116518505..116518524 59.99 55
upstream ENSMUSE00000669683 Chr11:116518852..116518920 CGGCTCAGACACAGACCTTC Chr11:116518888..116518907 61.01 60
upstream ENSMUSE00000669689 Chr11:116518852..116518920 CGGCTCAGACACAGACCTTC Chr11:116518888..116518907 61.01 60
upstream ENSMUSE00000669682 Chr11:116520612..116520690 No primer for this exon
upstream ENSMUSE00000669688 Chr11:116520612..116520690 No primer for this exon
upstream ENSMUSE00000645982 Chr11:116521047..116521141 GGAGAAACGGTCATGGAGAA Chr11:116521121..116521140 60.05 50
upstream ENSMUSE00000669687 Chr11:116521047..116521141 GGAGAAACGGTCATGGAGAA Chr11:116521121..116521140 60.05 50
upstream ENSMUSE00000705776 Chr11:116521079..116521096 No primer for this exon
upstream ENSMUSE00000645981 Chr11:116521099..116521141 GGAGAAACGGTCATGGAGAA Chr11:116521121..116521140 60.05 50

*** Putative Vector Insertion (Chr 11: 116521142 - 116529345) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000645980 Chr11:116529346..116529701 ATGGTAGAGACGCGATGCTT Chr11:116529439..116529458 59.87 50
downstream ENSMUSE00000669686 Chr11:116529346..116529701 ATGGTAGAGACGCGATGCTT Chr11:116529439..116529458 59.87 50
downstream ENSMUSE00000705775 Chr11:116529346..116529605 ATGGTAGAGACGCGATGCTT Chr11:116529439..116529458 59.87 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAATAATCGCCTTGCAGCAC Chr11:116527190..116527210 60.24 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTAGAGAGTGCTGCGTGACTG Chr11:116527180..116527201 59 57.14 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000075410