Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI11537
Trapped Gene
Stk38 (ENSMUSG00000024006)
Vector Insertion
Chr 17: 29137090 - 29144655
Public Clones (sanger) (sanger) P143D07 (ggtc) D137A04 (ggtc) D007B01 (ggtc)
W198E05 (ggtc) P127D04 (ggtc) D043E12 (ggtc) D143D01 (ggtc) D027G04 (ggtc)
P023D02 (ggtc) P135G06 (ggtc) D119G02 (ggtc) P094A04 (ggtc) D036H08 (ggtc)
D137A04 (ggtc) D027A07 (ggtc) W197E05 (ggtc) P135G06 (ggtc) D043E12 (ggtc)
E041B09 (ggtc) D031C07 (ggtc) PST8184-NR (escells) PST8725-NR (escells)
PSTVU01.HE35R (vanderbilt) PSTVU01.E456 (vanderbilt) IST14557E9 (tigm)
IST14567A8 (tigm) IST14579D2 (tigm) IST14183D2 (tigm) IST10551C3 (tigm)
IST14508A6 (tigm) IST10228H4 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000431121 (Chr17:29144656..29144882 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCAGTTGGGGTTCTTCCTTT Chr17:29144795..29144814 60.48 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000431121 (Chr17:29144656..29144882 -)
Downstram Exon
ENSMUSE00000710202 (Chr17:29136954..29137089 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCAGTTGGGGTTCTTCCTTT Chr17:29144795..29144814 60.48 50 TGAGCAAGGTGTTGATCCTG Chr17:29137033..29137052 59.83 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000431121 Chr17:29144656..29144882 GCAGTTGGGGTTCTTCCTTT Chr17:29144795..29144814 60.48 50

*** Putative Vector Insertion (Chr 17: 29137090 - 29144655) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000238312 Chr17:29136954..29137086 TGAGCAAGGTGTTGATCCTG Chr17:29137033..29137052 59.83 50
downstream ENSMUSE00000710202 Chr17:29136954..29137089 TGAGCAAGGTGTTGATCCTG Chr17:29137033..29137052 59.83 50
downstream ENSMUSE00000711234 Chr17:29136954..29137086 TGAGCAAGGTGTTGATCCTG Chr17:29137033..29137052 59.83 50
downstream ENSMUSE00000238301 Chr17:29129362..29129413 TCTTCGTCTTTCAGGCCTTC Chr17:29129341..29129360 59.55 50
downstream ENSMUSE00000137178 Chr17:29128243..29128365 GCGGATCTTCTGAGTCGTTT Chr17:29128324..29128343 59.43 50
downstream ENSMUSE00000137194 Chr17:29125123..29125206 CTTTGCGCAGGATTTTCATT Chr17:29125124..29125143 60.21 40
downstream ENSMUSE00000137186 Chr17:29121022..29121145 CACAAACTGTCTGCCTCCAC Chr17:29121071..29121090 59.31 55
downstream ENSMUSE00000137185 Chr17:29118977..29119131 TGCTGTCCAAGAGAAGGTTG Chr17:29118957..29118976 59.01 50
downstream ENSMUSE00000549113 Chr17:29117330..29117467 CCTCATGGCACAGCAAGTAA Chr17:29117383..29117402 59.86 50
downstream ENSMUSE00000137179 Chr17:29116148..29116250 AAAGGCCAAAGTCGGAAAGT Chr17:29116198..29116217 60.11 45
downstream ENSMUSE00000137183 Chr17:29114485..29114546 GCTGGCGTCTGTTTCTTTTC Chr17:29114465..29114484 60 50
downstream ENSMUSE00000137192 Chr17:29112764..29112881 TGTAACCCGTCTGCATGAAC Chr17:29112796..29112815 59.57 50
downstream ENSMUSE00000137180 Chr17:29111491..29111614 ATGTCTCTTGTGGGGTCTCG Chr17:29111554..29111573 60.11 55
downstream ENSMUSE00000238116 Chr17:29111227..29111322 AGGGGCTCCGATTCTATGTT Chr17:29111264..29111283 59.92 50
downstream ENSMUSE00000137176 Chr17:29109990..29110084 No primer for this exon
downstream ENSMUSE00000717891 Chr17:29109182..29109621 AGGCCCTATTTTGCTGCTTT Chr17:29109464..29109483 60.22 45
downstream ENSMUSE00000408447 Chr17:29107830..29109621 TAGGCAGTGTGTGCCTCAAG Chr17:29108677..29108696 60.05 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGATTGAACCAAATTATGTAGGG Chr17:29138675..29138699 59.19 33.33 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGATTGAACCAAATTATGTAGGG Chr17:29138675..29138699 59.19 33.33 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AACTAATCGCCTTGCAGCAC Chr17:29138815..29138835 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CTCCACAGTCTGAGGGGGTA Chr17:29138853..29138873 60.1 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024006