Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI16954
Trapped Gene
Smyd2 (ENSMUSG00000026603)
Vector Insertion
Chr 1: 191733794 - 191745985
Public Clones (sanger) (ggtc) IST14572C4 (tigm) IST10919E9 (tigm) IST14589E7 (tigm)
IST14983H7 (tigm) IST12280G1 (tigm) IST15086E12 (tigm) IST14910E10 (tigm)
IST14619B10 (tigm) IST14271H9 (tigm) IST11615B12 (tigm)
Private Clones OST451931 (lexicon) OST448696 (lexicon) OST437231 (lexicon) OST426767 (lexicon)
OST372742 (lexicon) OST364914 (lexicon) OST300568 (lexicon) OST266664 (lexicon)
OST252493 (lexicon) OST245778 (lexicon) OST238873 (lexicon) OST217400 (lexicon)
OST196462 (lexicon) OST194344 (lexicon) OST193875 (lexicon) OST187289 (lexicon)
OST181957 (lexicon) OST181138 (lexicon) OST179362 (lexicon) OST68545 (lexicon)
OST64438 (lexicon) OST45038 (lexicon) OST41521 (lexicon) OST41426 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000289243 (Chr1:191745986..191746170 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000289243 (Chr1:191745986..191746170 -)
Downstram Exon
ENSMUSE00000289238 (Chr1:191733730..191733793 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon GACATTCCACGTCGCAGTAG Chr1:191733710..191733729 59.32 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000289243 Chr1:191745986..191746170 No primer for this exon

*** Putative Vector Insertion (Chr 1: 191733794 - 191745985) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000289238 Chr1:191733730..191733793 GACATTCCACGTCGCAGTAG Chr1:191733710..191733729 59.32 55
downstream ENSMUSE00000289233 Chr1:191723697..191723807 GCACAGTCTCCGAAGGATTC Chr1:191723704..191723723 59.81 55
downstream ENSMUSE00000289226 Chr1:191721302..191721362 TGTCCTCTCTGGGTGGATTT Chr1:191721320..191721339 59.51 50
downstream ENSMUSE00000289221 Chr1:191720450..191720574 GCGATGTCACTCTGGATGAG Chr1:191720501..191720520 59.37 55
downstream ENSMUSE00000289217 Chr1:191715279..191715346 GAATATCGCCGATCCCAAAT Chr1:191715262..191715281 60.99 45
downstream ENSMUSE00000289209 Chr1:191712694..191712796 CAGGGTCCCTTTGTAGGTCA Chr1:191712714..191712733 59.96 55
downstream ENSMUSE00000160915 Chr1:191710400..191710510 CAGGTCGATGTAGCTGGTGA Chr1:191710465..191710484 59.85 55
downstream ENSMUSE00000160912 Chr1:191709178..191709298 CTGAGCTTTCGGACTTCCAC Chr1:191709245..191709264 59.99 55
downstream ENSMUSE00000160911 Chr1:191707703..191707877 TCTTCTGCCCGTATTTCAGG Chr1:191707697..191707716 60.21 50
downstream ENSMUSE00000160914 Chr1:191705988..191706096 TGAGGGAGTACACGGGGTAG Chr1:191706049..191706068 59.98 60
downstream ENSMUSE00000333082 Chr1:191704373..191704745 AAAGCTCAATCTGCCGAAAA Chr1:191704435..191704454 59.96 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAAGGAAACTCGGGCCTTTT Chr1:191736941..191736961 60.07 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAAGGAAACTCGGGCCTTTT Chr1:191736941..191736961 60.07 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TCTTAATCGCCTTGCAGCAC Chr1:191737103..191737123 61.44 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CTGGAGCGCTTCTCGTGACT Chr1:191737113..191737133 63.17 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026603