Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13365
Trapped Gene
Uba3 (ENSMUSG00000030061)
Vector Insertion
Chr 6: 97153589 - 97155299
Public Clones (sanger) CMHD-GT_329E2-3 (cmhd) IST12658E12 (tigm) IST14646B12 (tigm)
IST10468E5 (tigm)
Private Clones OST238315 (lexicon) OST197195 (lexicon) OST196716 (lexicon) OST126299 (lexicon)
OST110162 (lexicon)
Severity of mutation (?) Insertion after 5% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000244916 (Chr6:97155300..97155341 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TAGAGGAGCTGCTGGCTGAG Chr6:97155302..97155321 60.97 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000244916 (Chr6:97155300..97155341 -)
Downstram Exon
ENSMUSE00000244911 (Chr6:97153468..97153588 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TAGAGGAGCTGCTGGCTGAG Chr6:97155302..97155321 60.97 60 GACCTTCCCAGTCTCCAGTG Chr6:97153520..97153539 59.68 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000695343 Chr6:97155527..97155554 No primer for this exon
upstream ENSMUSE00000244916 Chr6:97155300..97155341 TAGAGGAGCTGCTGGCTGAG Chr6:97155302..97155321 60.97 60

*** Putative Vector Insertion (Chr 6: 97153589 - 97155299) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000244911 Chr6:97153468..97153588 GACCTTCCCAGTCTCCAGTG Chr6:97153520..97153539 59.68 60
downstream ENSMUSE00000244909 Chr6:97151911..97151991 ACATCCTAAGCCACCAGCTC Chr6:97151907..97151926 59.31 55
downstream ENSMUSE00000244906 Chr6:97149233..97149315 No primer for this exon
downstream ENSMUSE00000194806 Chr6:97146831..97146911 TTGGGTCTTCCGACATCTTT Chr6:97146866..97146885 59.53 45
downstream ENSMUSE00000194801 Chr6:97142735..97142778 No primer for this exon
downstream ENSMUSE00000194788 Chr6:97141520..97141584 GTCCAGGCCACATACAATGA Chr6:97141534..97141553 59.37 50
downstream ENSMUSE00000194797 Chr6:97141087..97141242 GCACTCAATACAAGCGGTCA Chr6:97141089..97141108 59.87 50
downstream ENSMUSE00000194803 Chr6:97139748..97139850 AGGCTGCTCTTTAGGCCATT Chr6:97139733..97139752 60.36 50
downstream ENSMUSE00000194791 Chr6:97139523..97139636 No primer for this exon
downstream ENSMUSE00000194785 Chr6:97136657..97136710 No primer for this exon
downstream ENSMUSE00000194799 Chr6:97136231..97136267 TTGAAAACCTCAGTGGCACA Chr6:97136221..97136240 60.28 45
downstream ENSMUSE00000194793 Chr6:97136063..97136144 CAGCCCATCTACATCATTGAA Chr6:97136071..97136091 58.59 42.86
downstream ENSMUSE00000194787 Chr6:97135644..97135744 TTGGCTACATGCTGGACAGT Chr6:97135699..97135718 59.32 50
downstream ENSMUSE00000194786 Chr6:97135477..97135540 GCTGTGATAGCCGGAGACTT Chr6:97135492..97135511 59.46 55
downstream ENSMUSE00000194795 Chr6:97135335..97135389 GGCCTGGTTCGTTCTTCAAT Chr6:97135336..97135355 61.38 50
downstream ENSMUSE00000695311 Chr6:97133813..97134859 TTCTTGGATGTTCCCCTCTG Chr6:97134646..97134665 60.04 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAGAGGAGCTGCTGGCTGAG Chr6:97155300..97155320 60.97 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAGAGGAGCTGCTGGCTGAG Chr6:97155300..97155320 60.97 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GAGCTGCTGGCTGAGAAGTT Chr6:97155295..97155315 59.9 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GAGCTGCTGGCTGAGAAGTT Chr6:97155295..97155315 59.9 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030061