Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12533
Trapped Gene
Tbc1d13 (ENSMUSG00000039678)
Vector Insertion
Chr 2: 29996078 - 29997781
Public Clones W074D06 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 32% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000285759 (Chr2:29995995..29996077 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGACAACGAGGTGCTACTCC Chr2:29996039..29996058 59.73 60 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000285759 (Chr2:29995995..29996077 +)
Downstram Exon
ENSMUSE00000285746 (Chr2:29997782..29997941 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGACAACGAGGTGCTACTCC Chr2:29996039..29996058 59.73 60 TTCAGTGTCGTCTGCTCCAC Chr2:29997904..29997923 60.03 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000646180 Chr2:29989310..29989432 AGTCCGGAAGTCAACACCAT Chr2:29989392..29989411 59.43 50
upstream ENSMUSE00000285790 Chr2:29990317..29990390 TGGAAAAGCTTCGAGAACTCA Chr2:29990361..29990381 60.12 42.86
upstream ENSMUSE00000285783 Chr2:29992193..29992233 No primer for this exon
upstream ENSMUSE00000351402 Chr2:29992641..29992702 GGAGAGAGCCTCGTGGACTT Chr2:29992664..29992683 60.93 60
upstream ENSMUSE00000285767 Chr2:29992802..29992901 GGCTCTATTCGCAGTTCCTG Chr2:29992804..29992823 59.98 55
upstream ENSMUSE00000285759 Chr2:29995995..29996077 GGACAACGAGGTGCTACTCC Chr2:29996039..29996058 59.73 60

*** Putative Vector Insertion (Chr 2: 29996078 - 29997781) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000285746 Chr2:29997782..29997941 TTCAGTGTCGTCTGCTCCAC Chr2:29997904..29997923 60.03 55
downstream ENSMUSE00000285707 Chr2:30002172..30002382 CAGGGTTGAGCTTGGCATAG Chr2:30002301..30002320 60.79 55
downstream ENSMUSE00000285697 Chr2:30002882..30003045 GATACCGCACTGGGAGTCAT Chr2:30002982..30003001 59.96 55
downstream ENSMUSE00000285737 Chr2:30004143..30004303 GGAGTCCCAGATACGGATGA Chr2:30004247..30004266 59.89 55
downstream ENSMUSE00000285726 Chr2:30004451..30004508 AGAAGCCGCATGTTGACAGT Chr2:30004507..30004526 60.87 50
downstream ENSMUSE00000370531 Chr2:30005220..30007529 AGGTACTGGGGATTCCTGCT Chr2:30006215..30006234 59.96 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GACAACGAGGTGCTACTCCA Chr2:29996041..29996061 58.88 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACAACGAGGTGCTACTCCAGA Chr2:29996042..29996063 59.92 52.38 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039678