Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14678
Trapped Gene
OTTMUSG00000016546 (ENSMUSG00000078905)
Vector Insertion
Chr 2: 174889368 - 174893265
Public Clones FHCRC-GT-S1-9D1 (fhcrc) PST13549-NL (escells) IST11532D1 (tigm)
Private Clones OST320483 (lexicon) OST319496 (lexicon) OST298958 (lexicon)
Severity of mutation (?) Insertion after 1% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000714617 (Chr2:174893201..174893264 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTGAGCGCCTCTACTGAGTG Chr2:174893239..174893258 59.34 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000714617 (Chr2:174893201..174893264 -)
Downstram Exon
ENSMUSE00000678927 (Chr2:174889369..174889495 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTGAGCGCCTCTACTGAGTG Chr2:174893239..174893258 59.34 55 AAGCCCATTCTTCCTGAGTG Chr2:174889419..174889438 59.28 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000678924 Chr2:174893201..174893282 AATGTGTTTTGAGCGCCTCT Chr2:174893247..174893266 59.88 45
upstream ENSMUSE00000714617 Chr2:174893201..174893264 TTGAGCGCCTCTACTGAGTG Chr2:174893239..174893258 59.34 55
upstream ENSMUSE00000678927 Chr2:174889369..174889495 TGCATGTCAACTTCACTCAGG Chr2:174889453..174889473 59.89 47.62

*** Putative Vector Insertion (Chr 2: 174889368 - 174893265) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000678926 Chr2:174889101..174889161 No primer for this exon
downstream ENSMUSE00000678923 Chr2:174888807..174889161 GCATGGCTCTACTAGGCTTGA Chr2:174888825..174888845 59.63 52.38
downstream ENSMUSE00000709461 Chr2:174887050..174887422 AACTCAGAGGGTTGCTCTGC Chr2:174887362..174887381 59.6 55
downstream ENSMUSE00000719886 Chr2:174887050..174887422 AACTCAGAGGGTTGCTCTGC Chr2:174887362..174887381 59.6 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AATGTGTTTTGAGCGCCTCT Chr2:174893245..174893265 59.88 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AATGTGTTTTGAGCGCCTCT Chr2:174893245..174893265 59.88 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CAACGAATTGCCAGTCAGAA Chr2:174893171..174893191 59.84 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CAACGAATTGCCAGTCAGAA Chr2:174893171..174893191 59.84 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000078905