Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI23288
Trapped Gene
She (ENSMUSG00000046280)
Vector Insertion
Chr 3: 89638193 - 89653289
Public Clones IST12575A5 (tigm)
Private Clones OST266777 (lexicon)
Severity of mutation (?) Insertion after 27% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000360671 (Chr3:89638066..89638192 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTGAGAACGACGGCTACAT Chr3:89638141..89638160 60.14 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000360671 (Chr3:89638066..89638192 +)
Downstram Exon
ENSMUSE00000385627 (Chr3:89653290..89653595 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTGAGAACGACGGCTACAT Chr3:89638141..89638160 60.14 55 TCCCAGGGCTGTTCATACTC Chr3:89653563..89653582 60.07 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000403332 Chr3:89635292..89636025 AGCTGGACAAGGCCAAGATA Chr3:89635988..89636007 59.84 50
upstream ENSMUSE00000672999 Chr3:89635426..89635487 CTGGGCCTCCTCACTCTTCT Chr3:89635467..89635486 60.92 60
upstream ENSMUSE00000672998 Chr3:89635944..89636025 AGCTGGACAAGGCCAAGATA Chr3:89635988..89636007 59.84 50
upstream ENSMUSE00000360671 Chr3:89638066..89638192 GGTGAGAACGACGGCTACAT Chr3:89638141..89638160 60.14 55

*** Putative Vector Insertion (Chr 3: 89638193 - 89653289) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000385627 Chr3:89653290..89653595 TCCCAGGGCTGTTCATACTC Chr3:89653563..89653582 60.07 55
downstream ENSMUSE00000350411 Chr3:89655531..89655672 GGTCGATCAGATCCCTCAAA Chr3:89655558..89655577 60.01 50
downstream ENSMUSE00000393714 Chr3:89656289..89656408 ACCAGGTAAGCGGCTTCTTT Chr3:89656366..89656385 60.26 50
downstream ENSMUSE00000348017 Chr3:89658453..89662758 AAGGCACCTGCATTACAACC Chr3:89662639..89662658 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAGCAGCCTCATTTTGAGTG Chr3:89653211..89653231 59.59 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGCAGCCTCATTTTGAGTG Chr3:89653211..89653231 59.59 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000046280