Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25255
Trapped Gene
She (ENSMUSG00000046280)
Vector Insertion
Chr 3: 89653596 - 89655530
Public Clones not available
Private Clones OST190103 (lexicon)
Severity of mutation (?) Insertion after 57% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000385627 (Chr3:89653290..89653595 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCCGCCACAACTCTATGAC Chr3:89653422..89653441 60.28 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000385627 (Chr3:89653290..89653595 +)
Downstram Exon
ENSMUSE00000350411 (Chr3:89655531..89655672 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCCGCCACAACTCTATGAC Chr3:89653422..89653441 60.28 55 GGTCGATCAGATCCCTCAAA Chr3:89655558..89655577 60.01 50

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
upstream ENSMUSE00000385627 Chr3:89653290..89653595 AGCCGCCACAACTCTATGAC Chr3:89653422..89653441 60.28 55

*** Putative Vector Insertion (Chr 3: 89653596 - 89655530) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 CTAATCGCCTTGCAGCACAT Chr3:89653646..89653666 61.32 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGAGCCCTGTCAGGTGAGG Chr3:89653583..89653603 62.36 65 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000046280