Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20606
Trapped Gene
Efna4 (ENSMUSG00000028040)
Vector Insertion
Chr 3: 89139395 - 89141759
Public Clones (sanger) IST14478F1 (tigm) IST14392E7 (tigm)
Private Clones OST357264 (lexicon) OST290128 (lexicon)
Severity of mutation (?) Insertion after 18% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000367369 (Chr3:89141760..89141950 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCCACCCAATCTACTGGAAC Chr3:89141774..89141793 59.41 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000367369 (Chr3:89141760..89141950 -)
Downstram Exon
ENSMUSE00000309999 (Chr3:89139099..89139394 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCCACCCAATCTACTGGAAC Chr3:89141774..89141793 59.41 55 AGAATCGAACAGGGCTGAAA Chr3:89139152..89139171 59.81 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000367369 Chr3:89141760..89141950 GCCACCCAATCTACTGGAAC Chr3:89141774..89141793 59.41 55

*** Putative Vector Insertion (Chr 3: 89139395 - 89141759) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000309999 Chr3:89139099..89139394 AGAATCGAACAGGGCTGAAA Chr3:89139152..89139171 59.81 45
downstream ENSMUSE00000175398 Chr3:89138704..89138772 CTTGCAGCAGACAGACACCT Chr3:89138689..89138708 59.21 55
downstream ENSMUSE00000367062 Chr3:89137660..89138354 CTCAGATCCTCCGACTTTGC Chr3:89138048..89138067 59.95 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCACCCAATCTACTGGAAC Chr3:89141772..89141792 59.41 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCACCCAATCTACTGGAAC Chr3:89141772..89141792 59.41 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TAATCGCCTTGCAGCACATC Chr3:89141880..89141900 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000028040