Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI11812
Trapped Gene
Rnf4 (ENSMUSG00000029110)
Vector Insertion
Chr 5: 34689551 - 34691312
Public Clones M041F05 (ggtc) PST10532-NR (escells)
Private Clones OST450392 (lexicon) OST168408 (lexicon) OST109755 (lexicon)
Severity of mutation (?) Insertion after 23% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000185707 (Chr5:34689424..34689550 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AACTTCGACCCCTGAGGTTT Chr5:34689495..34689514 59.97 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000185707 (Chr5:34689424..34689550 +)
Downstram Exon
ENSMUSE00000185703 (Chr5:34691313..34691392 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AACTTCGACCCCTGAGGTTT Chr5:34689495..34689514 59.97 50 CCACGGGCTCTAAAGATTCA Chr5:34691363..34691382 60.21 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000699069 Chr5:34688360..34688368 No primer for this exon
upstream ENSMUSE00000185707 Chr5:34689424..34689550 AACTTCGACCCCTGAGGTTT Chr5:34689495..34689514 59.97 50

*** Putative Vector Insertion (Chr 5: 34689551 - 34691312) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000185703 Chr5:34691313..34691392 CCACGGGCTCTAAAGATTCA Chr5:34691363..34691382 60.21 50
downstream ENSMUSE00000654188 Chr5:34692199..34692208 No primer for this exon
downstream ENSMUSE00000185704 Chr5:34692561..34692720 CTCCATCATCCTTGGTGCTT Chr5:34692710..34692729 60.07 50
downstream ENSMUSE00000185702 Chr5:34693439..34693487 No primer for this exon
downstream ENSMUSE00000654187 Chr5:34693880..34696083 TTCAGGCGGAATCATAGGTC Chr5:34694577..34694596 60.04 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTAATCGCCTTGCAGCACAT Chr5:34689601..34689621 61.2 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAGTGCGTGACTGGGAAAAC Chr5:34689597..34689617 58.78 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029110