Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5200
Trapped Gene
Rnf4 (ENSMUSG00000029110)
Vector Insertion
Chr 5: 34692721 - 34693438
Public Clones YTC007 (baygenomics) RRJ158 (baygenomics)
Private Clones OST35799 (lexicon)
Severity of mutation (?) Insertion after 66% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000185704 (Chr5:34692561..34692720 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTCGAAGCACCAAGGATGAT Chr5:34692684..34692703 60.22 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000185704 (Chr5:34692561..34692720 +)
Downstram Exon
ENSMUSE00000185702 (Chr5:34693439..34693487 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTCGAAGCACCAAGGATGAT Chr5:34692684..34692703 60.22 50 No primer for this exon

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
upstream ENSMUSE00000185703 Chr5:34691313..34691392 CTTTAGAGCCCGTGGTTGTG Chr5:34691346..34691365 60.68 55
upstream ENSMUSE00000654188 Chr5:34692199..34692208 No primer for this exon
upstream ENSMUSE00000185704 Chr5:34692561..34692720 CTCGAAGCACCAAGGATGAT Chr5:34692684..34692703 60.22 50

*** Putative Vector Insertion (Chr 5: 34692721 - 34693438) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 CTCGAAGCACCAAGGATGAT Chr5:34692685..34692705 60.22 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTCGAAGCACCAAGGATGAT Chr5:34692685..34692705 60.22 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029110