Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5378
Trapped Gene
Nufip2 (ENSMUSG00000037857)
Vector Insertion
Chr 11: 77506757 - 77519010
Public Clones XC697 (baygenomics) YHC305 (baygenomics) RST124 (baygenomics) SYA140 (baygenomics)
XC772 (baygenomics) XG095 (baygenomics) XE036 (baygenomics) YHC307 (baygenomics)
RST108 (baygenomics) A062B05 (ggtc) (ggtc) A059E02 (ggtc) (ggtc)
A061D08 (ggtc) PST5436-NR (escells)
Private Clones OST388281 (lexicon)
Severity of mutation (?) Insertion after 93% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000292192 (Chr11:77505044..77506756 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAACTCCTCCGTGTCACCAT Chr11:77505876..77505895 59.97 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000292192 (Chr11:77505044..77506756 +)
Downstram Exon
ENSMUSE00000292185 (Chr11:77519011..77519043 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAACTCCTCCGTGTCACCAT Chr11:77505876..77505895 59.97 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000292202 Chr11:77499641..77500009 AGCAGCCTCACCAATACCTG Chr11:77499887..77499906 60.28 55
upstream ENSMUSE00000292192 Chr11:77505044..77506756 GAACTCCTCCGTGTCACCAT Chr11:77505876..77505895 59.97 55

*** Putative Vector Insertion (Chr 11: 77506757 - 77519010) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000292185 Chr11:77519011..77519043 No primer for this exon
downstream ENSMUSE00000650373 Chr11:77523185..77524259 ATGAACGGTGGCTCTAATGC Chr11:77523293..77523312 60.1 50
downstream ENSMUSE00000650374 Chr11:77555188..77555294 ACCAATGTAACGCCAGTTCC Chr11:77555292..77555311 59.86 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGGGGTTCTTTTGACCTGA Chr11:77518711..77518731 60.08 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGGGGTTCTTTTGACCTGA Chr11:77518711..77518731 60.08 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037857