Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25248
Trapped Gene
Cnn3 (ENSMUSG00000053931)
Vector Insertion
Chr 3: 121154439 - 121154800
Public Clones not available
Private Clones OST190357 (lexicon)
Severity of mutation (?) Insertion after 39% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000463156 (Chr3:121154301..121154438 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCAGGCTTACGGTATGAAGC Chr3:121154333..121154352 59.73 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000463156 (Chr3:121154301..121154438 +)
Downstram Exon
ENSMUSE00000465196 (Chr3:121154801..121154917 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCAGGCTTACGGTATGAAGC Chr3:121154333..121154352 59.73 55 CGCCAATGTCAATGGTTGTA Chr3:121154843..121154862 60.38 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000359223 Chr3:121129452..121129746 AGGGTGACTGACCGCTAGAA Chr3:121129647..121129666 59.87 55
upstream ENSMUSE00000636208 Chr3:121152867..121152988 CTAGGCATTGGCACCAACTT Chr3:121152933..121152952 60.13 50
upstream ENSMUSE00000636205 Chr3:121153210..121153276 AGCCAGGCTCTGTGAAGAAA Chr3:121153227..121153246 60.13 50
upstream ENSMUSE00000463156 Chr3:121154301..121154438 CCAGGCTTACGGTATGAAGC Chr3:121154333..121154352 59.73 55

*** Putative Vector Insertion (Chr 3: 121154439 - 121154800) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000465196 Chr3:121154801..121154917 CGCCAATGTCAATGGTTGTA Chr3:121154843..121154862 60.38 45
downstream ENSMUSE00000563954 Chr3:121157865..121158011 CAGGCTAATCGTGGTCTGGT Chr3:121157984..121158003 60.13 55
downstream ENSMUSE00000391013 Chr3:121160000..121160867 GTCTGGGTACTCGCCATGAT Chr3:121160296..121160315 59.96 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGGTGGCTCTAGCAGGTCT Chr3:121154419..121154439 59.62 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGGTGGCTCTAGCAGGTCT Chr3:121154419..121154439 59.62 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000053931