Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27333
Trapped Gene
Nhedc1 (ENSMUSG00000050150)
Vector Insertion
Chr 3: 135037366 - 135045649
Public Clones not available
Private Clones OST62996 (lexicon)
Severity of mutation (?) Insertion after 69% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000425698 (Chr3:135037238..135037365 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAGTCTGTCTGCGCTTGTCA Chr3:135037257..135037276 60.34 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000425698 (Chr3:135037238..135037365 +)
Downstram Exon
ENSMUSE00000586688 (Chr3:135045650..135045825 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAGTCTGTCTGCGCTTGTCA Chr3:135037257..135037276 60.34 55 AGACAGCGCCTAGGACAAAA Chr3:135045672..135045691 60.01 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000705517 Chr3:135011001..135011086 GCGGGTGAGAGTTGCTAAAG Chr3:135011058..135011077 60.01 55
upstream ENSMUSE00000586687 Chr3:135011022..135011086 GCGGGTGAGAGTTGCTAAAG Chr3:135011058..135011077 60.01 55
upstream ENSMUSE00000719634 Chr3:135011291..135011737 TTTCCATCACGACTGACAGC Chr3:135011320..135011339 59.84 50
upstream ENSMUSE00000722138 Chr3:135011291..135011737 TTTCCATCACGACTGACAGC Chr3:135011320..135011339 59.84 50
upstream ENSMUSE00000362259 Chr3:135017975..135018035 CAAGAAGGATGATGGTTTCCA Chr3:135017996..135018016 59.92 42.86
upstream ENSMUSE00000705513 Chr3:135017975..135018035 CAAGAAGGATGATGGTTTCCA Chr3:135017996..135018016 59.92 42.86
upstream ENSMUSE00000413724 Chr3:135020421..135020718 CAGAACCGAAGGAACCAGAA Chr3:135020500..135020519 60.22 50
upstream ENSMUSE00000705512 Chr3:135020421..135020718 CAGAACCGAAGGAACCAGAA Chr3:135020500..135020519 60.22 50
upstream ENSMUSE00000425940 Chr3:135034809..135034979 TGGGCCCTTATAGGTCAAGA Chr3:135034841..135034860 59.52 50
upstream ENSMUSE00000425934 Chr3:135036083..135036225 CTAGTACGAGCTGGGCTTGG Chr3:135036193..135036212 60.03 60
upstream ENSMUSE00000425698 Chr3:135037238..135037365 GAGTCTGTCTGCGCTTGTCA Chr3:135037257..135037276 60.34 55

*** Putative Vector Insertion (Chr 3: 135037366 - 135045649) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000586688 Chr3:135045650..135045825 AGACAGCGCCTAGGACAAAA Chr3:135045672..135045691 60.01 50
downstream ENSMUSE00000176961 Chr3:135053386..135053492 CGCAAGGACGATAGGATGTT Chr3:135053422..135053441 60.1 50
downstream ENSMUSE00000466512 Chr3:135055064..135055213 CCATGTAAGCCAATGTGCTG Chr3:135055152..135055171 60.13 50
downstream ENSMUSE00000586686 Chr3:135055125..135055213 CCATGTAAGCCAATGTGCTG Chr3:135055152..135055171 60.13 50
downstream ENSMUSE00000705515 Chr3:135055125..135055172 CCATGTAAGCCAATGTGCTG Chr3:135055152..135055171 60.13 50
downstream ENSMUSE00000586685 Chr3:135055661..135056046 GGGGTAGGGACTTTTGCATT Chr3:135055935..135055954 60.19 50
downstream ENSMUSE00000462005 Chr3:135056924..135057032 GAAGCGGCTGAAAAACATTC Chr3:135056978..135056997 59.83 45
downstream ENSMUSE00000464747 Chr3:135057808..135057944 TCGAACAGATAGTGCCAAACC Chr3:135057850..135057870 60.12 47.62
downstream ENSMUSE00000467391 Chr3:135060560..135060788 CTTCGCGTATCCTTCCAAGT Chr3:135060631..135060650 59.34 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGGGGGTTCCTACTAGGGTA Chr3:135043350..135043370 58.38 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACATTTGCGTGACTGGGAAA Chr3:135040410..135040430 61.47 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000050150