Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI37311
Trapped Gene
Nhedc1 (ENSMUSG00000050150)
Vector Insertion
Chr 3: 135057945 - 135060559
Public Clones CMHD-GT_464D2-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 88% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000464747 (Chr3:135057808..135057944 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGGTTTGGCACTATCTGTTC Chr3:135057826..135057846 59.99 47.62 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000464747 (Chr3:135057808..135057944 +)
Downstram Exon
ENSMUSE00000467391 (Chr3:135060560..135060788 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGGTTTGGCACTATCTGTTC Chr3:135057826..135057846 59.99 47.62 CTTCGCGTATCCTTCCAAGT Chr3:135060631..135060650 59.34 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
upstream ENSMUSE00000586688 Chr3:135045650..135045825 TTTTGTCCTAGGCGCTGTCT Chr3:135045650..135045669 60.01 50
upstream ENSMUSE00000176961 Chr3:135053386..135053492 ACGTTCTTATTGGGGTGCTG Chr3:135053422..135053441 59.99 50
upstream ENSMUSE00000466512 Chr3:135055064..135055213 CAGCACATTGGCTTACATGG Chr3:135055130..135055149 60.13 50
upstream ENSMUSE00000586686 Chr3:135055125..135055213 CAGCACATTGGCTTACATGG Chr3:135055130..135055149 60.13 50
upstream ENSMUSE00000705515 Chr3:135055125..135055172 CAGCACATTGGCTTACATGG Chr3:135055130..135055149 60.13 50
upstream ENSMUSE00000586685 Chr3:135055661..135056046 ACCCACTGCGACAGTTTACC Chr3:135055824..135055843 60.03 55
upstream ENSMUSE00000462005 Chr3:135056924..135057032 GAATGTTTTTCAGCCGCTTC Chr3:135056956..135056975 59.83 45
upstream ENSMUSE00000464747 Chr3:135057808..135057944 TGGGTTTGGCACTATCTGTTC Chr3:135057826..135057846 59.99 47.62

*** Putative Vector Insertion (Chr 3: 135057945 - 135060559) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TAATAATCGCCTTGCAGCAC Chr3:135057993..135058013 58.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGATCCCTAAAGCTACAGTCCA Chr3:135057923..135057945 59.62 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000050150