Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13079
Trapped Gene
Nthl1 (ENSMUSG00000041429)
Vector Insertion
Chr 17: 24769800 - 24770871
Public Clones CMHD-GT_342C6-3 (cmhd) IST11081H6 (tigm)
Private Clones OST292892 (lexicon) OST285876 (lexicon) OST232616 (lexicon) OST102472 (lexicon)
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000302711 (Chr17:24769655..24769799 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGCTGCTCGGAGGAGTAGTT Chr17:24769665..24769684 60.92 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000302711 (Chr17:24769655..24769799 +)
Downstram Exon
ENSMUSE00000302698 (Chr17:24770872..24771110 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGCTGCTCGGAGGAGTAGTT Chr17:24769665..24769684 60.92 60 CTTCGCCTTCCTCACCATTA Chr17:24770967..24770986 60.21 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000302711 Chr17:24769655..24769799 GGCTGCTCGGAGGAGTAGTT Chr17:24769665..24769684 60.92 60

*** Putative Vector Insertion (Chr 17: 24769800 - 24770871) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000302698 Chr17:24770872..24771110 CTTCGCCTTCCTCACCATTA Chr17:24770967..24770986 60.21 50
downstream ENSMUSE00000302683 Chr17:24771670..24771840 GTCTGCCTAGCGTGTCATCA Chr17:24771817..24771836 60.02 55
downstream ENSMUSE00000302657 Chr17:24772533..24772692 CACAGCCATAGCCAAGTGTG Chr17:24772670..24772689 60.32 55
downstream ENSMUSE00000302632 Chr17:24775369..24775474 CACCTCAGTCGGTTGGCTAT Chr17:24775414..24775433 60.13 55
downstream ENSMUSE00000302605 Chr17:24775553..24775782 GTTGACCTCACTCCACAGCA Chr17:24775577..24775596 59.87 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAAAGGAGGAACGTGGAACTT Chr17:24769830..24769851 59.61 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGAACGTGGAACTTCGTGAC Chr17:24769837..24769857 60.56 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000041429