Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI15559
Trapped Gene
Hnrnpu (ENSMUSG00000039630)
Vector Insertion
Chr 1: 180260295 - 180260978
Public Clones PST3688-NR (escells)
Private Clones OST101327 (lexicon)
Severity of mutation (?) Insertion after 87% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000320702 (Chr1:180260723..180260977 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AACAGAGGTGGTGGCCATAG Chr1:180260770..180260789 59.99 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000320702 (Chr1:180260723..180260977 -)
Downstram Exon
ENSMUSE00000320695 (Chr1:180260296..180260477 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AACAGAGGTGGTGGCCATAG Chr1:180260770..180260789 59.99 55 TAGCCAATTCCACCACTTCC Chr1:180260374..180260393 59.93 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000591904 Chr1:180267084..180267915 GGCCCTCAACATGAGTTCTT Chr1:180267693..180267712 59.14 50
upstream ENSMUSE00000320768 Chr1:180266178..180266289 CGTTAAAAGACCGCGAGAAG Chr1:180266227..180266246 60.01 50
upstream ENSMUSE00000320763 Chr1:180266013..180266086 TCAGCCACCTGTTGAAGAAG Chr1:180266055..180266074 59.01 50
upstream ENSMUSE00000320756 Chr1:180264018..180264157 CGAGAGACCGTCTGAGTGCT Chr1:180264111..180264130 60.76 60
upstream ENSMUSE00000320749 Chr1:180263678..180263777 CGGATTGGCTGGTCACTAAC Chr1:180263698..180263717 60.52 55
upstream ENSMUSE00000320744 Chr1:180263128..180263240 No primer for this exon
upstream ENSMUSE00000320736 Chr1:180262224..180262487 TCCCCTTAGAGGACCGAGTT Chr1:180262263..180262282 60.07 55
upstream ENSMUSE00000320726 Chr1:180261966..180262085 AGCTGAAAACCCTGGGAAAT Chr1:180262007..180262026 59.94 45
upstream ENSMUSE00000320719 Chr1:180261480..180261608 ATTGAAATTGCTGCCCGTAA Chr1:180261505..180261524 60.46 40
upstream ENSMUSE00000320707 Chr1:180261224..180261392 AGGGGAAGGACCTACCAGAA Chr1:180261246..180261265 59.93 55
upstream ENSMUSE00000320702 Chr1:180260723..180260977 AACAGAGGTGGTGGCCATAG Chr1:180260770..180260789 59.99 55
upstream ENSMUSE00000320695 Chr1:180260296..180260477 GCCGAGGTGGTTACTCAAAC Chr1:180260347..180260366 59.6 55

*** Putative Vector Insertion (Chr 1: 180260295 - 180260978) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000320688 Chr1:180259999..180260070 GCCACGATTATTTCCTCGTC Chr1:180260019..180260038 59.53 50
downstream ENSMUSE00000591898 Chr1:180258431..180259538 TGCACAATGCTGAGGTTCTC Chr1:180259241..180259260 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTTCCAGAGGTTGCAGAAT Chr1:180260946..180260966 59.28 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTTCCAGAGGTTGCAGAAT Chr1:180260946..180260966 59.28 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GAGGTGGCAATTTCAGAGGA Chr1:180260725..180260745 60.19 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GAGGTGGCAATTTCAGAGGA Chr1:180260725..180260745 60.19 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039630