Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1901
Trapped Gene
Hnrnpul1 (ENSMUSG00000040725)
Vector Insertion
Chr 7: 26511923 - 26518034
Public Clones AR0147 (sanger) AY0354 (sanger)
Private Clones OST432578 (lexicon)
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000313137 (Chr7:26518035..26518163 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCCTCAACCGTCTTATTCA Chr7:26518075..26518094 59.27 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000313137 (Chr7:26518035..26518163 -)
Downstram Exon
ENSMUSE00000313129 (Chr7:26511754..26511922 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCCTCAACCGTCTTATTCA Chr7:26518075..26518094 59.27 45 GTCTCTGGGCTGACCCATAA Chr7:26511873..26511892 60.07 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000457808 Chr7:26539360..26539720 ACAACAACGAGGAGGTCGAG Chr7:26539460..26539479 60.3 55
upstream ENSMUSE00000676624 Chr7:26539360..26539749 GGTTACCTGGGCACAACAAC Chr7:26539472..26539491 60.28 55
upstream ENSMUSE00000313197 Chr7:26535884..26536009 CGAGACACCAGTCATCAAGC Chr7:26535953..26535972 59.42 55
upstream ENSMUSE00000313188 Chr7:26533342..26533495 GTACTTCGAGCACCGAGAGG Chr7:26533349..26533368 60.01 60
upstream ENSMUSE00000313182 Chr7:26531367..26531440 CTCAGCCTCCTGCTGAAGAG Chr7:26531410..26531429 60.42 60
upstream ENSMUSE00000313175 Chr7:26530112..26530251 ATTGACGATTGAGGGCTTTG Chr7:26530180..26530199 60.07 45
upstream ENSMUSE00000313167 Chr7:26527946..26528045 CTCCGTGAAGCATCTTCCAT Chr7:26528012..26528031 60.22 50
upstream ENSMUSE00000313159 Chr7:26525847..26525959 AACGATGTGATTGGCTGCTT Chr7:26525851..26525870 60.67 45
upstream ENSMUSE00000676620 Chr7:26521616..26521780 AATTGCAGGTGTGAGCCATT Chr7:26521754..26521773 60.53 45
upstream ENSMUSE00000313151 Chr7:26519578..26519844 ACCAAGAATGGCAAGTGGAT Chr7:26519789..26519808 59.41 45
upstream ENSMUSE00000313143 Chr7:26518263..26518385 CTGGGTACCAATGCCATCAT Chr7:26518276..26518295 60.6 50
upstream ENSMUSE00000313137 Chr7:26518035..26518163 TGCCTCAACCGTCTTATTCA Chr7:26518075..26518094 59.27 45

*** Putative Vector Insertion (Chr 7: 26511923 - 26518034) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000313129 Chr7:26511754..26511922 GTCTCTGGGCTGACCCATAA Chr7:26511873..26511892 60.07 55
downstream ENSMUSE00000313124 Chr7:26510943..26511233 TCGTTGTATTGCCTCACCAG Chr7:26511112..26511131 59.72 50
downstream ENSMUSE00000313118 Chr7:26509574..26509863 CCTCGGTTGTTGGAGTTGTT Chr7:26509757..26509776 60.01 50
downstream ENSMUSE00000313111 Chr7:26507825..26508016 GGGCCATAGCTCCCATAGTT Chr7:26507885..26507904 60.31 55
downstream ENSMUSE00000395476 Chr7:26506517..26507382 TCCAACTGAACAGACGCTTG Chr7:26506535..26506554 60.03 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGGGGTGGAAACGTAGTCAT Chr7:26514982..26515003 60.24 52.38 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGATGGTTTCCCTCGTGACT Chr7:26514976..26514996 60.51 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040725