Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3187
Trapped Gene
Ralgps2 (ENSMUSG00000026594)
Vector Insertion
Chr 1: 158743675 - 158747871
Public Clones XR0858 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 87% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000160839 (Chr1:158747872..158747964 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACTATGCCGCCAAATCTCTG Chr1:158747893..158747912 60.24 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000160839 (Chr1:158747872..158747964 -)
Downstram Exon
ENSMUSE00000274758 (Chr1:158743569..158743674 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACTATGCCGCCAAATCTCTG Chr1:158747893..158747912 60.24 50 TTTCTCGGAGTCAGTCAGCA Chr1:158743548..158743567 59.7 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000594883 Chr1:158869620..158869664 No primer for this exon
upstream ENSMUSE00000380719 Chr1:158837770..158837909 CTATCGCAGCCACTGTTTCC Chr1:158837773..158837792 60.8 55
upstream ENSMUSE00000274849 Chr1:158831917..158832021 CTAAGCGAGAAGGGCTCTGA Chr1:158831981..158832000 59.85 55
upstream ENSMUSE00000274840 Chr1:158830717..158830767 No primer for this exon
upstream ENSMUSE00000274832 Chr1:158818078..158818161 ACCAAATGCAGTTGCTTTCA Chr1:158818095..158818114 59.32 40
upstream ENSMUSE00000274824 Chr1:158817222..158817311 TCTCCATGCTCAAACACTGAA Chr1:158817265..158817285 59.43 42.86
upstream ENSMUSE00000274813 Chr1:158814664..158814756 CCGATTTTCCGGTTGACTAA Chr1:158814674..158814693 59.93 45
upstream ENSMUSE00000274806 Chr1:158799572..158799698 TGACTCCTTGCATTCCCTATTT Chr1:158799574..158799595 59.97 40.91
upstream ENSMUSE00000537110 Chr1:158763026..158763163 TTTGCAGCAGTCCTGTGAAT Chr1:158763029..158763048 59.44 45
upstream ENSMUSE00000160836 Chr1:158762796..158762886 TGCCTCATGTCCAAAAATACC Chr1:158762854..158762874 59.81 42.86
upstream ENSMUSE00000160835 Chr1:158760516..158760583 No primer for this exon
upstream ENSMUSE00000160840 Chr1:158759103..158759259 CTCATTCCACACGGACACAG Chr1:158759127..158759146 60.15 55
upstream ENSMUSE00000160832 Chr1:158758271..158758422 CAGAGTTTAAGAGCGCAACG Chr1:158758380..158758399 58.87 50
upstream ENSMUSE00000160837 Chr1:158754122..158754176 No primer for this exon
upstream ENSMUSE00000160834 Chr1:158751518..158751595 CTATCGAAGCCACACGAAGG Chr1:158751525..158751544 60.79 55
upstream ENSMUSE00000160831 Chr1:158749944..158750049 AAGAAGGCAAGAAACCCACA Chr1:158749944..158749963 59.71 45
upstream ENSMUSE00000160839 Chr1:158747872..158747964 ACTATGCCGCCAAATCTCTG Chr1:158747893..158747912 60.24 50

*** Putative Vector Insertion (Chr 1: 158743675 - 158747871) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000274758 Chr1:158743569..158743674 TTTCTCGGAGTCAGTCAGCA Chr1:158743548..158743567 59.7 50
downstream ENSMUSE00000385090 Chr1:158741576..158741667 AGCATTGCATTCATCCTGCT Chr1:158741600..158741619 60.78 45
downstream ENSMUSE00000537039 Chr1:158738253..158739324 AAGCGAAGTTCATGGCAGTT Chr1:158739061..158739080 59.88 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGAGCAGACATGCTTACATCC Chr1:158744858..158744879 58.89 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGAGCAGACATGCTTACATCC Chr1:158744858..158744879 58.89 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026594