Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8849
Trapped Gene
AC137156.3-201 (ENSMUSG00000052414)
Vector Insertion
Chr 15: 102377699 - 102378203
Public Clones XM081 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 53% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000415843 (Chr15:102378204..102378303 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTCCCTCTCGTCATGCATCT Chr15:102378268..102378287 60.37 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000415843 (Chr15:102378204..102378303 -)
Downstram Exon
ENSMUSE00000415840 (Chr15:102377585..102377698 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTCCCTCTCGTCATGCATCT Chr15:102378268..102378287 60.37 55 TTTGGCTTCTGACGGCATAG Chr15:102377566..102377585 61.29 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000678169 Chr15:102455793..102455852 No primer for this exon
upstream ENSMUSE00000678181 Chr15:102455470..102455519 AGGACTGAAGTGTGGGGAGA Chr15:102455477..102455496 59.68 55
upstream ENSMUSE00000678179 Chr15:102424103..102424171 GACAGACCGTTTGTGTGCAG Chr15:102424122..102424141 60.36 55
upstream ENSMUSE00000415854 Chr15:102393745..102393841 CGAACGGACTCAGTCATCATT Chr15:102393749..102393769 60.13 47.62
upstream ENSMUSE00000415868 Chr15:102387891..102388009 GTGGGGCTCTTCAATGAACT Chr15:102387946..102387965 59.14 50
upstream ENSMUSE00000415850 Chr15:102384215..102384352 GTCCTGCTTCTAGCCCCTGT Chr15:102384236..102384255 60.79 60
upstream ENSMUSE00000415847 Chr15:102381835..102381992 CCATCCAACAGGCAAATAGG Chr15:102381835..102381854 60.32 50
upstream ENSMUSE00000415843 Chr15:102378204..102378303 CTCCCTCTCGTCATGCATCT Chr15:102378268..102378287 60.37 55

*** Putative Vector Insertion (Chr 15: 102377699 - 102378203) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000415840 Chr15:102377585..102377698 TTTGGCTTCTGACGGCATAG Chr15:102377566..102377585 61.29 50
downstream ENSMUSE00000415836 Chr15:102376836..102376988 GTGCTGGATGAGGATCTGGT Chr15:102376844..102376863 60.08 55
downstream ENSMUSE00000415833 Chr15:102371171..102371368 TGCAGCTCTGTTTCGCTCTA Chr15:102371239..102371258 60.03 50
downstream ENSMUSE00000645707 Chr15:102368614..102368722 GAGCCACCTCATTGCGTAGT Chr15:102368667..102368686 60.28 55
downstream ENSMUSE00000678168 Chr15:102367085..102368722 CCAGGTACACGAGACAGCAA Chr15:102367528..102367547 59.9 55
downstream ENSMUSE00000645706 Chr15:102364056..102364869 TTCAGCTGCAGATCGAACAC Chr15:102364741..102364760 60.14 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGCCAAACCTACCAGCACAC Chr15:102378163..102378183 60.18 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGCCAAACCTACCAGCACAC Chr15:102378163..102378183 60.18 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000052414