Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI34140
Trapped Gene
Abhd6 (ENSMUSG00000025277)
Vector Insertion
Chr 14: 8860904 - 8872261
Public Clones IST12061D7 (tigm) IST11960F7 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000390530 (Chr14:8860751..8860903 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAGGTGTCAACAAGGCTCAA Chr14:8860757..8860776 59.87 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000390530 (Chr14:8860751..8860903 +)
Downstram Exon
ENSMUSE00000306381 (Chr14:8872262..8872418 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAGGTGTCAACAAGGCTCAA Chr14:8860757..8860776 59.87 50 GTCCTTGTGTGCGGAGAATC Chr14:8872400..8872419 60.67 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000350253 Chr14:8835457..8835477 No primer for this exon
upstream ENSMUSE00000390530 Chr14:8860751..8860903 CAGGTGTCAACAAGGCTCAA Chr14:8860757..8860776 59.87 50

*** Putative Vector Insertion (Chr 14: 8860904 - 8872261) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000306381 Chr14:8872262..8872418 GTCCTTGTGTGCGGAGAATC Chr14:8872400..8872419 60.67 55
downstream ENSMUSE00000149485 Chr14:8873633..8873746 ACTTGCCCCACTATGGACAG Chr14:8873733..8873752 59.99 55
downstream ENSMUSE00000149483 Chr14:8875208..8875340 AGCAGGACACACGAGAGACA Chr14:8875342..8875361 59.6 55
downstream ENSMUSE00000149487 Chr14:8877982..8878139 CCTTGAAGCGGACATAGGAG Chr14:8878131..8878150 59.83 55
downstream ENSMUSE00000149484 Chr14:8882088..8882142 GAATGCGAACATCGACAAGA Chr14:8882121..8882140 59.81 45
downstream ENSMUSE00000149480 Chr14:8882322..8882422 CTGTGTCGGGACCTTGATCT Chr14:8882401..8882420 60.11 55
downstream ENSMUSE00000149481 Chr14:8887985..8888423 CTACCGAATGGCCACAGTTT Chr14:8888075..8888094 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GATATAATCGCCTTGCAGCAC Chr14:8869951..8869972 59.72 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTAACCATATCGCCATTCG Chr14:8869937..8869957 59.4 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025277