Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI35686
Trapped Gene
3200002M19Rik (ENSMUSG00000030649)
Vector Insertion
Chr 7: 109047707 - 109047995
Public Clones IST14862H10 (tigm) IST12266C8 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 88% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000370783 (Chr7:109047708..109047994 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGGATCAGGACCAGTGGATG Chr7:109047730..109047749 59.92 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000370783 (Chr7:109047708..109047994 +)
Downstram Exon
ENSMUSE00000671733 (Chr7:109047708..109048054 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGGATCAGGACCAGTGGATG Chr7:109047730..109047749 59.92 55 GAGGGCTAGAAAGGGACCAC Chr7:109048028..109048047 60.07 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000671730 Chr7:109029839..109029916 GGCTGGAAGAGAACATCACC Chr7:109029857..109029876 59.66 55
upstream ENSMUSE00000671738 Chr7:109044854..109044964 GTGGGTTCTTCCGCTCAGAC Chr7:109044898..109044917 62.16 60
upstream ENSMUSE00000671721 Chr7:109044930..109044964 No primer for this exon
upstream ENSMUSE00000671727 Chr7:109044942..109044964 No primer for this exon
upstream ENSMUSE00000671732 Chr7:109046246..109046331 TGGAGCCAGGACTCAAACTC Chr7:109046310..109046329 60.39 55
upstream ENSMUSE00000589945 Chr7:109046247..109046301 ATTGGCCAAAATCAAAGAGC Chr7:109046280..109046299 59.16 40
upstream ENSMUSE00000716776 Chr7:109046247..109046331 TGGAGCCAGGACTCAAACTC Chr7:109046310..109046329 60.39 55
upstream ENSMUSE00000718870 Chr7:109046247..109046331 TGGAGCCAGGACTCAAACTC Chr7:109046310..109046329 60.39 55
upstream ENSMUSE00000721871 Chr7:109046247..109046331 TGGAGCCAGGACTCAAACTC Chr7:109046310..109046329 60.39 55
upstream ENSMUSE00000528854 Chr7:109046456..109046585 CACCTTGTTCCCGTCACTCT Chr7:109046471..109046490 60.15 55
upstream ENSMUSE00000633258 Chr7:109046456..109046585 CACCTTGTTCCCGTCACTCT Chr7:109046471..109046490 60.15 55
upstream ENSMUSE00000720972 Chr7:109046456..109046585 CACCTTGTTCCCGTCACTCT Chr7:109046471..109046490 60.15 55
upstream ENSMUSE00000633259 Chr7:109046461..109046585 CACCTTGTTCCCGTCACTCT Chr7:109046471..109046490 60.15 55
upstream ENSMUSE00000222469 Chr7:109047068..109047127 CAAAGCATCGCAGAGAAAGA Chr7:109047071..109047090 59.3 45
upstream ENSMUSE00000201583 Chr7:109047414..109047551 GGATTCCGAAGATGATGAGG Chr7:109047467..109047486 59.44 50

*** Putative Vector Insertion (Chr 7: 109047707 - 109047995) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000370783 Chr7:109047708..109047994 CATCCACTGGTCCTGATCCT Chr7:109047752..109047771 59.92 55
downstream ENSMUSE00000671726 Chr7:109047708..109047755 CATCCACTGGTCCTGATCCT Chr7:109047752..109047771 59.92 55
downstream ENSMUSE00000671731 Chr7:109047708..109048057 GAGGGCTAGAAAGGGACCAC Chr7:109048028..109048047 60.07 60
downstream ENSMUSE00000671733 Chr7:109047708..109048054 GAGGGCTAGAAAGGGACCAC Chr7:109048028..109048047 60.07 60
downstream ENSMUSE00000633257 Chr7:109049446..109050359 GGTAACCAGCCACAAATGCT Chr7:109050296..109050315 60 50
downstream ENSMUSE00000671722 Chr7:109049446..109049580 TTCATGAGGGACTCCCATTC Chr7:109049552..109049571 59.86 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGGATCAGGACCAGTGGATG Chr7:109047731..109047751 59.92 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTAGGCGTGACTGGGAAAAC Chr7:109047753..109047773 59.73 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030649