Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9938
Trapped Gene
AC166359.3 (ENSMUSG00000047146)
Vector Insertion
Chr 10: 62296377 - 62300923
Public Clones XD006 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 4% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000666241 (Chr10:62300924..62300993 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCTGGATTGAAGGAACAGGA Chr10:62300944..62300963 60.19 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000666241 (Chr10:62300924..62300993 -)
Downstram Exon
ENSMUSE00000643009 (Chr10:62296286..62296376 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCTGGATTGAAGGAACAGGA Chr10:62300944..62300963 60.19 50 GTCTCCATGAGCTCCCTGAC Chr10:62296267..62296286 59.8 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000666241 Chr10:62300924..62300993 GCTGGATTGAAGGAACAGGA Chr10:62300944..62300963 60.19 50

*** Putative Vector Insertion (Chr 10: 62296377 - 62300923) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000643009 Chr10:62296286..62296376 GTCTCCATGAGCTCCCTGAC Chr10:62296267..62296286 59.8 60
downstream ENSMUSE00000238699 Chr10:62295642..62295735 CCTTCCCCGTGAACACTATC Chr10:62295658..62295677 59.4 55
downstream ENSMUSE00000643008 Chr10:62285297..62285508 TGGTCTACACGCTCACGAAC Chr10:62285425..62285444 59.9 55
downstream ENSMUSE00000643006 Chr10:62282221..62282371 CCGTTGAAATACATGCTCCA Chr10:62282263..62282282 59.54 45
downstream ENSMUSE00000666240 Chr10:62281687..62281782 GTCTTGCGGTCTGGAATGAT Chr10:62281681..62281700 60.08 50
downstream ENSMUSE00000643005 Chr10:62279132..62279221 TGGAGCCATCTGCTTGTAAA Chr10:62279128..62279147 59.42 45
downstream ENSMUSE00000643003 Chr10:62277184..62277321 AATCCATGCAACAGGTGACA Chr10:62277215..62277234 59.97 45
downstream ENSMUSE00000643002 Chr10:62276349..62276572 TTGTTCATCCTCGGGACAAT Chr10:62276494..62276513 60.32 45
downstream ENSMUSE00000612637 Chr10:62276326..62276346 No primer for this exon
downstream ENSMUSE00000666239 Chr10:62275466..62276174 TCGGCGTAGATCTCCTCACT Chr10:62275637..62275656 59.97 55
downstream ENSMUSE00000351741 Chr10:62275115..62276160 TCGGCGTAGATCTCCTCACT Chr10:62275637..62275656 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGTTTGCTTTGGGGTCATC Chr10:62297926..62297946 59.53 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGTTTGCTTTGGGGTCATC Chr10:62297926..62297946 59.53 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000047146