Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9062
Trapped Gene
AC166359.3 (ENSMUSG00000047146)
Vector Insertion
Chr 10: 62279222 - 62281686
Public Clones XK152 (baygenomics)
Private Clones OST360057 (lexicon)
Severity of mutation (?) Insertion after 38% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000666240 (Chr10:62281687..62281782 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATCATTCCAGACCGCAAGAC Chr10:62281703..62281722 60.08 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000666240 (Chr10:62281687..62281782 -)
Downstram Exon
ENSMUSE00000643005 (Chr10:62279132..62279221 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATCATTCCAGACCGCAAGAC Chr10:62281703..62281722 60.08 50 TGGAGCCATCTGCTTGTAAA Chr10:62279128..62279147 59.42 45

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
upstream ENSMUSE00000643009 Chr10:62296286..62296376 GTCAGGGAGCTCATGGAGAC Chr10:62296289..62296308 59.8 60
upstream ENSMUSE00000238699 Chr10:62295642..62295735 GATAGTGTTCACGGGGAAGG Chr10:62295680..62295699 59.4 55
upstream ENSMUSE00000643008 Chr10:62285297..62285508 GTTCGTGAGCGTGTAGACCA Chr10:62285447..62285466 59.9 55
upstream ENSMUSE00000643006 Chr10:62282221..62282371 GAGGAGTGAAAACCCCAGAA Chr10:62282253..62282272 59.11 50
upstream ENSMUSE00000666240 Chr10:62281687..62281782 ATCATTCCAGACCGCAAGAC Chr10:62281703..62281722 60.08 50

*** Putative Vector Insertion (Chr 10: 62279222 - 62281686) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TATAATCGCCTTGCAGCACA Chr10:62281617..62281637 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000047146