Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27523
Trapped Gene
Alkbh3 (ENSMUSG00000040174)
Vector Insertion
Chr 2: 93848750 - 93850839
Public Clones not available
Private Clones OST57619 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000687190 (Chr2:93850840..93850887 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACGGCTGATTAGGGTCGTGT Chr2:93850867..93850886 61.86 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000687190 (Chr2:93850840..93850887 -)
Downstram Exon
ENSMUSE00000687189 (Chr2:93848600..93848749 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACGGCTGATTAGGGTCGTGT Chr2:93850867..93850886 61.86 55 TCAGACCAAGGGATGGCTAC Chr2:93848708..93848727 60.07 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000687186 Chr2:93850840..93850964 GGAGTTGGTGCCTCACTCTG Chr2:93850906..93850925 60.86 60
upstream ENSMUSE00000687190 Chr2:93850840..93850887 ACGGCTGATTAGGGTCGTGT Chr2:93850867..93850886 61.86 55

*** Putative Vector Insertion (Chr 2: 93848750 - 93850839) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000687189 Chr2:93848600..93848749 TCAGACCAAGGGATGGCTAC Chr2:93848708..93848727 60.07 55
downstream ENSMUSE00000336216 Chr2:93848581..93848749 TCAGACCAAGGGATGGCTAC Chr2:93848708..93848727 60.07 55
downstream ENSMUSE00000391510 Chr2:93848196..93848283 CAAATTGTCGGTCACATTGC Chr2:93848194..93848213 59.97 45
downstream ENSMUSE00000687188 Chr2:93848196..93848299 CAAATTGTCGGTCACATTGC Chr2:93848194..93848213 59.97 45
downstream ENSMUSE00000401397 Chr2:93847004..93847038 No primer for this exon
downstream ENSMUSE00000384525 Chr2:93844890..93844937 No primer for this exon
downstream ENSMUSE00000351013 Chr2:93843210..93843313 CCAGGGGACATCCTTACAAA Chr2:93843213..93843232 59.78 50
downstream ENSMUSE00000387408 Chr2:93841582..93841670 GAAGCTCTCCATACCATGCTG Chr2:93841601..93841621 59.85 52.38
downstream ENSMUSE00000295381 Chr2:93836340..93836549 TTCTCTTCAATGCGGCTCTT Chr2:93836484..93836503 60.1 45
downstream ENSMUSE00000295377 Chr2:93821673..93821771 TGGCTCCTTCCATGATTAGC Chr2:93821668..93821687 60.18 50
downstream ENSMUSE00000352091 Chr2:93820794..93821134 AGAAGCAAACACCACGCTTT Chr2:93820909..93820928 59.92 45
downstream ENSMUSE00000687184 Chr2:93820707..93821134 AGAAGCAAACACCACGCTTT Chr2:93820909..93820928 59.92 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACGGCTGATTAGGGTCGTGT Chr2:93850865..93850885 61.86 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACGGCTGATTAGGGTCGTGT Chr2:93850865..93850885 61.86 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040174