Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9458
Trapped Gene
Slc30a6 (ENSMUSG00000024069)
Vector Insertion
Chr 17: 74803429 - 74805024
Public Clones RRD082 (baygenomics)
Private Clones OST91016 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000394914 (Chr17:74803344..74803428 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTTCTGTTCGGTGCAATCAA Chr17:74803356..74803375 59.84 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000394914 (Chr17:74803344..74803428 +)
Downstram Exon
ENSMUSE00000369221 (Chr17:74805025..74805067 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTTCTGTTCGGTGCAATCAA Chr17:74803356..74803375 59.84 45 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000692249 Chr17:74794972..74795008 GCTGTACGGCTCCTTACCAT Chr17:74794988..74795007 59.22 55
upstream ENSMUSE00000383604 Chr17:74801252..74801338 TAGACTTGTCGCAGCTGACC Chr17:74801314..74801333 59.19 55
upstream ENSMUSE00000394914 Chr17:74803344..74803428 CTTCTGTTCGGTGCAATCAA Chr17:74803356..74803375 59.84 45

*** Putative Vector Insertion (Chr 17: 74803429 - 74805024) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000369221 Chr17:74805025..74805067 No primer for this exon
downstream ENSMUSE00000413190 Chr17:74806561..74806626 AGACAGGGCTAGGTTTCCTCA Chr17:74806618..74806638 60.25 52.38
downstream ENSMUSE00000367165 Chr17:74808186..74808266 CCCAATTGTGCCAAGACAGT Chr17:74808245..74808264 60.95 50
downstream ENSMUSE00000338492 Chr17:74808693..74808728 No primer for this exon
downstream ENSMUSE00000375948 Chr17:74809674..74809768 GCATCGTGAACAGGTTGAAA Chr17:74809732..74809751 59.7 45
downstream ENSMUSE00000335967 Chr17:74811614..74811662 TCCTGAAGCCAGCTCGTACT Chr17:74811641..74811660 60.16 55
downstream ENSMUSE00000137945 Chr17:74811947..74812066 CTGGGATAAGGCCACACAAG Chr17:74811969..74811988 60.51 55
downstream ENSMUSE00000137950 Chr17:74814960..74815062 TACATGGTGCCAAACGTCAT Chr17:74815028..74815047 59.85 45
downstream ENSMUSE00000137948 Chr17:74817960..74818007 No primer for this exon
downstream ENSMUSE00000137946 Chr17:74818872..74818940 CTAGCACCCCATCCAAGGTA Chr17:74818899..74818918 59.95 55
downstream ENSMUSE00000656979 Chr17:74822357..74823569 AAGGACCATTTGTTCGTTCG Chr17:74822413..74822432 59.97 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAACAGCATCGGTATGTTGC Chr17:74803419..74803439 60.14 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAACAGCATCGGTATGTTGC Chr17:74803419..74803439 60.14 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024069