Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1453
Trapped Gene
Csnk1a1 (ENSMUSG00000024576)
Vector Insertion
Chr 18: 61716264 - 61727917
Public Clones (sanger) CD0565 (sanger) XF099 (baygenomics) 5SE152E03 (ggtc) 3SE152E03 (ggtc)
PST19804-NR (escells)
Private Clones OST453549 (lexicon) OST436257 (lexicon) OST434855 (lexicon) OST309378 (lexicon)
OST281818 (lexicon)
Severity of mutation (?) Insertion after 23% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000291977 (Chr18:61716157..61716263 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTTGGCATCCCTCACATAC Chr18:61716243..61716262 60.2 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000291977 (Chr18:61716157..61716263 +)
Downstram Exon
ENSMUSE00000143439 (Chr18:61727918..61728044 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTTGGCATCCCTCACATAC Chr18:61716243..61716262 60.2 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000625344 Chr18:61714993..61715527 AGCGATCAACATCACCAATG Chr18:61715503..61715522 59.53 45
upstream ENSMUSE00000291977 Chr18:61716157..61716263 GGTTGGCATCCCTCACATAC Chr18:61716243..61716262 60.2 55

*** Putative Vector Insertion (Chr 18: 61716264 - 61727917) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000143439 Chr18:61727918..61728044 No primer for this exon
downstream ENSMUSE00000143437 Chr18:61729118..61729216 GTGACGCCCAATACCCATTA Chr18:61729210..61729229 60.58 50
downstream ENSMUSE00000291907 Chr18:61735064..61735203 GCAGTGCCAGTGAGGTTTTT Chr18:61735164..61735183 60.3 50
downstream ENSMUSE00000291890 Chr18:61736161..61736239 CCACGGCAGACTGGTTCTAT Chr18:61736230..61736249 60.13 55
downstream ENSMUSE00000372299 Chr18:61736832..61736906 CACCTCAACAGGAGTGGACA Chr18:61736900..61736919 59.71 55
downstream ENSMUSE00000143442 Chr18:61738321..61738427 GCAGCCCACGACAGTAATTT Chr18:61738372..61738391 60.14 50
downstream ENSMUSE00000371770 Chr18:61739993..61740141 CTGGGCTGCTTTCTGCTTTA Chr18:61740059..61740078 60.65 50
downstream ENSMUSE00000702159 Chr18:61739993..61740105 CTGGGCTGCTTTCTGCTTTA Chr18:61740059..61740078 60.65 50
downstream ENSMUSE00000702152 Chr18:61740390..61740394 No primer for this exon
downstream ENSMUSE00000353346 Chr18:61747080..61749035 TTAGGGAAAGCTGGACATGG Chr18:61748244..61748263 60.07 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTTCACCTGTAATCGCCTTG Chr18:61725306..61725326 58.77 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTTGGCATCCCTCACATAC Chr18:61725244..61725264 60.2 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024576