Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14581
Trapped Gene
Cks1b (ENSMUSG00000028044)
Vector Insertion
Chr 3: 89220195 - 89221940
Public Clones FHCRC-GT-S8-1H1 (fhcrc)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000673064 (Chr3:89221709..89221939 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTGGACGGAGGATGTAAAA Chr3:89221877..89221896 59.79 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000673064 (Chr3:89221709..89221939 -)
Downstram Exon
ENSMUSE00000673062 (Chr3:89220196..89220323 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTGGACGGAGGATGTAAAA Chr3:89221877..89221896 59.79 50 TAGTGGACCCATCCCTGACT Chr3:89220191..89220210 59.38 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000175427 Chr3:89222077..89222200 ATACGACGACGAGGAGTTCG Chr3:89222084..89222103 60.28 55
upstream ENSMUSE00000673064 Chr3:89221709..89221939 GGTGGACGGAGGATGTAAAA Chr3:89221877..89221896 59.79 50
upstream ENSMUSE00000566837 Chr3:89220196..89220323 CCGAAAACCCATCTGATGTC Chr3:89220267..89220286 60.32 50
upstream ENSMUSE00000673062 Chr3:89220196..89220323 CCGAAAACCCATCTGATGTC Chr3:89220267..89220286 60.32 50

*** Putative Vector Insertion (Chr 3: 89220195 - 89221940) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000507910 Chr3:89219479..89219885 CACGTCAGCAAATTCACACC Chr3:89219506..89219525 60.16 50
downstream ENSMUSE00000175425 Chr3:89219396..89219885 CACGTCAGCAAATTCACACC Chr3:89219506..89219525 60.16 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGATTGGGTACAGCAGCAAA Chr3:89221909..89221929 61.03 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTGGACGTGACTGGGAAAAC Chr3:89221874..89221894 60.41 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028044