Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI33553
Trapped Gene
Cdc2l6 (ENSMUSG00000038481)
Vector Insertion
Chr 10: 40156019 - 40173820
Public Clones IST13571D6 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 33% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000614593 (Chr10:40155878..40156018 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATTACCTCCACGCAAACTGG Chr10:40155981..40156000 59.99 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000614593 (Chr10:40155878..40156018 +)
Downstram Exon
ENSMUSE00000614592 (Chr10:40173821..40173878 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATTACCTCCACGCAAACTGG Chr10:40155981..40156000 59.99 50 TTTTGACTCTCCCCCTTTCA Chr10:40173878..40173897 59.64 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000488186 Chr10:40069114..40069527 ATGATTTCAAGGCGAAGCTG Chr10:40069407..40069426 60.35 45
upstream ENSMUSE00000483776 Chr10:40114131..40114206 CAAATCGAAGGCACAGGAAT Chr10:40114159..40114178 60.07 45
upstream ENSMUSE00000614594 Chr10:40154110..40154220 TGGCTGCTGTTTGACTATGC Chr10:40154185..40154204 60.02 50
upstream ENSMUSE00000614593 Chr10:40155878..40156018 ATTACCTCCACGCAAACTGG Chr10:40155981..40156000 59.99 50

*** Putative Vector Insertion (Chr 10: 40156019 - 40173820) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000614592 Chr10:40173821..40173878 TTTTGACTCTCCCCCTTTCA Chr10:40173878..40173897 59.64 45
downstream ENSMUSE00000498551 Chr10:40186444..40186575 CTGGATCCAAATCTGCGAGT Chr10:40186509..40186528 60.22 50
downstream ENSMUSE00000614591 Chr10:40189385..40189528 No primer for this exon
downstream ENSMUSE00000614590 Chr10:40189692..40189761 TTGGGTACTCTGGCATTTTTCT Chr10:40189734..40189755 60 40.91
downstream ENSMUSE00000614589 Chr10:40195375..40195447 GCTGTCAGGCTTGACCTTGT Chr10:40195435..40195454 60.45 55
downstream ENSMUSE00000614588 Chr10:40195963..40196060 GTTGGATCCATGGTGAGGAG Chr10:40195994..40196013 60.33 55
downstream ENSMUSE00000614587 Chr10:40196695..40196773 CTTTTGGGGTACGGAATCTG Chr10:40196733..40196752 59.42 50
downstream ENSMUSE00000614586 Chr10:40197508..40197774 GATAATCCGACGGCATAACG Chr10:40197775..40197794 60.31 50
downstream ENSMUSE00000614585 Chr10:40199481..40203624 TTGATCAGCGTGACTCCTTG Chr10:40200465..40200484 59.98 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGTTGACTAATCGCCTTGC Chr10:40171062..40171082 58.92 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTGCTTTTGTTGACCGTGA Chr10:40171055..40171075 60.43 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000038481