Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28357
Trapped Gene
Cdk8 (ENSMUSG00000029635)
Vector Insertion
Chr 5: 147071157 - 147079790
Public Clones (sanger) (sanger) (sanger) (sanger) IST12755F10 (tigm) IST15054A7 (tigm)
IST10906F9 (tigm) IST14842F4 (tigm) IST14888C11 (tigm) IST11968F10 (tigm)
IST14445D5 (tigm) IST11529B5 (tigm) IST15088E9 (tigm) IST14135B1 (tigm)
Private Clones OST32975 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000684565 (Chr5:147071081..147071156 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTCGGCATGCAGAGAGATA Chr5:147071134..147071153 60.53 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000684565 (Chr5:147071081..147071156 +)
Downstram Exon
ENSMUSE00000684568 (Chr5:147079791..147079862 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTCGGCATGCAGAGAGATA Chr5:147071134..147071153 60.53 50 TTCCGATCAGCATGAGACAG Chr5:147079864..147079883 59.94 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000684566 Chr5:147042826..147042910 No primer for this exon
upstream ENSMUSE00000684569 Chr5:147042961..147043396 CACTTACGGGCACGTCTACA Chr5:147043358..147043377 59.78 55
upstream ENSMUSE00000453178 Chr5:147043251..147043396 CACTTACGGGCACGTCTACA Chr5:147043358..147043377 59.78 55
upstream ENSMUSE00000452610 Chr5:147071081..147071156 TGTCGGCATGCAGAGAGATA Chr5:147071134..147071153 60.53 50
upstream ENSMUSE00000684565 Chr5:147071081..147071156 TGTCGGCATGCAGAGAGATA Chr5:147071134..147071153 60.53 50

*** Putative Vector Insertion (Chr 5: 147071157 - 147079790) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000452605 Chr5:147079791..147079901 TTCCGATCAGCATGAGACAG Chr5:147079864..147079883 59.94 50
downstream ENSMUSE00000684568 Chr5:147079791..147079862 TTCCGATCAGCATGAGACAG Chr5:147079864..147079883 59.94 50
downstream ENSMUSE00000452599 Chr5:147083171..147083311 GTTGGCTTTCGAAGCTCTGT Chr5:147083209..147083228 59.62 50
downstream ENSMUSE00000684567 Chr5:147083171..147083240 GTTGGCTTTCGAAGCTCTGT Chr5:147083209..147083228 59.62 50
downstream ENSMUSE00000452594 Chr5:147095205..147095262 GCTCAGGACCTTCACCCATA Chr5:147095247..147095266 60.07 55
downstream ENSMUSE00000452593 Chr5:147097684..147097815 CGCTCCGAGGAGTAATTCTG Chr5:147097796..147097815 59.97 55
downstream ENSMUSE00000452591 Chr5:147104200..147104343 TGCAGGGAATCCCATTACAT Chr5:147104345..147104364 60.15 45
downstream ENSMUSE00000684564 Chr5:147104215..147104343 TGCAGGGAATCCCATTACAT Chr5:147104345..147104364 60.15 45
downstream ENSMUSE00000684562 Chr5:147106486..147106808 GTTGAATGTTCGGGCATCTT Chr5:147106784..147106803 59.94 45
downstream ENSMUSE00000452590 Chr5:147106739..147106808 GTTGAATGTTCGGGCATCTT Chr5:147106784..147106803 59.94 45
downstream ENSMUSE00000190928 Chr5:147107935..147108007 TTGATAAGGCTGCAATTGGT Chr5:147107961..147107980 58.24 40
downstream ENSMUSE00000190917 Chr5:147110379..147110476 GCCTGCTCTGAGGTAATTCG Chr5:147110434..147110453 59.98 55
downstream ENSMUSE00000190935 Chr5:147111074..147111152 TCGTTTGGGATATGGGATCT Chr5:147111113..147111132 59.2 45
downstream ENSMUSE00000190931 Chr5:147111268..147111426 GCCAGTTCCGTTAGTGTGGT Chr5:147111318..147111337 60.03 55
downstream ENSMUSE00000333428 Chr5:147113152..147114395 AGCTACCACCCCAATCTGTG Chr5:147113440..147113459 59.99 55
downstream ENSMUSE00000684563 Chr5:147113152..147114407 AGCTACCACCCCAATCTGTG Chr5:147113440..147113459 59.99 55
downstream ENSMUSE00000684571 Chr5:147113152..147114450 AGCTACCACCCCAATCTGTG Chr5:147113440..147113459 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATTGGTGGTGGTGTGTGTGT Chr5:147071134..147071154 59.6 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATTGGTGGTGGTGTGTGTGT Chr5:147071134..147071154 59.6 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029635