Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI17546
Trapped Gene
Cdk7 (ENSMUSG00000069089)
Vector Insertion
Chr 13: 101489326 - 101490540
Public Clones IST14841F7 (tigm)
Private Clones OST440842 (lexicon) OST353692 (lexicon) OST244925 (lexicon) OST129081 (lexicon)
OST67775 (lexicon)
Severity of mutation (?) Insertion after 22% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000569288 (Chr13:101490541..101490608 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000569288 (Chr13:101490541..101490608 -)
Downstram Exon
ENSMUSE00000569286 (Chr13:101489257..101489325 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon TGTCCAAATGCATCAAGGAG Chr13:101489284..101489303 59.65 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000569295 Chr13:101500729..101500878 TCGGACGCTTTAAATTCCTG Chr13:101500843..101500862 60.2 45
upstream ENSMUSE00000569293 Chr13:101500413..101500472 ACCAAATCGTCGCCATTAAG Chr13:101500416..101500435 59.96 45
upstream ENSMUSE00000569289 Chr13:101492635..101492668 No primer for this exon
upstream ENSMUSE00000569288 Chr13:101490541..101490608 No primer for this exon

*** Putative Vector Insertion (Chr 13: 101489326 - 101490540) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000569286 Chr13:101489257..101489325 TGTCCAAATGCATCAAGGAG Chr13:101489284..101489303 59.65 45
downstream ENSMUSE00000569283 Chr13:101487527..101487637 TCAGCACAAGGCTGTTATCCT Chr13:101487585..101487605 59.89 47.62
downstream ENSMUSE00000569281 Chr13:101486456..101486574 GCCAAAATCTGCCAGTTTCA Chr13:101486490..101486509 61.15 45
downstream ENSMUSE00000569278 Chr13:101481452..101481551 CCCACATGTCTACTCCCACA Chr13:101481465..101481484 59.39 55
downstream ENSMUSE00000569276 Chr13:101480029..101480115 TCTCCAGGCAAAAATGGAAC Chr13:101480074..101480093 60.05 45
downstream ENSMUSE00000569275 Chr13:101476322..101476471 AAGAACAGGCCTTGGATGAG Chr13:101476334..101476353 59.28 50
downstream ENSMUSE00000569272 Chr13:101474346..101474493 TCTGCTCTTTTCCGCTTTGT Chr13:101474338..101474357 60.13 45
downstream ENSMUSE00000640048 Chr13:101473270..101473461 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AATTAATCGCCTTGCAGCAC Chr13:101490472..101490492 60.24 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAAGTAATCGCCTTGCAGCAC Chr13:101490541..101490562 60.41 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000069089