Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI11714
Trapped Gene
Cdk7 (ENSMUSG00000069089)
Vector Insertion
Chr 13: 101500473 - 101500728
Public Clones M119H07 (ggtc) PST17500-NR (escells) IST11018F1 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 6% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000569295 (Chr13:101500729..101500878 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCGGACGCTTTAAATTCCTG Chr13:101500843..101500862 60.2 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000569295 (Chr13:101500729..101500878 -)
Downstram Exon
ENSMUSE00000569293 (Chr13:101500413..101500472 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCGGACGCTTTAAATTCCTG Chr13:101500843..101500862 60.2 45 CTTAATGGCGACGATTTGGT Chr13:101500394..101500413 59.96 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

*** Putative Vector Insertion (Chr 13: 101500473 - 101500728) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000569293 Chr13:101500413..101500472 CTTAATGGCGACGATTTGGT Chr13:101500394..101500413 59.96 45
downstream ENSMUSE00000569289 Chr13:101492635..101492668 No primer for this exon
downstream ENSMUSE00000569288 Chr13:101490541..101490608 No primer for this exon
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 GCGAAGCGCTATGAGAAACT Chr13:101500749..101500769 59.76 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCGAAGCGCTATGAGAAACT Chr13:101500749..101500769 59.76 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GTAGCTGTTGGGCAGCTTTC Chr13:101500859..101500879 60.02 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GTAGCTGTTGGGCAGCTTTC Chr13:101500859..101500879 60.02 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000069089