Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5537
Trapped Gene
Cdk7 (ENSMUSG00000069089)
Vector Insertion
Chr 13: 101490609 - 101492634
Public Clones (sanger) (sanger) (sanger) (sanger) (sanger) (sanger)
YTA130 (baygenomics) RRJ012 (baygenomics) XK283 (baygenomics)
Private Clones OST442367 (lexicon) OST391705 (lexicon) OST388257 (lexicon) OST383099 (lexicon)
OST347838 (lexicon) OST283415 (lexicon) OST282978 (lexicon) OST246044 (lexicon)
OST245165 (lexicon) OST244888 (lexicon) OST207954 (lexicon) OST184292 (lexicon)
OST138541 (lexicon) OST105600 (lexicon) OST67776 (lexicon)
Severity of mutation (?) Insertion after 15% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000569289 (Chr13:101492635..101492668 -)
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
ENSMUSE00000569289 (Chr13:101492635..101492668 -)
Downstram Exon
ENSMUSE00000569288 (Chr13:101490541..101490608 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

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

*** Putative Vector Insertion (Chr 13: 101490609 - 101492634) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TCCCAGATCAAACTTGGACA Chr13:101492653..101492673 59.06 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAAATGCGTGACTGGGAAAA Chr13:101492569..101492589 60.48 40 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CTCCCAGATCAAACTTGGACA Chr13:101492653..101492674 60.1 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 ATGTCGTGACTGGGAAAACC Chr13:101492602..101492622 59.83 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000069089