Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI470
Trapped Gene
Cdk7 (ENSMUSG00000069089)
Vector Insertion
Chr 13: 101473462 - 101474345
Public Clones DA0124 (sanger) DB0212 (sanger) XE148 (baygenomics)
Private Clones OST439355 (lexicon) OST403253 (lexicon) OST346796 (lexicon) OST233111 (lexicon)
Severity of mutation (?) Insertion after 97% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000569272 (Chr13:101474346..101474493 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACAAAGCGGAAAAGAGCAGA Chr13:101474360..101474379 60.13 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000569272 (Chr13:101474346..101474493 -)
Downstram Exon
ENSMUSE00000640048 (Chr13:101473270..101473461 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACAAAGCGGAAAAGAGCAGA Chr13:101474360..101474379 60.13 45 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
upstream ENSMUSE00000569288 Chr13:101490541..101490608 No primer for this exon
upstream ENSMUSE00000569286 Chr13:101489257..101489325 CTCCTTGATGCATTTGGACAT Chr13:101489305..101489325 59.95 42.86
upstream ENSMUSE00000569283 Chr13:101487527..101487637 AGGATAACAGCCTTGTGCTGA Chr13:101487607..101487627 59.89 47.62
upstream ENSMUSE00000569281 Chr13:101486456..101486574 CCCCAATAGGGCTTACACAC Chr13:101486472..101486491 59.31 55
upstream ENSMUSE00000569278 Chr13:101481452..101481551 CGGGCTCCTGAGTTATTGTT Chr13:101481525..101481544 59.19 50
upstream ENSMUSE00000569276 Chr13:101480029..101480115 GTTCCATTTTTGCCTGGAGA Chr13:101480096..101480115 60.05 45
upstream ENSMUSE00000569275 Chr13:101476322..101476471 CTCATCCAAGGCCTGTTCTT Chr13:101476356..101476375 59.28 50
upstream ENSMUSE00000569272 Chr13:101474346..101474493 ACAAAGCGGAAAAGAGCAGA Chr13:101474360..101474379 60.13 45

*** Putative Vector Insertion (Chr 13: 101473462 - 101474345) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 CAAAGCGGAAAAGAGCAGAG Chr13:101474357..101474377 60.26 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAAAGCGGAAAAGAGCAGAG Chr13:101474357..101474377 60.26 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000069089