Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI16633
Trapped Gene
Zdhhc20 (ENSMUSG00000021969)
Vector Insertion
Chr 14: 58484479 - 58492729
Public Clones IST12107B2 (tigm)
Private Clones OST456598 (lexicon) OST364544 (lexicon) OST303795 (lexicon)
Severity of mutation (?) Insertion after 23% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000122526 (Chr14:58492730..58492833 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCTTGTGGCTTTCCATCTGT Chr14:58492798..58492817 60.11 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000122526 (Chr14:58492730..58492833 -)
Downstram Exon
ENSMUSE00000122540 (Chr14:58484358..58484478 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCTTGTGGCTTTCCATCTGT Chr14:58492798..58492817 60.11 50 AGGTCTCTTGCCGCTCTTCT Chr14:58484365..58484384 60.67 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000558391 Chr14:58508900..58509099 ACCTTTGTGGTCGTCTGGTC Chr14:58508932..58508951 60.01 55
upstream ENSMUSE00000122547 Chr14:58497270..58497296 No primer for this exon
upstream ENSMUSE00000122526 Chr14:58492730..58492833 CCTTGTGGCTTTCCATCTGT Chr14:58492798..58492817 60.11 50

*** Putative Vector Insertion (Chr 14: 58484479 - 58492729) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000122540 Chr14:58484358..58484478 AGGTCTCTTGCCGCTCTTCT Chr14:58484365..58484384 60.67 55
downstream ENSMUSE00000122541 Chr14:58477377..58477446 GGCTCGGTCAGGTTTAATCA Chr14:58477378..58477397 60.07 50
downstream ENSMUSE00000558401 Chr14:58476465..58476497 No primer for this exon
downstream ENSMUSE00000307301 Chr14:58475447..58475567 AAAACTGTTGCAGCCACAAA Chr14:58475450..58475469 59.37 40
downstream ENSMUSE00000558399 Chr14:58468982..58469017 No primer for this exon
downstream ENSMUSE00000307294 Chr14:58465758..58465899 CGAAGAACATTGCAGACACAA Chr14:58465799..58465819 59.9 42.86
downstream ENSMUSE00000307283 Chr14:58462025..58462151 TGCATCCAAGAGAGAAACCAT Chr14:58462067..58462087 59.69 42.86
downstream ENSMUSE00000122534 Chr14:58459666..58459755 AGCTGGAAAACTGCAACCAT Chr14:58459706..58459725 59.74 45
downstream ENSMUSE00000122556 Chr14:58457927..58458042 TCACTGTCCAATAAGCGGTTT Chr14:58457952..58457972 59.62 42.86
downstream ENSMUSE00000354959 Chr14:58456428..58456504 No primer for this exon
downstream ENSMUSE00000615304 Chr14:58451539..58455483 TTTTGAGCTGTGAGGCAATG Chr14:58455259..58455278 59.99 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTAATCGCCTTGCAGCACAT Chr14:58492659..58492679 61.2 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGAGATTGCCAGCGTGACTG Chr14:58489670..58489690 61.57 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AAATAATCGCCTTGCAGCAC Chr14:58492766..58492786 60.24 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TGTTCGTGACTGGGAAAACC Chr14:58492767..58492787 60.93 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000021969