Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2874
Trapped Gene
Mark2 (ENSMUSG00000024969)
Vector Insertion
Chr 19: 7359479 - 7360221
Public Clones AG0190 (sanger) AF0004 (sanger) RRK203 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 30% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000146736 (Chr19:7360222..7360458 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCAACGAATTCACCTTTGG Chr19:7360382..7360401 60.11 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000146736 (Chr19:7360222..7360458 -)
Downstram Exon
ENSMUSE00000146729 (Chr19:7359359..7359478 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCAACGAATTCACCTTTGG Chr19:7360382..7360401 60.11 45 TACGGTATTTCCCCCTCAGT Chr19:7359420..7359439 58.38 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000695304 Chr19:7415658..7416334 AACCTCGGTCTTCGGAATCT Chr19:7416262..7416281 60.07 50
upstream ENSMUSE00000695218 Chr19:7369528..7369927 TGGAAGTCGCTGGTAGTCCT Chr19:7369547..7369566 59.87 55
upstream ENSMUSE00000695217 Chr19:7365093..7365272 ACCGGCTCCTTAAGACCATT Chr19:7365150..7365169 59.96 50
upstream ENSMUSE00000695301 Chr19:7365093..7365272 ACCGGCTCCTTAAGACCATT Chr19:7365150..7365169 59.96 50
upstream ENSMUSE00000146730 Chr19:7364806..7364859 ATCGACAAGACCCAGCTGAA Chr19:7364825..7364844 60.8 50
upstream ENSMUSE00000146723 Chr19:7361820..7361868 AGGTTTTGAATCATCCCAACA Chr19:7361823..7361843 59.28 38.1
upstream ENSMUSE00000146738 Chr19:7361491..7361556 TTGTTTGAAGTGATCGAGACTGA Chr19:7361529..7361551 59.91 39.13
upstream ENSMUSE00000146735 Chr19:7361324..7361394 AAAAAGAAGCTCGAGCCAAA Chr19:7361333..7361352 59.22 40
upstream ENSMUSE00000146737 Chr19:7361059..7361115 No primer for this exon
upstream ENSMUSE00000146736 Chr19:7360222..7360458 AGCAACGAATTCACCTTTGG Chr19:7360382..7360401 60.11 45

*** Putative Vector Insertion (Chr 19: 7359479 - 7360221) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000146729 Chr19:7359359..7359478 TACGGTATTTCCCCCTCAGT Chr19:7359420..7359439 58.38 50
downstream ENSMUSE00000695224 Chr19:7359177..7359249 CACGTTCATCCACCGATCTT Chr19:7359198..7359217 60.92 50
downstream ENSMUSE00000146726 Chr19:7359150..7359249 CACGTTCATCCACCGATCTT Chr19:7359198..7359217 60.92 50
downstream ENSMUSE00000486614 Chr19:7359043..7359089 CCCATTGACACCATCAACTC Chr19:7359027..7359046 58.77 50
downstream ENSMUSE00000550698 Chr19:7358955..7359067 CTGGATCTCTTCCCGTGTGT Chr19:7359005..7359024 60.11 55
downstream ENSMUSE00000550711 Chr19:7358955..7359038 CGTTGTACCTCTGGCCTACC Chr19:7358977..7358996 59.62 60
downstream ENSMUSE00000550710 Chr19:7357926..7358058 GGGGCTTCAAAGTGATGGTA Chr19:7358006..7358025 59.93 50
downstream ENSMUSE00000550709 Chr19:7357523..7357695 CCGCTTATTTTCTGCGTTGT Chr19:7357603..7357622 60.26 45
downstream ENSMUSE00000550708 Chr19:7357216..7357313 AAAAGTGGGGAGTTCCTGCT Chr19:7357242..7357261 60.11 50
downstream ENSMUSE00000550707 Chr19:7356288..7356449 CCGAGGCACCTCACAGTTAC Chr19:7356271..7356290 60.71 60
downstream ENSMUSE00000550706 Chr19:7355488..7355745 AAGGTGCTTCGACTGGACAC Chr19:7355610..7355629 60.31 55
downstream ENSMUSE00000643494 Chr19:7354476..7354502 TCTGGCAAACCTGAAAGACA Chr19:7354456..7354475 59.42 45
downstream ENSMUSE00000550704 Chr19:7352532..7352576 TCTCCACTCGGTCTTTGCTT Chr19:7352517..7352536 59.99 50
downstream ENSMUSE00000550701 Chr19:7349886..7351940 GATCTCCCGCATCATCTCAT Chr19:7351783..7351802 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGTGAAATGCAGGCTTCGAT Chr19:7360196..7360216 59.84 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGTGAAATGCAGGCTTCGAT Chr19:7360196..7360216 59.84 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024969