Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28777
Trapped Gene
Actn2 (ENSMUSG00000052374)
Vector Insertion
Chr 13: 12363204 - 12364965
Public Clones not available
Private Clones OST20835 (lexicon)
Severity of mutation (?) Insertion after 88% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000116672 (Chr13:12364966..12365031 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GATTTCAGAGCCTGCCTCAT Chr13:12364985..12365004 59.39 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000116672 (Chr13:12364966..12365031 -)
Downstram Exon
ENSMUSE00000571885 (Chr13:12363045..12363203 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GATTTCAGAGCCTGCCTCAT Chr13:12364985..12365004 59.39 50 TTGGGGTCAACCAAAGTCAT Chr13:12363138..12363157 60.21 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000342528 Chr13:12432642..12432999 CGGCGTGCAGTACAACTATG Chr13:12432731..12432750 60.34 55
upstream ENSMUSE00000711006 Chr13:12432642..12432999 CGGCGTGCAGTACAACTATG Chr13:12432731..12432750 60.34 55
upstream ENSMUSE00000571897 Chr13:12403114..12403228 GCACCCAGATCGAGAACATC Chr13:12403169..12403188 60.63 55
upstream ENSMUSE00000571896 Chr13:12401862..12401981 TCCACAAGATTGCGAATGTC Chr13:12401923..12401942 59.65 45
upstream ENSMUSE00000571895 Chr13:12401167..12401253 GACCCTGGGTATGATCTGGA Chr13:12401209..12401228 59.74 55
upstream ENSMUSE00000684611 Chr13:12400486..12401253 AAAAGACCGAGGCAGTGCTA Chr13:12400995..12401014 60.01 50
upstream ENSMUSE00000571894 Chr13:12398541..12398628 AAAGAAGGGCTGCTGCTATG Chr13:12398598..12398617 59.62 50
upstream ENSMUSE00000571893 Chr13:12396581..12396659 GCCCGACCTCATTGACTACT Chr13:12396595..12396614 59.17 55
upstream ENSMUSE00000571892 Chr13:12393202..12393283 GGCCATGGAAATAGCAGAGA Chr13:12393238..12393257 60.18 50
upstream ENSMUSE00000571891 Chr13:12388742..12388827 ACTCCCAAACCCGATGAAAG Chr13:12388797..12388816 61.24 50
upstream ENSMUSE00000298103 Chr13:12386577..12386669 CCGAGACAGCAGCTAACAGA Chr13:12386649..12386668 59.34 55
upstream ENSMUSE00000571890 Chr13:12383927..12384157 AGAACAGGACGCCTGAGAAG Chr13:12384101..12384120 59.6 55
upstream ENSMUSE00000114863 Chr13:12382941..12383088 CAGGCTGAGAAGGGCTATGA Chr13:12383039..12383058 60.49 55
upstream ENSMUSE00000571889 Chr13:12380774..12380924 ACGGAAGTTCGAGCCCTACT Chr13:12380858..12380877 60.27 55
upstream ENSMUSE00000116667 Chr13:12374782..12374890 ATCACGATGCTGTGAACGTC Chr13:12374860..12374879 59.71 50
upstream ENSMUSE00000571888 Chr13:12372696..12372836 GTTCATTGTCCACAGCATCG Chr13:12372707..12372726 60.12 50
upstream ENSMUSE00000298063 Chr13:12371061..12371243 ATCCAGAACGAGGTGGAGAA Chr13:12371149..12371168 59.65 50
upstream ENSMUSE00000298054 Chr13:12369666..12369800 ACATGCTAATGAGCGTCTGC Chr13:12369725..12369744 59.06 50
upstream ENSMUSE00000571887 Chr13:12368630..12368809 CGACAACAAGCACACGAACT Chr13:12368641..12368660 59.95 50
upstream ENSMUSE00000571886 Chr13:12367345..12367491 CCATCAATGAGGTGGAGACC Chr13:12367426..12367445 60.33 55
upstream ENSMUSE00000116672 Chr13:12364966..12365031 GATTTCAGAGCCTGCCTCAT Chr13:12364985..12365004 59.39 50

*** Putative Vector Insertion (Chr 13: 12363204 - 12364965) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000571885 Chr13:12363045..12363203 TTGGGGTCAACCAAAGTCAT Chr13:12363138..12363157 60.21 45
downstream ENSMUSE00000406318 Chr13:12361696..12361919 CTCTCGACGAAGCTCCTCTG Chr13:12361865..12361884 60.42 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTCAGAGCCTGCCTCATTTC Chr13:12364980..12365000 60.48 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTCAGAGCCTGCCTCATTTC Chr13:12364980..12365000 60.48 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000052374