Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9157
Trapped Gene
Mysm1 (ENSMUSG00000062627)
Vector Insertion
Chr 4: 94641984 - 94645694
Public Clones RRE042 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 3% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000390662 (Chr4:94645695..94645791 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTGGATGTGGAAGGAGATGT Chr4:94645716..94645736 60.38 47.62 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000390662 (Chr4:94645695..94645791 -)
Downstram Exon
ENSMUSE00000349848 (Chr4:94641908..94641983 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTGGATGTGGAAGGAGATGT Chr4:94645716..94645736 60.38 47.62 TCCCTTCTCCACGTTGAATC Chr4:94641899..94641918 60.05 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000390662 Chr4:94645695..94645791 TGTGGATGTGGAAGGAGATGT Chr4:94645716..94645736 60.38 47.62

*** Putative Vector Insertion (Chr 4: 94641984 - 94645694) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000349848 Chr4:94641908..94641983 TCCCTTCTCCACGTTGAATC Chr4:94641899..94641918 60.05 50
downstream ENSMUSE00000358844 Chr4:94639609..94639679 TGGTGCTATCCAGAGTCCAA Chr4:94639636..94639655 59.24 50
downstream ENSMUSE00000402969 Chr4:94637315..94637392 CCCAGAATTTTCCTGGAAGT Chr4:94637330..94637349 58.09 45
downstream ENSMUSE00000497581 Chr4:94637203..94637226 TGGCTTTTGATGACTTCTGC Chr4:94637182..94637201 59 45
downstream ENSMUSE00000394760 Chr4:94635671..94635749 GCTGGTTTTGCAGGAGAATC Chr4:94635704..94635723 59.82 50
downstream ENSMUSE00000298939 Chr4:94634561..94634659 No primer for this exon
downstream ENSMUSE00000525934 Chr4:94631820..94632562 TCCACTTGAGTCCTGCCTCT Chr4:94632001..94632020 59.99 55
downstream ENSMUSE00000525933 Chr4:94628394..94628524 GTTCTTCAGGCCAGGACGTA Chr4:94628445..94628464 60.26 55
downstream ENSMUSE00000525932 Chr4:94627019..94627122 CAAGTGGTTGTGGCCTGTTA Chr4:94627068..94627087 59.61 50
downstream ENSMUSE00000525931 Chr4:94625604..94625681 TTTGCATCACACCAGTTTCC Chr4:94625607..94625626 59.55 45
downstream ENSMUSE00000525930 Chr4:94623741..94623829 TTGCCATCTCCTCCACAGAC Chr4:94623783..94623802 61.23 55
downstream ENSMUSE00000525929 Chr4:94620563..94620617 No primer for this exon
downstream ENSMUSE00000525928 Chr4:94620189..94620239 No primer for this exon
downstream ENSMUSE00000471179 Chr4:94619554..94619628 TCACCTCTGCCATAGACACG Chr4:94619579..94619598 59.85 55
downstream ENSMUSE00000506734 Chr4:94618865..94619053 TTCTGAGGCCTGTGTCTGTG Chr4:94618948..94618967 60.02 55
downstream ENSMUSE00000520119 Chr4:94617617..94617749 CCAAGCAGGTTATCTGGGAAT Chr4:94617631..94617651 60.33 47.62
downstream ENSMUSE00000508790 Chr4:94615020..94615125 TTCCCACTGAGGTTCTTCTAACA Chr4:94615051..94615073 60.15 43.48
downstream ENSMUSE00000509687 Chr4:94614793..94614850 CGGCGAAAGATTCTATCCAT Chr4:94614799..94614818 59.14 45
downstream ENSMUSE00000510826 Chr4:94608732..94613814 GACAGCTTAGGCTGGAATGC Chr4:94610326..94610345 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTAGGCAAGGGTCTAATCG Chr4:94645637..94645657 58.95 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTGGATGTGGAAGGAGATGT Chr4:94645714..94645735 60.38 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000062627