Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI192
Trapped Gene
Plec1 (ENSMUSG00000022565)
Vector Insertion
Chr 15: 76014536 - 76015740
Public Clones GC0596 (tigem)
Private Clones not available
Severity of mutation (?) Insertion after 22% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000648420 (Chr15:76015741..76015919 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCCTGTCTGCCATCTACCTG Chr15:76015746..76015765 60.82 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000648420 (Chr15:76015741..76015919 -)
Downstram Exon
ENSMUSE00000648419 (Chr15:76014397..76014535 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCCTGTCTGCCATCTACCTG Chr15:76015746..76015765 60.82 60 TACTGCGAATCACCAAGCTG Chr15:76014482..76014501 60.01 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000559353 Chr15:76061604..76061808 CGAAGTGGAGGTGGTTCTGT Chr15:76061657..76061676 60.15 55
upstream ENSMUSE00000559019 Chr15:76059788..76059927 GAGGTGCGGGAGAAGTACAA Chr15:76059790..76059809 60.26 55
upstream ENSMUSE00000466268 Chr15:76039395..76039595 ACGAGATCAGCTCCCTCAAA Chr15:76039396..76039415 59.95 50
upstream ENSMUSE00000623212 Chr15:76038854..76039083 TGGCTCTTTGTCCAGGGTTA Chr15:76038974..76038993 60.63 50
upstream ENSMUSE00000623180 Chr15:76038492..76038683 TGGAGATCATTAGGGGATGG Chr15:76038494..76038513 59.7 50
upstream ENSMUSE00000471415 Chr15:76036028..76036751 ATGAGGTGCTCTTCCGTGAG Chr15:76036503..76036522 60.41 55
upstream ENSMUSE00000366194 Chr15:76029979..76030265 TCGTGGGTCATGTTGTCACT Chr15:76030034..76030053 60.01 50
upstream ENSMUSE00000513487 Chr15:76028410..76028639 GGGAGTCTTCACTTCGCAGA Chr15:76028500..76028519 60.53 55
upstream ENSMUSE00000401097 Chr15:76025854..76026140 ACCTCTACCTGGCTGTGCTC Chr15:76025876..76025895 59.48 60
upstream ENSMUSE00000648409 Chr15:76025181..76025242 TCACCAAGTGGGTCAACAAA Chr15:76025193..76025212 59.98 45
upstream ENSMUSE00000648470 Chr15:76025181..76025242 TCACCAAGTGGGTCAACAAA Chr15:76025193..76025212 59.98 45
upstream ENSMUSE00000648396 Chr15:76024989..76025003 No primer for this exon
upstream ENSMUSE00000648408 Chr15:76024771..76024860 TCAGAGGCACATCAGTGACC Chr15:76024839..76024858 59.83 55
upstream ENSMUSE00000648468 Chr15:76024771..76024860 TCAGAGGCACATCAGTGACC Chr15:76024839..76024858 59.83 55
upstream ENSMUSE00000682091 Chr15:76024396..76024431 CGGGACGTAATCAGGAGTGT Chr15:76024403..76024422 59.99 55
upstream ENSMUSE00000648403 Chr15:76023840..76023917 GTGCAGATTGCCCTGGACTA Chr15:76023856..76023875 61.21 55
upstream ENSMUSE00000648465 Chr15:76023840..76023917 GTGCAGATTGCCCTGGACTA Chr15:76023856..76023875 61.21 55
upstream ENSMUSE00000648464 Chr15:76023651..76023743 TCTGGACAATCATCCTGCAC Chr15:76023657..76023676 59.64 50
upstream ENSMUSE00000648463 Chr15:76022611..76022777 CGCTGTGACAACTTCACCAC Chr15:76022659..76022678 60.36 55
upstream ENSMUSE00000648462 Chr15:76021850..76021965 ACCTAGACCAGGCATTCTCG Chr15:76021896..76021915 59.31 55
upstream ENSMUSE00000648459 Chr15:76021672..76021778 TCCCTCAGCCTGATGAAAAG Chr15:76021750..76021769 60.33 50
upstream ENSMUSE00000648458 Chr15:76021447..76021566 CTTTTGAGGAGCGCAAGTTC Chr15:76021471..76021490 60.13 50
upstream ENSMUSE00000648457 Chr15:76021279..76021374 CAGACAAAAACCGGTCCAAA Chr15:76021300..76021319 60.89 45
upstream ENSMUSE00000648456 Chr15:76020889..76021016 AACTGCGAAGCGAGTTTGAG Chr15:76020891..76020910 60.71 50
upstream ENSMUSE00000648454 Chr15:76020532..76020625 AGTGTCTTCAGCGCATTGTG Chr15:76020601..76020620 60.06 50
upstream ENSMUSE00000648452 Chr15:76019687..76019841 TATGATCCGGCTGTTGTTCA Chr15:76019745..76019764 60.07 45
upstream ENSMUSE00000648451 Chr15:76019301..76019610 GGAGAACCAGCGTCGAATAG Chr15:76019420..76019439 59.84 55
upstream ENSMUSE00000648448 Chr15:76019138..76019215 GGTCGCCTAGACCTGCAGTA Chr15:76019151..76019170 60.42 60
upstream ENSMUSE00000648447 Chr15:76018894..76019055 AGTGGGCTTTGATTGGAGTG Chr15:76018935..76018954 60.11 50
upstream ENSMUSE00000648443 Chr15:76018603..76018707 TGATGCGAGAACTGGAAATG Chr15:76018684..76018703 59.8 45
upstream ENSMUSE00000648440 Chr15:76018409..76018504 GCTGCATTGAAGCACACTTG Chr15:76018433..76018452 60.61 50
upstream ENSMUSE00000648438 Chr15:76018067..76018192 AGGAGACGTTACGCAGGAAG Chr15:76018127..76018146 59.5 55
upstream ENSMUSE00000648437 Chr15:76017041..76017193 GCCAAGGCTATTGTGCAGTT Chr15:76017117..76017136 60.28 50
upstream ENSMUSE00000648436 Chr15:76016790..76016944 ACTGGAAGGTGCTCAGTGGT Chr15:76016870..76016889 59.76 55
upstream ENSMUSE00000648435 Chr15:76016571..76016697 ATACAGCTCATCCGGTCCTG Chr15:76016584..76016603 60.1 55
upstream ENSMUSE00000648431 Chr15:76016284..76016467 GAGGACCGTCTAGTGGCAGA Chr15:76016343..76016362 60.41 60
upstream ENSMUSE00000648424 Chr15:76016039..76016196 CTGTGAGACTCGGACTGTGC Chr15:76016107..76016126 59.6 60
upstream ENSMUSE00000648420 Chr15:76015741..76015919 GCCTGTCTGCCATCTACCTG Chr15:76015746..76015765 60.82 60

*** Putative Vector Insertion (Chr 15: 76014536 - 76015740) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000648419 Chr15:76014397..76014535 TACTGCGAATCACCAAGCTG Chr15:76014482..76014501 60.01 50
downstream ENSMUSE00000648417 Chr15:76013953..76014309 CCCCGCAACTCATCTCTTAG Chr15:76014223..76014242 59.83 55
downstream ENSMUSE00000648416 Chr15:76013792..76013875 CTTCTCACCATGACGCTCAA Chr15:76013818..76013837 59.98 50
downstream ENSMUSE00000648415 Chr15:76013521..76013625 TCCGATCCAGACTGAACCTT Chr15:76013515..76013534 59.65 50
downstream ENSMUSE00000648414 Chr15:76013340..76013438 CGAAGGGTCTCACTGATGAA Chr15:76013337..76013356 58.8 50
downstream ENSMUSE00000648413 Chr15:76008949..76012329 GTAACTTCGCCTCCTGCTTG Chr15:76008947..76008966 60.01 55
downstream ENSMUSE00000648412 Chr15:76001406..76008815 GTGAGGTTCTCGTGGGTGTT Chr15:76005657..76005676 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGCCTGTCTGCCATCTACCT Chr15:76015745..76015765 58.92 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAGCCTGTCTGCCATCTACC Chr15:76015746..76015766 59.31 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000022565