Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8640
Trapped Gene
Smarca5 (ENSMUSG00000031715)
Vector Insertion
Chr 8: 83248137 - 83249888
Public Clones RRK347 (baygenomics) RRK134 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 34% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000212321 (Chr8:83249889..83250020 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGACGCCTCTTCAGAACAAC Chr8:83249949..83249968 59.85 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000212321 (Chr8:83249889..83250020 -)
Downstram Exon
ENSMUSE00000212320 (Chr8:83248068..83248136 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGACGCCTCTTCAGAACAAC Chr8:83249949..83249968 59.85 55 CTTTTGATCCCCAAGGCAAT Chr8:83248067..83248086 61.17 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000342996 Chr8:83262822..83263358 TTCCGTTTTCCTTTCCCTTT Chr8:83263307..83263326 59.92 40
upstream ENSMUSE00000212317 Chr8:83260588..83260662 TTGATCATGGATCACCTGGA Chr8:83260636..83260655 59.85 45
upstream ENSMUSE00000212324 Chr8:83257589..83257755 GACTCCAACCTCACCCTTGA Chr8:83257653..83257672 60.09 55
upstream ENSMUSE00000284972 Chr8:83253994..83254094 ACACCGTAGAACGGAGCAAG Chr8:83254069..83254088 60.31 55
upstream ENSMUSE00000581645 Chr8:83252372..83252472 ATGGGATCCTTGCAGATGAA Chr8:83252375..83252394 60.43 45
upstream ENSMUSE00000212322 Chr8:83251515..83251694 CATTGCACAACTGGATGAGTG Chr8:83251577..83251597 60.17 47.62
upstream ENSMUSE00000581644 Chr8:83250110..83250265 TGCATTTGTCAGGGATGTTT Chr8:83250244..83250263 58.98 40
upstream ENSMUSE00000212321 Chr8:83249889..83250020 GGACGCCTCTTCAGAACAAC Chr8:83249949..83249968 59.85 55

*** Putative Vector Insertion (Chr 8: 83248137 - 83249888) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000212320 Chr8:83248068..83248136 CTTTTGATCCCCAAGGCAAT Chr8:83248067..83248086 61.17 45
downstream ENSMUSE00000212328 Chr8:83244587..83244696 No primer for this exon
downstream ENSMUSE00000581643 Chr8:83243477..83243703 AGGTTCAGCTCCATCGAAGA Chr8:83243546..83243565 59.95 50
downstream ENSMUSE00000212313 Chr8:83241421..83241542 CTCTCATCATGGGGTGTCTG Chr8:83241403..83241422 59.05 55
downstream ENSMUSE00000212315 Chr8:83240348..83240500 AGATCAACTTGCGGATTCCA Chr8:83240336..83240355 60.6 45
downstream ENSMUSE00000212310 Chr8:83237833..83237965 AAGCGAAACACTCGGACAGT Chr8:83237894..83237913 59.91 50
downstream ENSMUSE00000212312 Chr8:83235556..83235704 CATGTCGAATCATTTGAAGCA Chr8:83235617..83235637 59.68 38.1
downstream ENSMUSE00000212319 Chr8:83234456..83234575 TCACCCATCTTGGAGAGCTT Chr8:83234516..83234535 59.8 50
downstream ENSMUSE00000212325 Chr8:83233555..83233665 GGCTCACTAACACGGAGAGC Chr8:83233546..83233565 60.02 60
downstream ENSMUSE00000212330 Chr8:83233012..83233125 CAAATAAACGCGGAGGAAAG Chr8:83233040..83233059 59.72 45
downstream ENSMUSE00000212309 Chr8:83232582..83232704 CTGTGCCTGTGCTGCATTAG Chr8:83232641..83232660 60.62 55
downstream ENSMUSE00000212323 Chr8:83229346..83229478 ATCATCACGACCCCACTTCT Chr8:83229385..83229404 59.38 50
downstream ENSMUSE00000212318 Chr8:83229118..83229236 TGCATCTTTCCCAGAACACA Chr8:83229194..83229213 60.24 45
downstream ENSMUSE00000581636 Chr8:83228504..83228716 CATCGCAGTTCTGGACTTGA Chr8:83228482..83228501 59.98 50
downstream ENSMUSE00000212307 Chr8:83226027..83226134 No primer for this exon
downstream ENSMUSE00000334946 Chr8:83223845..83225027 GCACCGTCCATCTTACGTTT Chr8:83224980..83224999 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTTAATCGCCTTGCAGCACA Chr8:83249819..83249839 62.74 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATTTTCGTGACTGGGAAAACC Chr8:83249821..83249842 60.21 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000031715