Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3166
Trapped Gene
Rfx1 (ENSMUSG00000031706)
Vector Insertion
Chr 8: 86611972 - 86614009
Public Clones XT0268 (sanger) XT0107 (sanger) RRR141 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 44% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000372199 (Chr8:86611605..86611971 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACCTACCAGTACCCGGAGA Chr8:86611614..86611633 59.98 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000372199 (Chr8:86611605..86611971 +)
Downstram Exon
ENSMUSE00000212111 (Chr8:86614010..86614191 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACCTACCAGTACCCGGAGA Chr8:86611614..86611633 59.98 60 ATGAATACCGAGCGGATGAG Chr8:86614164..86614183 60.06 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000407950 Chr8:86590765..86590947 CAACGCCAGTCAACAACAAC Chr8:86590800..86590819 60.2 50
upstream ENSMUSE00000269634 Chr8:86597630..86597968 TATGTCACCGAGCTGCAAAG Chr8:86597812..86597831 60.01 50
upstream ENSMUSE00000269601 Chr8:86603762..86603871 GCGGGCTAGTGAGACTGTGT Chr8:86603772..86603791 60.48 60
upstream ENSMUSE00000269573 Chr8:86604024..86604107 CCCTGCAGCTTACCAACATT Chr8:86604073..86604092 60.13 50
upstream ENSMUSE00000269550 Chr8:86605014..86605121 No primer for this exon
upstream ENSMUSE00000269524 Chr8:86606547..86606660 GCAGCAACTACAGGTCCACA Chr8:86606609..86606628 59.9 55
upstream ENSMUSE00000269502 Chr8:86607981..86608073 CCAGTTCACGTTGCTCAAGA Chr8:86608053..86608072 60.03 50
upstream ENSMUSE00000269483 Chr8:86609472..86609566 AGGTGCAGTACGTGGAAGGT Chr8:86609518..86609537 59.65 55
upstream ENSMUSE00000372199 Chr8:86611605..86611971 CACCTACCAGTACCCGGAGA Chr8:86611614..86611633 59.98 60

*** Putative Vector Insertion (Chr 8: 86611972 - 86614009) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000212111 Chr8:86614010..86614191 ATGAATACCGAGCGGATGAG Chr8:86614164..86614183 60.06 50
downstream ENSMUSE00000212119 Chr8:86614849..86614968 CGCAGGCCGTAATAGTGGTA Chr8:86614884..86614903 61.03 55
downstream ENSMUSE00000269363 Chr8:86615265..86615377 CAGGAACTGCTGGTACTGCT Chr8:86615379..86615398 58.12 55
downstream ENSMUSE00000269328 Chr8:86616434..86616552 CTCAGCAAAATCAGGCAAGC Chr8:86616468..86616487 61.05 50
downstream ENSMUSE00000212122 Chr8:86616679..86616788 TTACCATGACGTCCACGATG Chr8:86616703..86616722 60.39 50
downstream ENSMUSE00000269268 Chr8:86616873..86617024 TTGGAGAGGAGCACCAGACT Chr8:86616929..86616948 59.99 55
downstream ENSMUSE00000269248 Chr8:86617102..86617199 TCTCCTCAGGGATGTTCACC Chr8:86617188..86617207 60.05 55
downstream ENSMUSE00000581443 Chr8:86618626..86618775 CAAGTGGTTGAGCGATGTGT Chr8:86618688..86618707 59.75 50
downstream ENSMUSE00000581442 Chr8:86618849..86619057 TCCAGTGAGTTCTGCTGCTG Chr8:86618946..86618965 60.33 55
downstream ENSMUSE00000581441 Chr8:86619295..86619448 GTCAGGTCCCGGATTACCAT Chr8:86619321..86619340 60.97 55
downstream ENSMUSE00000269135 Chr8:86619527..86619572 CCAAGGGATTCAGTGAGGTG Chr8:86619563..86619582 60.5 55
downstream ENSMUSE00000269117 Chr8:86619696..86620901 CAAGCGGCACTCACTAATCA Chr8:86620600..86620619 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCGAGAAATAATCGCCTTGC Chr8:86612015..86612035 60.31 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCAGCCACAGTAAGTGTTCG Chr8:86611964..86611984 59.36 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000031706