Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI409
Trapped Gene
Rnf10 (ENSMUSG00000041740)
Vector Insertion
Chr 5: 115722265 - 115722902
Public Clones GC1453 (tigem) CSH651 (baygenomics) XH178 (baygenomics) CSH634 (baygenomics)
CSH587 (baygenomics) XC366 (baygenomics) CSH675 (baygenomics) BGC001 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000709339 (Chr5:115722266..115722901 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAAAATGTCGCCATGAAGG Chr5:115722531..115722550 60.45 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000709339 (Chr5:115722266..115722901 -)
Downstram Exon
ENSMUSE00000690456 (Chr5:115722266..115722901 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAAAATGTCGCCATGAAGG Chr5:115722531..115722550 60.45 45 CCTTCATGGCGACATTTTTC Chr5:115722509..115722528 60.45 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000690452 Chr5:115722355..115722380 No primer for this exon
upstream ENSMUSE00000650744 Chr5:115722328..115722903 GAAAAATGTCGCCATGAAGG Chr5:115722531..115722550 60.45 45
upstream ENSMUSE00000650743 Chr5:115722266..115722326 GGCGAGTCTAAACCCAAGAG Chr5:115722268..115722287 58.93 55
upstream ENSMUSE00000690456 Chr5:115722266..115722901 GAAAAATGTCGCCATGAAGG Chr5:115722531..115722550 60.45 45
upstream ENSMUSE00000690459 Chr5:115722266..115722907 GAAAAATGTCGCCATGAAGG Chr5:115722531..115722550 60.45 45
upstream ENSMUSE00000709339 Chr5:115722266..115722901 GAAAAATGTCGCCATGAAGG Chr5:115722531..115722550 60.45 45

*** Putative Vector Insertion (Chr 5: 115722265 - 115722902) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000268179 Chr5:115710128..115710324 TTCACGCTTGCGATTGTAAC Chr5:115710256..115710275 59.88 45
downstream ENSMUSE00000690450 Chr5:115710128..115710158 CTCATCTCGTCTTCCACCATT Chr5:115710106..115710126 59.15 47.62
downstream ENSMUSE00000268172 Chr5:115706983..115707182 GCTCCTTGTTGAAAGGCTTG Chr5:115706977..115706996 59.99 50
downstream ENSMUSE00000268168 Chr5:115705359..115705449 TGTCAGGGTCAGCAAAGTGA Chr5:115705369..115705388 60.44 50
downstream ENSMUSE00000268162 Chr5:115701286..115701470 GTTATCTTGGCCGCAGTAGG Chr5:115701381..115701400 59.73 55
downstream ENSMUSE00000268151 Chr5:115701075..115701211 No primer for this exon
downstream ENSMUSE00000268142 Chr5:115699979..115700139 AGCAGCCTCAATGAAACAGG Chr5:115699972..115699991 60.4 50
downstream ENSMUSE00000268120 Chr5:115699406..115699531 AGCCACAACACCAGTGACCT Chr5:115699447..115699466 60.63 55
downstream ENSMUSE00000268111 Chr5:115698924..115699179 CTCCTCCTGGCTCATCTCAG Chr5:115698963..115698982 60.09 60
downstream ENSMUSE00000650742 Chr5:115698924..115699182 TTAGTGATGGGCTCCTCCTG Chr5:115698952..115698971 60.21 55
downstream ENSMUSE00000268104 Chr5:115698591..115698724 CAGACATGGAATACCCAGCA Chr5:115698571..115698590 59.52 50
downstream ENSMUSE00000268096 Chr5:115697178..115697295 TGCAGAGCCAGTTCACAGAT Chr5:115697197..115697216 59.58 50
downstream ENSMUSE00000268090 Chr5:115696889..115696990 CCATCTCAATTCTGCGCTCT Chr5:115696891..115696910 60.5 50
downstream ENSMUSE00000268085 Chr5:115695858..115696013 GGACCCAAAGCAGAATCAGA Chr5:115695904..115695923 60.19 50
downstream ENSMUSE00000268074 Chr5:115694030..115694130 TCGTCTTCCAGACTCCCAAC Chr5:115694033..115694052 60.24 55
downstream ENSMUSE00000268066 Chr5:115692643..115692700 No primer for this exon
downstream ENSMUSE00000453219 Chr5:115692402..115692560 AAGGCTGCTTCGATAGCTTG Chr5:115692421..115692440 59.75 50
downstream ENSMUSE00000495809 Chr5:115691786..115692070 GCCCCAAGCTAATCAATCTG Chr5:115691867..115691886 59.67 50
downstream ENSMUSE00000690447 Chr5:115691782..115692067 GCCCCAAGCTAATCAATCTG Chr5:115691867..115691886 59.67 50
downstream ENSMUSE00000690454 Chr5:115691779..115692067 GCCCCAAGCTAATCAATCTG Chr5:115691867..115691886 59.67 50
downstream ENSMUSE00000690458 Chr5:115691421..115692070 TGTAAAGAGGGGAAGCTGGA Chr5:115691786..115691805 59.81 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGATGCTGTTTGGCGACTC Chr5:115722885..115722905 60.96 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGATGCTGTTTGGCGACTC Chr5:115722885..115722905 60.96 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000041740