Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8116
Trapped Gene
Klhl13 (ENSMUSG00000036782)
Vector Insertion
Chr X: 22805814 - 22812351
Public Clones RRG185 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 67% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000318923 (ChrX:22812352..22813147 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCGCCTGGAAGAACCTAGAA ChrX:22812904..22812923 59.95 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000318923 (ChrX:22812352..22813147 -)
Downstram Exon
ENSMUSE00000318908 (ChrX:22805700..22805813 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCGCCTGGAAGAACCTAGAA ChrX:22812904..22812923 59.95 50 TGGCAACATAGGTCCATTCA ChrX:22805741..22805760 59.92 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000702439 ChrX:22942082..22942208 AGCTTGGAACAGGGACTTTG ChrX:22942112..22942131 59.33 50
upstream ENSMUSE00000702438 ChrX:22938620..22938710 GCCTTCAGACTGGGACTGAG ChrX:22938684..22938703 59.99 60
upstream ENSMUSE00000624545 ChrX:22892256..22892333 TGCTCAACCCTGAGAAGTGA ChrX:22892305..22892324 59.54 50
upstream ENSMUSE00000702437 ChrX:22892256..22892327 TGCTCAACCCTGAGAAGTGA ChrX:22892305..22892324 59.54 50
upstream ENSMUSE00000702446 ChrX:22862284..22862363 CTGTTGCAGCTCAAAAGAAGAA ChrX:22862316..22862337 59.81 40.91
upstream ENSMUSE00000702444 ChrX:22861686..22861783 ATGGAAAACGAGCTCTCCTG ChrX:22861753..22861772 59.43 50
upstream ENSMUSE00000702442 ChrX:22843811..22843866 No primer for this exon
upstream ENSMUSE00000370594 ChrX:22838561..22838699 GGCAGGAAGTACACGCATCT ChrX:22838596..22838615 60.28 55
upstream ENSMUSE00000702457 ChrX:22838561..22838699 GGCAGGAAGTACACGCATCT ChrX:22838596..22838615 60.28 55
upstream ENSMUSE00000318948 ChrX:22825238..22825370 GGCTTGATGGATTGCTTTGT ChrX:22825335..22825354 60.08 45
upstream ENSMUSE00000318938 ChrX:22824487..22824683 CTTCAGGATACGCTGGAAGC ChrX:22824548..22824567 59.98 55
upstream ENSMUSE00000318923 ChrX:22812352..22813147 TCGCCTGGAAGAACCTAGAA ChrX:22812904..22812923 59.95 50

*** Putative Vector Insertion (Chr X: 22805814 - 22812351) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000318908 ChrX:22805700..22805813 TGGCAACATAGGTCCATTCA ChrX:22805741..22805760 59.92 45
downstream ENSMUSE00000345795 ChrX:22796397..22797978 TGATGGTGTGGCTTCTTCAG ChrX:22797502..22797521 59.83 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCAGCTGGAGAACTCCGTAA ChrX:22809346..22809366 60.54 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GACATGACGTGACTGGGAAA ChrX:22809287..22809307 59.53 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036782