Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9419
Trapped Gene
Ftsj1 (ENSMUSG00000031171)
Vector Insertion
Chr X: 7824048 - 7826104
Public Clones RRD143 (baygenomics) IST14270F12 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 39% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000239642 (ChrX:7826105..7826183 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCAAGGAGATCATCCAGCAC ChrX:7826154..7826173 60.62 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000239642 (ChrX:7826105..7826183 -)
Downstram Exon
ENSMUSE00000207055 (ChrX:7823995..7824047 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCAAGGAGATCATCCAGCAC ChrX:7826154..7826173 60.62 55 CATCCACATCATGGAGACCA ChrX:7824002..7824021 60.34 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000383729 ChrX:7829298..7829532 GTCCACTCCGAACACCAACT ChrX:7829372..7829391 60.01 55
upstream ENSMUSE00000703517 ChrX:7829298..7829436 GTCCACTCCGAACACCAACT ChrX:7829372..7829391 60.01 55
upstream ENSMUSE00000703521 ChrX:7829298..7829521 GTCCACTCCGAACACCAACT ChrX:7829372..7829391 60.01 55
upstream ENSMUSE00000239660 ChrX:7828006..7828163 ACTGAGATGGGACGGACATC ChrX:7828113..7828132 59.93 55
upstream ENSMUSE00000239653 ChrX:7827695..7827764 No primer for this exon
upstream ENSMUSE00000207056 ChrX:7827522..7827612 TACAGGGCGACATCACTCAG ChrX:7827522..7827541 59.85 55
upstream ENSMUSE00000239642 ChrX:7826105..7826183 CCAAGGAGATCATCCAGCAC ChrX:7826154..7826173 60.62 55

*** Putative Vector Insertion (Chr X: 7824048 - 7826104) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000207055 ChrX:7823995..7824047 CATCCACATCATGGAGACCA ChrX:7824002..7824021 60.34 50
downstream ENSMUSE00000207066 ChrX:7823853..7823906 GCCCCCTAGCTTCAAGACAT ChrX:7823846..7823865 60.6 55
downstream ENSMUSE00000207064 ChrX:7823658..7823760 CTAGAGTTCCGGCTGCTCTT ChrX:7823641..7823660 58.84 55
downstream ENSMUSE00000207063 ChrX:7823462..7823545 GGTCAGGTCTGGAATGAAGC ChrX:7823465..7823484 59.66 55
downstream ENSMUSE00000207062 ChrX:7822678..7822781 GAGTAAGTGCGGTCCGAATC ChrX:7822663..7822682 59.7 55
downstream ENSMUSE00000703520 ChrX:7822678..7822775 GAGTAAGTGCGGTCCGAATC ChrX:7822663..7822682 59.7 55
downstream ENSMUSE00000343131 ChrX:7822410..7822598 TGTTGATGGAGCATTCTTGG ChrX:7822441..7822460 59.65 45
downstream ENSMUSE00000703516 ChrX:7822410..7822556 TGTTGATGGAGCATTCTTGG ChrX:7822441..7822460 59.65 45
downstream ENSMUSE00000207058 ChrX:7822186..7822227 No primer for this exon
downstream ENSMUSE00000703519 ChrX:7817546..7817956 GAATTCCTGGGCCTTCTAGG ChrX:7817674..7817693 60.03 55
downstream ENSMUSE00000422171 ChrX:7815794..7817956 TTCAGGCATTTCTTGCTCCT ChrX:7815786..7815805 59.96 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GATGGTAAATGCGCTGTGAG ChrX:7826087..7826107 59.3 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GATGGTAAATGCGCTGTGAG ChrX:7826087..7826107 59.3 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCAAGGAGATCATCCAGCAC ChrX:7826152..7826172 60.62 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCAAGGAGATCATCCAGCAC ChrX:7826152..7826172 60.62 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000031171