Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8919
Trapped Gene
Gpc3 (ENSMUSG00000055653)
Vector Insertion
Chr X: 49668174 - 49718898
Public Clones RST606 (baygenomics) IST14990F11 (tigm)
Private Clones OST64914 (lexicon)
Severity of mutation (?) Insertion after 81% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000436223 (ChrX:49718899..49719019 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGGTGGTTAGCCAGATCATT ChrX:49718923..49718942 59.96 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000436223 (ChrX:49718899..49719019 -)
Downstram Exon
ENSMUSE00000436221 (ChrX:49668014..49668173 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGGTGGTTAGCCAGATCATT ChrX:49718923..49718942 59.96 50 GGAAGCGCAGTTGATTCTTC ChrX:49667998..49668017 59.96 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000520286 ChrX:49966810..49967127 TCTTGCTCTGTCGGGCTACT ChrX:49967062..49967081 60.16 55
upstream ENSMUSE00000719933 ChrX:49966810..49967127 TCTTGCTCTGTCGGGCTACT ChrX:49967062..49967081 60.16 55
upstream ENSMUSE00000436250 ChrX:49935974..49936135 TGCTCCAGTCTGCGAGTATG ChrX:49936017..49936036 60.16 55
upstream ENSMUSE00000436236 ChrX:49781617..49782311 TGCTCTTACTGCCAGGGACT ChrX:49781846..49781865 60.01 55
upstream ENSMUSE00000436230 ChrX:49750250..49750383 CCCAGCAACGCCAATATAGA ChrX:49750342..49750361 60.98 50
upstream ENSMUSE00000436226 ChrX:49741286..49741411 TGCTGGAACGGACAAGAACT ChrX:49741295..49741314 60.83 50
upstream ENSMUSE00000700805 ChrX:49740841..49741411 TGCTGGAACGGACAAGAACT ChrX:49741295..49741314 60.83 50
upstream ENSMUSE00000436223 ChrX:49718899..49719019 CGGTGGTTAGCCAGATCATT ChrX:49718923..49718942 59.96 50

*** Putative Vector Insertion (Chr X: 49668174 - 49718898) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000436221 ChrX:49668014..49668173 GGAAGCGCAGTTGATTCTTC ChrX:49667998..49668017 59.96 50
downstream ENSMUSE00000624027 ChrX:49625610..49626131 AGGTGGTGATCTCGTTGTCC ChrX:49626029..49626048 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CATCTCTTCAGGGAGCCACT ChrX:49676921..49676941 59.4 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CATCTCTTCAGGGAGCCACT ChrX:49676921..49676941 59.4 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 ATAATCGCCTTGCAGCACAT ChrX:49679950..49679970 60.64 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCAGAGATGTTTCACCCACAC ChrX:49700970..49700991 60.42 52.38 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000055653