Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9642
Trapped Gene
Snx8 (ENSMUSG00000029560)
Vector Insertion
Chr 5: 140836337 - 140865101
Public Clones (sanger) (sanger) XG226 (baygenomics) E118D01 (ggtc) W055D01 (ggtc)
D144B06 (ggtc) W183B03 (ggtc) IST11632D12 (tigm) IST14112D3 (tigm)
IST10099B6 (tigm) IST11711C7 (tigm) IST10394F4 (tigm) IST12016H1 (tigm)
IST14224E1 (tigm) IST14120D3 (tigm) IST12016H1 (tigm) IST14116D3 (tigm)
Private Clones OST383003 (lexicon) OST276969 (lexicon) OST274696 (lexicon) OST179367 (lexicon)
OST168862 (lexicon)
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000367862 (Chr5:140865102..140865216 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000367862 (Chr5:140865102..140865216 -)
Downstram Exon
ENSMUSE00000190062 (Chr5:140836146..140836336 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon TGGCTGGAAACCTCGTACTC Chr5:140836125..140836144 60.26 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000367862 Chr5:140865102..140865216 No primer for this exon

*** Putative Vector Insertion (Chr 5: 140836337 - 140865101) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000190062 Chr5:140836146..140836336 TGGCTGGAAACCTCGTACTC Chr5:140836125..140836144 60.26 55
downstream ENSMUSE00000190051 Chr5:140834011..140834128 AGCGTCTGTACACGGAGGAC Chr5:140834079..140834098 60.33 60
downstream ENSMUSE00000190056 Chr5:140831914..140832035 AAGGAGCACGTCCTCAGAGA Chr5:140831919..140831938 60.13 55
downstream ENSMUSE00000190052 Chr5:140829387..140829467 GAACTCATCTCCCACGCACT Chr5:140829395..140829414 60.27 55
downstream ENSMUSE00000190061 Chr5:140828989..140829149 GGCTCTGTCTCGAAGCTTGT Chr5:140829032..140829051 59.75 55
downstream ENSMUSE00000298718 Chr5:140828087..140828219 No primer for this exon
downstream ENSMUSE00000190059 Chr5:140822231..140822299 No primer for this exon
downstream ENSMUSE00000190057 Chr5:140820663..140820809 TTCATCAGGCCGTACTTGTG Chr5:140820714..140820733 59.72 50
downstream ENSMUSE00000190058 Chr5:140820240..140820389 GGATCTGGGAGTTCACGAAG Chr5:140820232..140820251 59.65 55
downstream ENSMUSE00000427267 Chr5:140816258..140817596 GCCCAAGGCTAGAGTCACTG Chr5:140817066..140817085 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGTGCATGTGTGGGTTCCTA Chr5:140862121..140862141 61.79 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTGCATGTGTGGGTTCCTA Chr5:140862121..140862141 61.79 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TTTTAATCGCCTTGCAGCAC Chr5:140862149..140862169 61.26 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 AGTGTGCGTGACTGGGAAAA Chr5:140862152..140862172 61.69 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029560