Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8861
Trapped Gene
Snx8 (ENSMUSG00000029560)
Vector Insertion
Chr 5: 140820810 - 140822230
Public Clones XL179 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 71% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000190059 (Chr5:140822231..140822299 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTCTTGGATTTGTTGCAGTCC Chr5:140822237..140822257 60.1 42.86 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000190059 (Chr5:140822231..140822299 -)
Downstram Exon
ENSMUSE00000190057 (Chr5:140820663..140820809 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTCTTGGATTTGTTGCAGTCC Chr5:140822237..140822257 60.1 42.86 TTCATCAGGCCGTACTTGTG Chr5:140820714..140820733 59.72 50

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
upstream ENSMUSE00000190062 Chr5:140836146..140836336 GTGGAGCTCATCCCTGAGAA Chr5:140836192..140836211 60.35 55
upstream ENSMUSE00000190051 Chr5:140834011..140834128 TCGTGGTCTTCCATGAAGTG Chr5:140834072..140834091 59.68 50
upstream ENSMUSE00000190056 Chr5:140831914..140832035 TCTCTGAGGACGTGCTCCTT Chr5:140831941..140831960 60.13 55
upstream ENSMUSE00000190052 Chr5:140829387..140829467 AGTGCGTGGGAGATGAGTTC Chr5:140829417..140829436 60.27 55
upstream ENSMUSE00000190061 Chr5:140828989..140829149 CAACGCTGCTGATCTTCTCA Chr5:140829008..140829027 60.29 50
upstream ENSMUSE00000298718 Chr5:140828087..140828219 CTCTCCGTGGAGTTTGCACT Chr5:140828112..140828131 60.44 55
upstream ENSMUSE00000190059 Chr5:140822231..140822299 TTCTTGGATTTGTTGCAGTCC Chr5:140822237..140822257 60.1 42.86

*** Putative Vector Insertion (Chr 5: 140820810 - 140822230) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 ATCTGATGGTGGGTGACCTT Chr5:140822190..140822210 59.23 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTCTGCGTGACTGGGAAAAC Chr5:140822164..140822184 60.7 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029560