Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7294
Trapped Gene
Sin3b (ENSMUSG00000031622)
Vector Insertion
Chr 8: 75255178 - 75257243
Public Clones RRT473 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 64% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000211251 (Chr8:75254980..75255177 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTTTCTGGACCACCCTGAGA Chr8:75255120..75255139 60.23 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000211251 (Chr8:75254980..75255177 +)
Downstram Exon
ENSMUSE00000325260 (Chr8:75257244..75257387 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTTTCTGGACCACCCTGAGA Chr8:75255120..75255139 60.23 55 GCCCTTAGTGTGCAGCTGTT Chr8:75257270..75257289 60.46 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000325243 Chr8:75247203..75247307 No primer for this exon
upstream ENSMUSE00000211240 Chr8:75247943..75248049 TACAACGGCTTCCTGGAGAT Chr8:75248006..75248025 59.69 50
upstream ENSMUSE00000211246 Chr8:75249436..75249589 TCGTGGGGTTTAATGCTTTC Chr8:75249498..75249517 59.94 45
upstream ENSMUSE00000211251 Chr8:75254980..75255177 CTTTCTGGACCACCCTGAGA Chr8:75255120..75255139 60.23 55

*** Putative Vector Insertion (Chr 8: 75255178 - 75257243) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000325260 Chr8:75257244..75257387 GCCCTTAGTGTGCAGCTGTT Chr8:75257270..75257289 60.46 55
downstream ENSMUSE00000211258 Chr8:75263268..75263387 CGAGAGCGTTTCTTGTTGTG Chr8:75263353..75263372 59.63 50
downstream ENSMUSE00000682179 Chr8:75263629..75263800 CCTCAGCTGTGCAGTAACCA Chr8:75263686..75263705 60.05 55
downstream ENSMUSE00000211256 Chr8:75265373..75265462 ATTCCTGCAGTGTGCCGTAT Chr8:75265448..75265467 60.55 50
downstream ENSMUSE00000211247 Chr8:75265709..75265827 CCCAGGAATGGACTGACAAG Chr8:75265830..75265849 60.5 55
downstream ENSMUSE00000325221 Chr8:75268357..75268564 CATAGGTGGTGCAAAGGACA Chr8:75268432..75268451 59.57 50
downstream ENSMUSE00000211243 Chr8:75268793..75268909 TTCAGACCAGGATGGAAAGG Chr8:75268837..75268856 60.04 50
downstream ENSMUSE00000211249 Chr8:75270309..75270547 GCCATCCGTGACAACTTCTT Chr8:75270388..75270407 60.12 50
downstream ENSMUSE00000581754 Chr8:75271584..75271767 TCCAGGGACTTGAGGTATGC Chr8:75271682..75271701 60.07 55
downstream ENSMUSE00000211252 Chr8:75273618..75274167 GCGTCCTCTAGGATCTGTCG Chr8:75273712..75273731 59.97 60
downstream ENSMUSE00000211248 Chr8:75274335..75274504 CATACTGTGTGGGGTCGATG Chr8:75274424..75274443 59.83 55
downstream ENSMUSE00000211241 Chr8:75277066..75277239 CTGCACGAACACATCTGGAG Chr8:75277180..75277199 60.46 55
downstream ENSMUSE00000211242 Chr8:75277444..75277536 GTACCTCCACAGGGTCCTCA Chr8:75277537..75277556 59.96 60
downstream ENSMUSE00000581753 Chr8:75280372..75280466 TTCAGCAGGAAGCCTTCAGT Chr8:75280451..75280470 60.13 50
downstream ENSMUSE00000581752 Chr8:75280747..75280951 CTCGGAATTGACGATGAACA Chr8:75280912..75280931 59.65 45
downstream ENSMUSE00000635998 Chr8:75281074..75281304 CTTGCAGGGTACCATGTCCT Chr8:75281223..75281242 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGCATTGTTTGGCATTAGGA Chr8:75255195..75255215 60.84 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGTCGTGACTGGGAAAACC Chr8:75255225..75255245 59.56 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000031622