Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29621
Trapped Gene
Rprd2 (ENSMUSG00000028106)
Vector Insertion
Chr 3: 95578034 - 95580721
Public Clones E133G03 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 84% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000448220 (Chr3:95580438..95580720 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGGAATCACCAGTCCCCTCT Chr3:95580622..95580641 59.93 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000448220 (Chr3:95580438..95580720 -)
Downstram Exon
ENSMUSE00000566199 (Chr3:95578035..95578295 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGGAATCACCAGTCCCCTCT Chr3:95580622..95580641 59.93 55 AAAACCAAAGTTGGGGAAGG Chr3:95578090..95578109 60.19 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000566196 Chr3:95622470..95622876 GGCTTGTCGTCCTGGTGTAT Chr3:95622529..95622548 60 55
upstream ENSMUSE00000176218 Chr3:95594023..95594152 TCCCCATCGTTTGAATCTCT Chr3:95594126..95594145 59.48 45
upstream ENSMUSE00000392753 Chr3:95591207..95591307 TCTGGGAAGATCGAAATGTG Chr3:95591247..95591266 58.64 45
upstream ENSMUSE00000176217 Chr3:95590243..95590320 CAACCGAATAAGCAGTGGAA Chr3:95590254..95590273 58.77 45
upstream ENSMUSE00000566202 Chr3:95590243..95590374 CCATAATGCCAGACTGCAAA Chr3:95590339..95590358 59.69 45
upstream ENSMUSE00000176223 Chr3:95588977..95589029 ATCCACGAATCCAAAAGCTG Chr3:95589009..95589028 60.07 45
upstream ENSMUSE00000393155 Chr3:95588137..95588263 AGGCCCTCATTGAAGAGTTG Chr3:95588240..95588259 59.28 50
upstream ENSMUSE00000448226 Chr3:95584338..95584513 TGGGCCCTCACTAACAGAAG Chr3:95584400..95584419 60.25 55
upstream ENSMUSE00000448220 Chr3:95580438..95580720 AGGAATCACCAGTCCCCTCT Chr3:95580622..95580641 59.93 55
upstream ENSMUSE00000448213 Chr3:95578183..95578295 AGTGTCTCGAAAGCCTCACC Chr3:95578205..95578224 59.46 55
upstream ENSMUSE00000448268 Chr3:95578064..95578180 CCTTCCCCAACTTTGGTTTT Chr3:95578112..95578131 60.19 45
upstream ENSMUSE00000566199 Chr3:95578035..95578295 CCTTCCCCAACTTTGGTTTT Chr3:95578112..95578131 60.19 45

*** Putative Vector Insertion (Chr 3: 95578034 - 95580721) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000566198 Chr3:95575919..95576119 GTTGCTGGGACTGGTAGGAA Chr3:95576045..95576064 60.11 55
downstream ENSMUSE00000566197 Chr3:95563796..95570343 ACAGCTGAGGCCTAACTCCA Chr3:95564490..95564509 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGTTGGTAATCGCCTTGCAG Chr3:95580656..95580676 60.27 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGAAGAAGTTGGCGTGACTG Chr3:95580662..95580682 58.09 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028106